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Suzuki T. Current research on mechanisms of limb bud development, and challenges for the next decade. Genes Genet Syst 2024; 99:n/a. [PMID: 38382923 DOI: 10.1266/ggs.23-00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Abstract
The developmental mechanisms of limb buds have been studied in developmental biology as an excellent model of pattern formation. Chick embryos have contributed to the discovery of new principles in developmental biology, as it is easy to observe live embryos and manipulate embryonic tissues. Herein, I outline recent findings and future issues over the next decade regarding three themes, based on my research: limb positioning, proximal-distal limb elongation and digit identity determination. First, how hindlimb position is determined at the molecular level is described, with a focus on the transforming growth factor-β signaling molecule GDF11. Second, I explain how the cell population in the limb bud deforms with developmental progress, shaping the limb bud with elongation along the proximal-distal axis. Finally, I describe the developmental mechanisms that determine digit identity through the interdigits.
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Affiliation(s)
- Takayuki Suzuki
- Division of Biology, Graduate School of Science, Osaka Metropolitan University
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2
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Leung AOW, Poon ACH, Wang X, Feng C, Chen P, Zheng Z, To MK, Chan WCW, Cheung M, Chan D. Suppression of apoptosis impairs phalangeal joint formation in the pathogenesis of brachydactyly type A1. Nat Commun 2024; 15:2229. [PMID: 38472182 PMCID: PMC10933404 DOI: 10.1038/s41467-024-45053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/12/2024] [Indexed: 03/14/2024] Open
Abstract
Apoptosis occurs during development when a separation of tissues is needed. Synovial joint formation is initiated at the presumptive site (interzone) within a cartilage anlagen, with changes in cellular differentiation leading to cavitation and tissue separation. Apoptosis has been detected in phalangeal joints during development, but its role and regulation have not been defined. Here, we use a mouse model of brachydactyly type A1 (BDA1) with an IhhE95K mutation, to show that a missing middle phalangeal bone is due to the failure of the developing joint to cavitate, associated with reduced apoptosis, and a joint is not formed. We showed an intricate relationship between IHH and interacting partners, CDON and GAS1, in the interzone that regulates apoptosis. We propose a model in which CDON/GAS1 may act as dependence receptors in this context. Normally, the IHH level is low at the center of the interzone, enabling the "ligand-free" CDON/GAS1 to activate cell death for cavitation. In BDA1, a high concentration of IHH suppresses apoptosis. Our findings provided new insights into the role of IHH and CDON in joint formation, with relevance to hedgehog signaling in developmental biology and diseases.
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Affiliation(s)
- Adrian On Wah Leung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Andrew Chung Hin Poon
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xue Wang
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Chen Feng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- Hebei Orthopedic Clinical Research Center, The Third Hospital of Hebei Medical University, 050051, Shijiazhuang, Hebei, China
| | - Peikai Chen
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Orthopaedics Surgery and Traumatology, The University of Hong Kong -Shenzhen Hospital (HKU-SZH), Shenzhen, China
| | - Zhengfan Zheng
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Michael KaiTsun To
- Department of Orthopaedics Surgery and Traumatology, The University of Hong Kong -Shenzhen Hospital (HKU-SZH), Shenzhen, China
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wilson Cheuk Wing Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
- Department of Orthopaedics Surgery and Traumatology, The University of Hong Kong -Shenzhen Hospital (HKU-SZH), Shenzhen, China.
| | - Martin Cheung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Danny Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
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Tsutsumi R, Eiraku M. How might we build limbs in vitro informed by the modular aspects and tissue-dependency in limb development? Front Cell Dev Biol 2023; 11:1135784. [PMID: 37283945 PMCID: PMC10241304 DOI: 10.3389/fcell.2023.1135784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Building limb morphogenesis in vitro would substantially open up avenues for research and applications of appendage development. Recently, advances in stem cell engineering to differentiate desired cell types and produce multicellular structures in vitro have enabled the derivation of limb-like tissues from pluripotent stem cells. However, in vitro recapitulation of limb morphogenesis is yet to be achieved. To formulate a method of building limbs in vitro, it is critically important to understand developmental mechanisms, especially the modularity and the dependency of limb development on the external tissues, as those would help us to postulate what can be self-organized and what needs to be externally manipulated when reconstructing limb development in vitro. Although limbs are formed on the designated limb field on the flank of embryo in the normal developmental context, limbs can also be regenerated on the amputated stump in some animals and experimentally induced at ectopic locations, which highlights the modular aspects of limb morphogenesis. The forelimb-hindlimb identity and the dorsal-ventral, proximal-distal, and anterior-posterior axes are initially instructed by the body axis of the embryo, and maintained in the limb domain once established. In contrast, the aspects of dependency on the external tissues are especially underscored by the contribution of incoming tissues, such as muscles, blood vessels, and peripheral nerves, to developing limbs. Together, those developmental mechanisms explain how limb-like tissues could be derived from pluripotent stem cells. Prospectively, the higher complexity of limb morphologies is expected to be recapitulated by introducing the morphogen gradient and the incoming tissues in the culture environment. Those technological developments would dramatically enhance experimental accessibility and manipulability for elucidating the mechanisms of limb morphogenesis and interspecies differences. Furthermore, if human limb development can be modeled, drug development would be benefited by in vitro assessment of prenatal toxicity on congenital limb deficiencies. Ultimately, we might even create a future in which the lost appendage would be recovered by transplanting artificially grown human limbs.
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Affiliation(s)
- Rio Tsutsumi
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mototsugu Eiraku
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Laboratory of Developmental Systems, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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Luxey M, Stieger G, Berki B, Tschopp P. Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies. Front Cell Dev Biol 2023; 11:1154205. [PMID: 37215090 PMCID: PMC10192688 DOI: 10.3389/fcell.2023.1154205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.
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Affiliation(s)
- Maëva Luxey
- *Correspondence: Maëva Luxey, ; Patrick Tschopp,
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Arostegui M, Scott RW, Underhill TM. Hic1 identifies a specialized mesenchymal progenitor population in the embryonic limb responsible for bone superstructure formation. Cell Rep 2023; 42:112325. [PMID: 37002923 DOI: 10.1016/j.celrep.2023.112325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/21/2022] [Accepted: 03/17/2023] [Indexed: 06/19/2023] Open
Abstract
The musculoskeletal system relies on the integration of multiple components with diverse physical properties, such as striated muscle, tendon, and bone, that enable locomotion and structural stability. This relies on the emergence of specialized, but poorly characterized, interfaces between these various elements during embryonic development. Within the appendicular skeleton, we show that a subset of mesenchymal progenitors (MPs), identified by Hic1, do not contribute to the primary cartilaginous anlagen but represent the MP population, whose progeny directly contribute to the interfaces that connect bone to tendon (entheses), tendon to muscle (myotendinous junctions), and the associated superstructures. Furthermore, deletion of Hic1 leads to skeletal defects reflective of deficient muscle-bone coupling and, consequently, perturbation of ambulation. Collectively, these findings show that Hic1 identifies a unique MP population that contributes to a secondary wave of bone sculpting critical to skeletal morphogenesis.
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Affiliation(s)
- Martin Arostegui
- Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - R Wilder Scott
- Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - T Michael Underhill
- Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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Matsuhashi Y, Horiuchi K, Nakagawa T, Takahashi Y, Imabayashi H, Hosogane N, Watanabe K, Matsumoto M, Chiba K. Abrogation of LBX1 in skeletal muscle results in hypoplastic limbs and progressive kyphosis in mice. J Orthop Res 2023; 41:884-890. [PMID: 35856296 DOI: 10.1002/jor.25417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 02/04/2023]
Abstract
LBX1 is a gene located near a single-nucleotide polymorphism, rs11190870, which is highly associated with susceptibility to adolescent idiopathic scoliosis. However, the potential involvement of LBX1 in the etiology of this spinal deformity has not been elucidated. In this study, we aimed to determine whether the lack of LBX1 in skeletal muscle results in spinal deformities in mice. We generated mutant mice in which the Lbx1 allele was conditionally excised under the control of a human muscle actin promoter. Mice lacking LBX1 from the skeletal muscle were fertile and available. The mutant mice had hypoplastic forelimbs and weighed less than control animals, but otherwise, there were no overt anomalies. The mice did not exhibit a scoliosis-like spinal deformity; however, they developed moderate kyphosis as they grew old. These observations indicated that LBX1 is involved in limb development and potentially in the maintenance of spinal curvature/alignment in mice.
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Affiliation(s)
- Yusuke Matsuhashi
- Department of Orthopedic Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Keisuke Horiuchi
- Department of Orthopedic Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Takahiro Nakagawa
- Department of Orthopedic Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yohei Takahashi
- Department of Orthopaedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Hideaki Imabayashi
- Department of Orthopedic Surgery, Saiseikai Central Hospital, Tokyo, Japan
| | - Naobumi Hosogane
- Department of Orthopedic Surgery, Kyorin University, Mitaka, Tokyo, Japan
| | - Kota Watanabe
- Department of Orthopaedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Kazuhiro Chiba
- Department of Orthopedic Surgery, National Defense Medical College, Tokorozawa, Saitama, Japan
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7
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Andrey G, Duboule D. Genetic cold cases; lessons from solving complex congenital limb disorders. Genes Dev 2023; 37:261-276. [PMID: 36990510 PMCID: PMC10153463 DOI: 10.1101/gad.350450.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Congenital genetic disorders affecting limb morphology in humans and other mammals are particularly well described, due to both their rather high frequencies of occurrence and the ease of their detection when expressed as severe forms. In most cases, their molecular and cellular etiology remained unknown long after their initial description, often for several decades, and sometimes close to a century. Over the past 20 yr, however, experimental and conceptual advances in our understanding of gene regulation, in particular over large genomic distances, have allowed these cold cases to be reopened and, eventually, for some of them to be solved. These investigations led not only to the isolation of the culprit genes and mechanisms, but also to the understanding of the often complex regulatory processes that are disturbed in such mutant genetic configurations. Here, we present several cases in which dormant regulatory mutations have been retrieved from the archives, starting from a historical perspective up to their molecular explanations. While some cases remain open, waiting for new tools and/or concepts to bring their investigations to an end, the solutions to others have contributed to our understanding of particular features often found in the regulation of developmental genes and hence can be used as benchmarks to address the impact of noncoding variants in the future.
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Affiliation(s)
- Guillaume Andrey
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland;
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva 4, Switzerland
| | - Denis Duboule
- Collège de France, 75231 Paris, France;
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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8
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Cova G, Glaser J, Schöpflin R, Prada-Medina CA, Ali S, Franke M, Falcone R, Federer M, Ponzi E, Ficarella R, Novara F, Wittler L, Timmermann B, Gentile M, Zuffardi O, Spielmann M, Mundlos S. Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3. Nat Commun 2023; 14:1475. [PMID: 36928426 PMCID: PMC10020157 DOI: 10.1038/s41467-023-37057-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigate the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice results in restructuring of the chromatin architecture. This leads to ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern induced by AER-specific enhancers of Fgf8. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression in the developing limb. Our results reveal insights into the molecular mechanism underlying SHFM3 and provide conceptual framework for how genomic rearrangements can cause gene misexpression and disease.
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Affiliation(s)
- Giulia Cova
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Department of Pathology, New York University School of Medicine, Langone Health Medical Center, New York, NY, 10016, USA.
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Cesar Augusto Prada-Medina
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Rita Falcone
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Miriam Federer
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Universität Innsbruck, Innsbruck, 6020, Austria
| | - Emanuela Ponzi
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Romina Ficarella
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | | | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Mattia Gentile
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, 27100, Italy
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig Holstein Campus Kiel and Christian-Albrechts-Universität, Kiel, 24118, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, 13353, Germany.
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Markman S, Zada M, David E, Giladi A, Amit I, Zelzer E. A single-cell census of mouse limb development identifies complex spatiotemporal dynamics of skeleton formation. Dev Cell 2023; 58:565-581.e4. [PMID: 36931270 DOI: 10.1016/j.devcel.2023.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 10/20/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023]
Abstract
Limb development has long served as a model system for coordinated spatial patterning of progenitor cells. Here, we identify a population of naive limb progenitors and show that they differentiate progressively to form the skeleton in a complex, non-consecutive, three-dimensional pattern. Single-cell RNA sequencing of the developing mouse forelimb identified three progenitor states: naive, proximal, and autopodial, as well as Msx1 as a marker for the naive progenitors. In vivo lineage tracing confirmed this role and localized the naive progenitors to the outer margin of the limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that the progressive transition of Msx1+ naive progenitors into proximal and autopodial progenitors coincides with their differentiation to Sox9+ chondroprogenitors, which occurs along all the forming skeletal segments. Indeed, tracking the spatiotemporal sequence of differentiation showed that the skeleton forms progressively in a complex pattern. These findings suggest an alternative model for limb skeleton development.
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Affiliation(s)
- Svetlana Markman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mor Zada
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Nojiri T, Werneburg I, Tu VT, Fukui D, Takechi M, Iseki S, Furutera T, Koyabu D. Timing of organogenesis underscores the evolution of neonatal life histories and powered flight in bats. Proc Biol Sci 2023; 290:20221928. [PMID: 36629110 PMCID: PMC9832570 DOI: 10.1098/rspb.2022.1928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
Bats have undergone one of the most drastic limb innovations in vertebrate history, associated with the evolution of powered flight. Knowledge of the genetic basis of limb organogenesis in bats has increased but little has been documented regarding the differences between limb organogenesis in bats and that of other vertebrates. We conducted embryological comparisons of the timelines of limb organogenesis in 24 bat species and 72 non-bat amniotes. In bats, the time invested for forelimb organogenesis has been considerably extended and the appearance timing of the forelimb ridge has been significantly accelerated, whereas the timing of the finger and first appearance of the claw development has been delayed, facilitating the enlargement of the manus. Furthermore, we discovered that bats initiate the development of their hindlimbs earlier than their forelimbs compared with other placentals. Bat neonates are known to be able to cling continuously with their well-developed foot to the maternal bodies or habitat substrates soon after birth. We suggest that this unique life history of neonates, which possibly coevolved with powered flight, has driven the accelerated development of the hindlimb and precocious foot.
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Affiliation(s)
- Taro Nojiri
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Environmental Science, Hokkaido University, North 11, West 10, Sapporo 060-0811, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ingmar Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment an der Eberhard Karls Universität, Sigwartstraße 10, D-72076 Tübingen, Germany
- Fachbereich Geowissenschaften, Eberhard Karls Universität, Hölderlinstraße 12, 72074 Tübingen, Germany
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet road, Cau Giay district, Hanoi, Vietnam
- Vietnam Academy of Science and Technology, Graduate University of Science and Technology, No. 18, Hoang Quac Viet road, Cau Giay district, Hanoi, Vietnam
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 9-61, Yamabe-Higashimachi, Furano, Hokkaido 079-1563, Japan
| | - Masaki Takechi
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Sachiko Iseki
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Toshiko Furutera
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Daisuke Koyabu
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba-shi, Ibaraki 305-8550, Japan
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11
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H’ng CH, Khaladkar A, Rosello-Diez A. Look who's TORking: mTOR-mediated integration of cell status and external signals during limb development and endochondral bone growth. Front Cell Dev Biol 2023; 11:1153473. [PMID: 37152288 PMCID: PMC10154674 DOI: 10.3389/fcell.2023.1153473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
The balance of cell proliferation and size is key for the control of organ development and repair. Moreover, this balance has to be coordinated within tissues and between tissues to achieve robustness in the organ's pattern and size. The tetrapod limb has been used to study these topics during development and repair, and several conserved pathways have emerged. Among them, mechanistic target of rapamycin (mTOR) signaling, despite being active in several cell types and developmental stages, is one of the least understood in limb development, perhaps because of its multiple potential roles and interactions with other pathways. In the body of this review, we have collated and integrated what is known about the role of mTOR signaling in three aspects of tetrapod limb development: 1) limb outgrowth; 2) chondrocyte differentiation after mesenchymal condensation and 3) endochondral ossification-driven longitudinal bone growth. We conclude that, given its ability to interact with the most common signaling pathways, its presence in multiple cell types, and its ability to influence cell proliferation, size and differentiation, the mTOR pathway is a critical integrator of external stimuli and internal status, coordinating developmental transitions as complex as those taking place during limb development. This suggests that the study of the signaling pathways and transcription factors involved in limb patterning, morphogenesis and growth could benefit from probing the interaction of these pathways with mTOR components.
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Affiliation(s)
- Chee Ho H’ng
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Ashwini Khaladkar
- Department of Biochemistry, Central University of Hyderabad, Hyderabad, India
| | - Alberto Rosello-Diez
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Alberto Rosello-Diez, ,
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12
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Berenguer M, Duester G. Genetic loss-of-function does not support gain-of-function studies suggesting retinoic acid controls limb bud timing and scaling. Front Cell Dev Biol 2023; 11:1149009. [PMID: 37123409 PMCID: PMC10133474 DOI: 10.3389/fcell.2023.1149009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
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13
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Zhu M, Tabin CJ. The role of timing in the development and evolution of the limb. Front Cell Dev Biol 2023; 11:1135519. [PMID: 37200627 PMCID: PMC10185760 DOI: 10.3389/fcell.2023.1135519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023] Open
Abstract
The term heterochrony was coined to describe changes in the timing of developmental processes relative to an ancestral state. Limb development is a well-suited system to address the contribution of heterochrony to morphological evolution. We illustrate how timing mechanisms have been used to establish the correct pattern of the limb and provide cases where natural variations in timing have led to changes in limb morphology.
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14
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Lex RK, Vokes SA. Timing is everything: Transcriptional repression is not the default mode for regulating Hedgehog signaling. Bioessays 2022; 44:e2200139. [PMID: 36251875 PMCID: PMC9691524 DOI: 10.1002/bies.202200139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022]
Abstract
Hedgehog (HH) signaling is a conserved pathway that drives developmental growth and is essential for the formation of most organs. The expression of HH target genes is regulated by a dual switch mechanism where GLI proteins function as bifunctional transcriptional activators (in the presence of HH signaling) and transcriptional repressors (in the absence of HH signaling). This results in a tight control of GLI target gene expression during rapidly changing levels of pathway activity. It has long been presumed that GLI proteins also repress target genes prior to the initial expression of HH in a given tissue. This idea forms the basis for the limb bud pre-patterning model for regulating digit number. Recent findings indicate that GLI repressor proteins are indeed present prior to HH signaling but contrary to this model, GLI proteins are inert as they do not regulate transcriptional responses or enhancer chromatin modifications at this time. These findings suggest that GLI transcriptional repressor activity is not a default state as assumed, but is itself regulated in an unknown fashion. We discuss these findings and their implications for understanding pre-patterning, digit regulation, and HH-driven disease.
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Affiliation(s)
- Rachel K. Lex
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109 USA
| | - Steven A. Vokes
- Department of Molecular Bioscienc es, University of Texas at Austin, 100 E 24th Street Stop A5000, Austin, TX 78712 USA
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15
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Johnson GL, Glasser MB, Charles JF, Duryea J, Lehoczky JA. En1 and Lmx1b do not recapitulate embryonic dorsal-ventral limb patterning functions during mouse digit tip regeneration. Cell Rep 2022; 41:111701. [PMID: 36417876 PMCID: PMC9727699 DOI: 10.1016/j.celrep.2022.111701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/09/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The mouse digit tip regenerates following amputation. How the regenerate is patterned is unknown, but a long-standing hypothesis proposes developmental patterning mechanisms are re-used during regeneration. The digit tip bone exhibits dorsal-ventral (DV) polarity, so we focus on En1 and Lmx1b, two factors necessary for DV patterning during limb development. We investigate whether they are re-expressed during regeneration in a developmental-like pattern and whether they direct DV morphology of the regenerate. We find that both En1 and Lmx1b are expressed in the regenerating digit tip epithelium and mesenchyme, respectively, but without DV polarity. Conditional genetics and quantitative analysis of digit tip bone morphology determine that genetic deletion of En1 or Lmx1b in adult digit tip regeneration modestly reduces bone regeneration but does not affect DV patterning. Collectively, our data suggest that, while En1 and Lmx1b are re-expressed during mouse digit tip regeneration, they do not define the DV axis during regeneration.
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Affiliation(s)
- Gemma L. Johnson
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Morgan B. Glasser
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Julia F. Charles
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jeffrey Duryea
- Department of Radiology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessica A. Lehoczky
- Department of Orthopedic Surgery, Brigham and Women’s Hospital, Boston, MA 02115, USA,Lead contact,Correspondence:
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16
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Yamaguchi Y, Murase A, Kodama R, Yamamoto A, Imai H, Yoneyama A, Yamada S. Three-dimensional visualization and quantitative analysis of embryonic and fetal thigh muscles using magnetic resonance and phase-contrast X-ray imaging. J Anat 2022; 241:1310-1323. [PMID: 36123316 DOI: 10.1111/joa.13764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/04/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
The musculoskeletal system around the human hip joint has acquired a suitable structure for erect bipedal walking. However, little is known about the process of separation and maturation of individual muscles during the prenatal period, when muscle composition is acquired. Understanding the maturation process of the normal musculoskeletal system contributes to elucidating the acquisition of bipedal walking in humans and to predicting normal growth and detecting congenital muscle disorders and anomalies. In this study, we clarify the process of thigh muscle maturation from the embryonic stage to the mid-fetal stage using serial sections, phase-contrast X-ray computed tomography, and magnetic resonance imaging. We also provide a 4D atlas of human thigh muscles between 8 and 23 weeks of gestation. As a result, we first show that muscle separation in the lower thigh tends to progress from the superficial to the deep layers and that all musculoskeletal components are formed by Carnegie Stage 22. Next, we show that femur and muscle volume grow in correlation with crown-rump length. Finally, we show that the anterior, abductor, and posterior muscle groups in the thigh contain a high percentage of monoarticular muscle volume by the end of the embryonic period. This ratio approaches that of adult muscle composition during normal early fetal development and is typical of bipedal walking. This study of fetal muscle composition suggests that preparation for postnatal walking may begin in early fetal period.
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Affiliation(s)
- Yutaka Yamaguchi
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ami Murase
- Human Health Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryota Kodama
- Human Health Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akira Yamamoto
- Medical Education Center, Kyoto University, Kyoto, Japan
| | - Hirohiko Imai
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | | | - Shigehito Yamada
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Human Health Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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17
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Zhu J, Patel R, Trofka A, Harfe BD, Mackem S. Sonic hedgehog is not a limb morphogen but acts as a trigger to specify all digits in mice. Dev Cell 2022; 57:2048-2062.e4. [PMID: 35977544 PMCID: PMC9709693 DOI: 10.1016/j.devcel.2022.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/03/2022] [Accepted: 07/26/2022] [Indexed: 11/03/2022]
Abstract
Limb patterning by Sonic hedgehog (Shh), via either graded spatial or temporal signal integration, is a paradigm for "morphogen" function, yet how Shh instructs distinct digit identities remains controversial. Here, we bypass the Shh requirement in cell survival during outgrowth and demonstrate that a transient, early Shh pulse is both necessary and sufficient for normal mouse limb development. Shh response is only short range and is limited to the Shh-expressing zone during this time window. Shh patterns digits 1-3, anterior to this zone, by an indirect mechanism rather than direct spatial or temporal signal integration. Using a genetic relay-signaling assay, we discover that Shh also specifies digit 1/thumb (thought to be exclusively Shh independent) indirectly, and this finding implicates Shh in a unique regulatory hierarchy for digit 1 evolutionary adaptations such as opposable thumbs. This study illuminates Shh as a trigger for an indirect downstream network that becomes rapidly self-sustaining, with mechanistic relevance for limb development, regeneration, and evolution.
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Affiliation(s)
- Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Rashmi Patel
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Anna Trofka
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Brian D Harfe
- College of Medicine, Department of Molecular Genetics and Microbiology and the Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA.
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18
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Lancman JJ, Hasso SM, Suzuki T, Kherdjemil Y, Kmita M, Ferris A, Dong PDS, Ros MA, Fallon JF. Downregulation of Grem1 expression in the distal limb mesoderm is a necessary precondition for phalanx development. Dev Dyn 2022; 251:1439-1455. [PMID: 34719843 PMCID: PMC9054941 DOI: 10.1002/dvdy.431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The phalanges are the final skeletal elements to form in the vertebrate limb and their identity is regulated by signaling at the phalanx forming region (PFR) located at the tip of the developing digit ray. Here, we seek to explore the relationship between PFR activity and phalanx morphogenesis, which define the most distal limb skeletal elements, and signals associated with termination of limb outgrowth. RESULTS As Grem1 is extinguished in the distal chick limb mesoderm, the chondrogenesis marker Aggrecan is up-regulated in the metatarsals and phalanges. Fate mapping confirms that subridge mesoderm cells contribute to the metatarsal and phalanges when subridge Grem1 is down-regulated. Grem1 overexpression specifically blocks chick phalanx development by inhibiting PFR activity. PFR activity and digit development are also disrupted following overexpression of a Gli3 repressor, which results in Grem1 expression in the distal limb and downregulation of Bmpr1b. CONCLUSIONS Based on expression and fate mapping studies, we propose that downregulation of Grem1 in the distal limb marks the transition from metatarsal to phalanx development. This suggests that downregulation of Grem1 in the distal limb mesoderm is necessary for phalanx development. Grem1 downregulation allows for full PFR activity and phalanx progenitor cell commitment to digit fate.
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Affiliation(s)
- Joseph J Lancman
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Sean M Hasso
- Heat Biologics, Morrisville, North Carolina, USA
| | - Takayuki Suzuki
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yacine Kherdjemil
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Andrea Ferris
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - P Duc S Dong
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas-Universidad de Cantabria-Sociedad para al Desarrollo Cantabria, Santander, Spain
- Departamento de Anatomía y Biología Celular, Facultad de Medicina, Universidad de Cantabria, Santander, Spain
| | - John F Fallon
- Department of Anatomy, University of Wisconsin Madison, Madison, Wisconsin, USA
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19
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García-García RD, Garay-Pacheco E, Marín-Llera JC, Chimal-Monroy J. Recombinant Limb Assay as in Vivo Organoid Model. Front Cell Dev Biol 2022; 10:863140. [PMID: 35557939 PMCID: PMC9086426 DOI: 10.3389/fcell.2022.863140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Organ formation initiates once cells become committed to one of the three embryonic germ layers. In the early stages of embryogenesis, different gene transcription networks regulate cell fate after each germ layer is established, thereby directing the formation of complex tissues and functional organs. These events can be modeled in vitro by creating organoids from induced pluripotent, embryonic, or adult stem cells to study organ formation. Under these conditions, the induced cells are guided down the developmental pathways as in embryonic development, resulting in an organ of a smaller size that possesses the essential functions of the organ of interest. Although organoids are widely studied, the formation of skeletal elements in an organoid model has not yet been possible. Therefore, we suggest that the formation of skeletal elements using the recombinant limb (RL) assay system can serve as an in vivo organoid model. RLs are formed from undissociated or dissociated-reaggregated undifferentiated mesodermal cells introduced into an ectodermal cover obtained from an early limb bud. Next, this filled ectoderm is grafted into the back of a donor chick embryo. Under these conditions, the cells can receive the nascent embryonic signals and develop complex skeletal elements. We propose that the formation of skeletal elements induced through the RL system may occur from stem cells or other types of progenitors, thus enabling the study of morphogenetic properties in vivo from these cells for the first time.
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Affiliation(s)
- Roberto Damián García-García
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Estefanía Garay-Pacheco
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Jessica Cristina Marín-Llera
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Jesús Chimal-Monroy
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
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20
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Miyamoto K, Kawakami K, Tamura K, Abe G. Developmental independence of median fins from the larval fin fold revises their evolutionary origin. Sci Rep 2022; 12:7521. [PMID: 35525860 PMCID: PMC9079066 DOI: 10.1038/s41598-022-11180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
The median fins of modern fish that show discrete forms (dorsal, anal, and caudal fins) are derived from a continuous fold-like structure, both in ontogeny and phylogeny. The median fin fold (MFF) hypothesis assumes that the median fins evolved by reducing some positions in the continuous fin fold of basal chordates, based on the classical morphological observation of developmental reduction in the larval fin folds of living fish. However, the developmental processes of median fins are still unclear at the cellular and molecular levels. Here, we describe the transition from the larval fin fold into the median fins in zebrafish at the cellular and molecular developmental level. We demonstrate that reduction does not play a role in the emergence of the dorsal fin primordium. Instead, the reduction occurs along with body growth after primordium formation, rather than through actively scrapping the non-fin forming region by inducing cell death. We also report that the emergence of specific mesenchymal cells and their proliferation promote dorsal fin primordium formation. Based on these results, we propose a revised hypothesis for median fin evolution in which the acquisition of de novo developmental mechanisms is a crucial evolutionary component of the discrete forms of median fins.
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Affiliation(s)
- Kazuhide Miyamoto
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Koji Tamura
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Gembu Abe
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan.
- Division of Developmental Biology, Department of Functional Morphology, School of Life Science, Faculty of Medicine, Tottori University, Nishi-cho 86, Yonago, 683-8503, Japan.
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21
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Lovely AM, Duerr TJ, Qiu Q, Galvan S, Voss SR, Monaghan JR. Wnt Signaling Coordinates the Expression of Limb Patterning Genes During Axolotl Fore limb Development and Regeneration. Front Cell Dev Biol 2022; 10:814250. [PMID: 35531102 PMCID: PMC9068880 DOI: 10.3389/fcell.2022.814250] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
After amputation, axolotl salamanders can regenerate their limbs, but the degree to which limb regeneration recapitulates limb development remains unclear. One limitation in answering this question is our lack of knowledge about salamander limb development. Here, we address this question by studying expression patterns of genes important for limb patterning during axolotl salamander limb development and regeneration. We focus on the Wnt signaling pathway because it regulates multiple functions during tetrapod limb development, including limb bud initiation, outgrowth, patterning, and skeletal differentiation. We use fluorescence in situ hybridization to show the expression of Wnt ligands, Wnt receptors, and limb patterning genes in developing and regenerating limbs. Inhibition of Wnt ligand secretion permanently blocks limb bud outgrowth when treated early in limb development. Inhibiting Wnt signaling during limb outgrowth decreases the expression of critical signaling genes, including Fgf10, Fgf8, and Shh, leading to the reduced outgrowth of the limb. Patterns of gene expression are similar between developing and regenerating limbs. Inhibition of Wnt signaling during regeneration impacted patterning gene expression similarly. Overall, our findings suggest that limb development and regeneration utilize Wnt signaling similarly. It also provides new insights into the interaction of Wnt signaling with other signaling pathways during salamander limb development and regeneration.
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Affiliation(s)
| | - Timothy J. Duerr
- Department of Biology, Northeastern University, Boston, MA, United States
| | - Qingchao Qiu
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, United States
| | | | - S. Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, United States
| | - James R. Monaghan
- Department of Biology, Northeastern University, Boston, MA, United States
- Institute for Chemical Imaging of Living Systems, Northeastern University, Boston, MA, United States
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22
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Parada C, Banavar SP, Khalilian P, Rigaud S, Michaut A, Liu Y, Joshy DM, Campàs O, Gros J. Mechanical feedback defines organizing centers to drive digit emergence. Dev Cell 2022; 57:854-866.e6. [PMID: 35413235 DOI: 10.1016/j.devcel.2022.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/25/2022] [Accepted: 03/10/2022] [Indexed: 11/03/2022]
Abstract
During embryonic development, digits gradually emerge in a periodic pattern. Although genetic evidence indicates that digit formation results from a self-organizing process, the underlying mechanisms are still unclear. Here, we find that convergent-extension tissue flows driven by active stresses underlie digit formation. These active stresses simultaneously shape cartilage condensations and lead to the emergence of a compressive stress region that promotes high activin/p-SMAD/SOX9 expression, thereby defining digit-organizing centers via a mechanical feedback. In Wnt5a mutants, such mechanical feedback is disrupted due to the loss of active stresses, organizing centers do not emerge, and digit formation is precluded. Thus, digit emergence does not result solely from molecular interactions, as was previously thought, but requires a mechanical feedback that ensures continuous coupling between phalanx specification and elongation. Our work, which links mechanical and molecular signals, provides a mechanistic context for the emergence of organizing centers that may underlie various developmental processes.
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Affiliation(s)
- Carolina Parada
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75724 Paris Cedex 15, France; CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Samhita P Banavar
- Department of Physics, University of California, Santa Barbara, CA 93106-5070, USA
| | - Parisa Khalilian
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75724 Paris Cedex 15, France; CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Stephane Rigaud
- Image Analysis Hub, C2RT, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Arthur Michaut
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75724 Paris Cedex 15, France; CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Yucen Liu
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106-5070, USA
| | - Dennis Manjaly Joshy
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106-5070, USA
| | - Otger Campàs
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106-5070, USA; Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA, USA; Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany.
| | - Jerome Gros
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75724 Paris Cedex 15, France; CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France.
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23
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Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Curr Biol 2022; 32:289-303.e6. [PMID: 34793695 PMCID: PMC8792248 DOI: 10.1016/j.cub.2021.10.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/16/2021] [Accepted: 10/28/2021] [Indexed: 01/26/2023]
Abstract
Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Pushpanathan Muthuirulan
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - Stanley J Neufeld
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Mai P Tran
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Haydee L Gutierrez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kevin D Chen
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Joel M Erberich
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138, USA
| | - John Cobb
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany; Max Planck Institute for the Physics of Complex Systems, Nothnitzerstraße 38, Dresden 01187, Germany
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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24
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Li J, Glover JD, Zhang H, Peng M, Tan J, Mallick CB, Hou D, Yang Y, Wu S, Liu Y, Peng Q, Zheng SC, Crosse EI, Medvinsky A, Anderson RA, Brown H, Yuan Z, Zhou S, Xu Y, Kemp JP, Ho YYW, Loesch DZ, Wang L, Li Y, Tang S, Wu X, Walters RG, Lin K, Meng R, Lv J, Chernus JM, Neiswanger K, Feingold E, Evans DM, Medland SE, Martin NG, Weinberg SM, Marazita ML, Chen G, Chen Z, Zhou Y, Cheeseman M, Wang L, Jin L, Headon DJ, Wang S. Limb development genes underlie variation in human fingerprint patterns. Cell 2022; 185:95-112.e18. [PMID: 34995520 PMCID: PMC8740935 DOI: 10.1016/j.cell.2021.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022]
Abstract
Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint type across the digits, including a genetic basis for the long-recognized “pattern-block” correlations among the middle three digits. In particular, we identified a variant near EVI1 that alters regulatory activity and established a role for EVI1 in dermatoglyph patterning in mice. Dynamic EVI1 expression during human development supports its role in shaping the limbs and digits, rather than influencing skin patterning directly. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci, with nearby genes being strongly enriched for general limb development pathways. We also found that fingerprint patterns were genetically correlated with hand proportions. Taken together, these findings support the key role of limb development genes in influencing the outcome of fingerprint patterning. GWAS identifies variants associated with fingerprint type across all digits Fingerprint-associated genes are strongly enriched for limb development functions Evi1 alters dermatoglyphs in mice by modulating limb rather than skin development Fingerprint patterns are genetically correlated with hand and finger proportions
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Affiliation(s)
- Jinxi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - James D Glover
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Haiguo Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Meifang Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Chandana Basu Mallick
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Dan Hou
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Edie I Crosse
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, PRC
| | - Shen Zhou
- Shanghai Foreign Language School, Shanghai 200083, PRC
| | - Yanqing Xu
- Forest Ridge School of the Sacred Heart, Bellevue, WA 98006, USA
| | - John P Kemp
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia
| | - Yvonne Y W Ho
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | - Danuta Z Loesch
- Psychology Department, La Trobe University, Melbourne, VIC, Australia
| | | | | | | | - Xiaoli Wu
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ruogu Meng
- Center for Data Science in Health and Medicine, Peking University, Beijing 100191, PRC
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, PRC
| | - Jonathan M Chernus
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | | | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Clinical and Translational Science, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gang Chen
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PRC
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Lan Wang
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, PRC.
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, PRC.
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25
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Wells KM, Baumel M, McCusker CD. The Regulation of Growth in Developing, Homeostatic, and Regenerating Tetrapod Limbs: A Minireview. Front Cell Dev Biol 2022; 9:768505. [PMID: 35047496 PMCID: PMC8763381 DOI: 10.3389/fcell.2021.768505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/19/2021] [Indexed: 01/29/2023] Open
Abstract
The size and shape of the tetrapod limb play central roles in their functionality and the overall physiology of the organism. In this minireview we will discuss observations on mutant animal models and humans, which show that the growth and final size of the limb is most impacted by factors that regulate either limb bud patterning or the elongation of the long bones. We will also apply the lessons that have been learned from embryos to how growth could be regulated in regenerating limb structures and outline the challenges that are unique to regenerating animals.
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26
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Díaz-Hernández ME, Galván-Hernández CI, Marín-Llera JC, Camargo-Sosa K, Bustamante M, Wischin S, Chimal-Monroy J. Activation of the WNT-BMP-FGF Regulatory Network Induces the Onset of Cell Death in Anterior Mesodermal Cells to Establish the ANZ. Front Cell Dev Biol 2021; 9:703836. [PMID: 34820367 PMCID: PMC8606791 DOI: 10.3389/fcell.2021.703836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
The spatiotemporal control of programmed cell death (PCD) plays a significant role in sculpting the limb. In the early avian limb bud, the anterior necrotic zone (ANZ) and the posterior necrotic zone are two cell death regions associated with digit number reduction. In this study, we evaluated the first events triggered by the FGF, BMP, and WNT signaling interactions to initiate cell death in the anterior margin of the limb to establish the ANZ. This study demonstrates that in a period of two to 8 h after the inhibition of WNT or FGF signaling or the activation of BMP signaling, cell death was induced in the anterior margin of the limb concomitantly with the regulation of Dkk, Fgf8, and Bmp4 expression. Comparing the gene expression profile between the ANZ and the undifferentiated zone at 22HH and 25HH and between the ANZ of 22HH and 25HH stages correlates with functional programs controlled by the regulatory network FGF, BMP, and WNT signaling in the anterior margin of the limb. This work provides novel insights to recognize a negative feedback loop between FGF8, BMP4, and DKK to control the onset of cell death in the anterior margin of the limb to the establishment of the ANZ.
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Affiliation(s)
- Martha Elena Díaz-Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Claudio Iván Galván-Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Jessica Cristina Marín-Llera
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Karen Camargo-Sosa
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Marcia Bustamante
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Sabina Wischin
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
| | - Jesús Chimal-Monroy
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, Mexico
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27
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Huang BL, Mackem S. Rethinking positional information and digit identity: The role of late interdigit signaling. Dev Dyn 2021; 251:1414-1422. [PMID: 34811837 DOI: 10.1002/dvdy.440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 12/22/2022] Open
Abstract
Seminal work from John Fallon's lab has illuminated how digit identity determination involves ongoing late regulation and occurs progressively during phalanx formation. Complementary genetic analyses in mice and several papers in this special issue have begun to flesh out how interdigit signaling accomplishes this, but major questions remain unaddressed, including how uncommitted progenitors from which phalanges arise are maintained, and what factors set limits on digit extension and phalanx number, particularly in mammals. This review summarizes what has been learned in the two decades since control of digit identity by late interdigit signals was first identified and what remains poorly understood, and will hopefully spark renewed interest in a process that is critical to evolutionary limb adaptations but nevertheless remains enigmatic.
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Affiliation(s)
- Bau-Lin Huang
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, Maryland, USA
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, Maryland, USA
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28
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Fujii K, Zhulyn O, Byeon GW, Genuth NR, Kerr CH, Walsh EM, Barna M. Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c. Dev Cell 2021; 56:2928-2937.e9. [PMID: 34752747 DOI: 10.1016/j.devcel.2021.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/06/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022]
Abstract
Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning. Analysis of loss-of-function eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor patched 1 (Ptch1) dosage. Genome-wide in vivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine-rich motif present in subsets of 5'-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find a transcript specific effect in Eif3c loss-of-function embryos whereby translation of Ptch1 through this pyrimidine-rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.
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Affiliation(s)
- Kotaro Fujii
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.
| | - Olena Zhulyn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Gun Woo Byeon
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Naomi R Genuth
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin M Walsh
- Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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29
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Matsuda S, Schaefer JV, Mii Y, Hori Y, Bieli D, Taira M, Plückthun A, Affolter M. Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nat Commun 2021; 12:6435. [PMID: 34750371 PMCID: PMC8576045 DOI: 10.1038/s41467-021-26726-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
How morphogen gradients control patterning and growth in developing tissues remains largely unknown due to lack of tools manipulating morphogen gradients. Here, we generate two membrane-tethered protein binders that manipulate different aspects of Decapentaplegic (Dpp), a morphogen required for overall patterning and growth of the Drosophila wing. One is "HA trap" based on a single-chain variable fragment (scFv) against the HA tag that traps HA-Dpp to mainly block its dispersal, the other is "Dpp trap" based on a Designed Ankyrin Repeat Protein (DARPin) against Dpp that traps Dpp to block both its dispersal and signaling. Using these tools, we found that, while posterior patterning and growth require Dpp dispersal, anterior patterning and growth largely proceed without Dpp dispersal. We show that dpp transcriptional refinement from an initially uniform to a localized expression and persistent signaling in transient dpp source cells render the anterior compartment robust against the absence of Dpp dispersal. Furthermore, despite a critical requirement of dpp for the overall wing growth, neither Dpp dispersal nor direct signaling is critical for lateral wing growth after wing pouch specification. These results challenge the long-standing dogma that Dpp dispersal is strictly required to control and coordinate overall wing patterning and growth.
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Affiliation(s)
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- JST PRESTO, Kawaguchi, Saitama, Japan
| | - Yutaro Hori
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | | | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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30
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Amândio AR, Beccari L, Lopez-Delisle L, Mascrez B, Zakany J, Gitto S, Duboule D. Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster. Genes Dev 2021; 35:1490-1509. [PMID: 34711654 PMCID: PMC8559674 DOI: 10.1101/gad.348934.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022]
Abstract
Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their importance in organizing a TAD border, which isolates the most posterior genes from the rest of the cluster, the positions and orientations of these sites suggest that CTCF may be instrumental in the selection of various subsets of contiguous genes, which are targets of distinct remote enhancers located in the flanking regulatory landscapes. We examined this possibility by producing an allelic series of cumulative in cis mutations in these sites, up to the abrogation of CTCF binding in the five sites located on one side of the TAD border. In the most impactful alleles, the global chromatin architecture of the locus was modified, yet not drastically, illustrating that CTCF sites located on one side of a strong TAD border are sufficient to organize at least part of this insulation. Spatial colinearity in the expression of these genes along the major body axis was nevertheless maintained, despite abnormal expression boundaries. In contrast, strong effects were scored in the selection of target genes responding to particular enhancers, leading to the misregulation of Hoxd genes in specific structures. Altogether, while most enhancer-promoter interactions can occur in the absence of this series of CTCF sites, the binding of CTCF in the Hox cluster is required to properly transform a rather unprecise process into a highly discriminative mechanism of interactions, which is translated into various patterns of transcription accompanied by the distinctive chromatin topology found at this locus. Our allelic series also allowed us to reveal the distinct functional contributions for CTCF sites within this Hox cluster, some acting as insulator elements, others being necessary to anchor or stabilize enhancer-promoter interactions, and some doing both, whereas they all together contribute to the formation of a TAD border. This variety of tasks may explain the amazing evolutionary conservation in the distribution of these sites among paralogous Hox clusters or between various vertebrates.
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Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland
- Collège de France, 75231 Paris, France
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31
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Bruneau BG. Dissecting CTCF site function in a tense HoxD locus. Genes Dev 2021; 35:1401-1402. [PMID: 34725128 PMCID: PMC8559678 DOI: 10.1101/gad.349089.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this issue of Genes & Development, Amândio and colleagues (pp. 1490-1509) dissect the function of a cluster of several CTCF binding sites in the HoxD cluster by iterative deletions in mice. They found additive functions for some, and intriguingly found that some sites function as insulators, while others function as anchors for enhancer-promoter interactions. These functions vary depending on developmental context. The work provides new insights into the roles played by CTCF in regulating developmental patterns and 3D chromatin organization.
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Affiliation(s)
- Benoit G Bruneau
- Gladstone Institutes, San Francisco, California 94158 USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, California 94158, USA; Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, USA; Department of Pediatrics, University of California at San Francisco, San Francisco, California 94143, USA
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Royle SR, Tabin CJ, Young JJ. Limb positioning and initiation: An evolutionary context of pattern and formation. Dev Dyn 2021; 250:1264-1279. [PMID: 33522040 PMCID: PMC10623539 DOI: 10.1002/dvdy.308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 12/22/2022] Open
Abstract
Before limbs or fins, can be patterned and grow they must be initiated. Initiation of the limb first involves designating a portion of lateral plate mesoderm along the flank as the site of the future limb. Following specification, a myriad of cellular and molecular events interact to generate a bud that will grow and form the limb. The past three decades has provided a wealth of understanding on how those events generate the limb bud and how variations in them result in different limb forms. Comparatively, much less attention has been given to the earliest steps of limb formation and what impacts altering the position and initiation of the limb have had on evolution. Here, we first review the processes and pathways involved in these two phases of limb initiation, as determined from amniote model systems. We then broaden our scope to examine how variation in the limb initiation module has contributed to biological diversity in amniotes. Finally, we review what is known about limb initiation in fish and amphibians, and consider what mechanisms are conserved across vertebrates.
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Affiliation(s)
- Samantha R Royle
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Clifford J Tabin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John J Young
- Department of Biology, Simmons University, Boston, Massachusetts, USA
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Smith‐Paredes D, Griffith O, Fabbri M, Yohe L, Blackburn DG, Siler CD, Bhullar BS, Wagner GP. Hidden limbs in the "limbless skink" Brachymeles lukbani: Developmental observations. J Anat 2021; 239:693-703. [PMID: 33870497 PMCID: PMC8349411 DOI: 10.1111/joa.13447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/21/2021] [Accepted: 03/31/2021] [Indexed: 12/15/2022] Open
Abstract
Reduced limbs and limblessness have evolved independently in many lizard clades. Scincidae exhibit a wide range of limb-reduced morphologies, but only some species have been used to study the embryology of limb reduction (e.g., digit reduction in Chalcides and limb reduction in Scelotes). The genus Brachymeles, a Southeast Asian clade of skinks, includes species with a range of limb morphologies, from pentadactyl to functionally and structurally limbless species. Adults of the small, snake-like species Brachymeles lukbani show no sign of external limbs in the adult except for small depressions where they might be expected to occur. Here, we show that embryos of B. lukbani in early stages of development, on the other hand, show a truncated but well-developed limb with a stylopod and a zeugopod, but no signs of an autopod. As development proceeds, the limb's small size persists even while the embryo elongates. These observations are made based on external morphology. We used florescent whole-mount immunofluorescence to visualize the morphology of skeletal elements and muscles within the embryonic limb of B. lukabni. Early stages have a humerus and separated ulna and radius cartilages; associated with these structures are dorsal and ventral muscle masses as those found in the embryos of other limbed species. While the limb remains small, the pectoral girdle grows in proportion to the rest of the body, with well-developed skeletal elements and their associated muscles. In later stages of development, we find the small limb is still present under the skin, but there are few indications of its presence, save for the morphology of the scale covering it. By use of CT scanning, we find that the adult morphology consists of a well-developed pectoral girdle, small humerus, extremely reduced ulna and radius, and well-developed limb musculature connected to the pectoral girdle. These muscles form in association with a developing limb during embryonic stages, a hint that "limbless" lizards that possess these muscles may have or have had at least transient developing limbs, as we find in B. lukbani. Overall, this newly observed pattern of ontogenetic reduction leads to an externally limbless adult in which a limb rudiment is hidden and covered under the trunk skin, a situation called cryptomelia. The results of this work add to our growing understanding of clade-specific patterns of limb reduction and the convergent evolution of limbless phenotypes through different developmental processes.
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Affiliation(s)
- Daniel Smith‐Paredes
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Oliver Griffith
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Matteo Fabbri
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Laurel Yohe
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Daniel G. Blackburn
- Department of Biology, and Electron Microscopy CenterTrinity CollegeHartfordCTUSA
| | - Cameron D. Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural HistoryUniversity of OklahomaNormanOKUSA
| | - Bhart‐Anjan S. Bhullar
- Department of Earth and Planetary Science and Peabody Museum of Natural HistoryYale UniversityNew HavenCTUSA
| | - Günter P. Wagner
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
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Nord H, Kahsay A, Dennhag N, Pedrosa Domellöf F, von Hofsten J. Genetic compensation between Pax3 and Pax7 in zebrafish appendicular muscle formation. Dev Dyn 2021; 251:1423-1438. [PMID: 34435397 DOI: 10.1002/dvdy.415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Migrating muscle progenitors delaminate from the somite and subsequently form muscle tissue in distant anatomical regions such as the paired appendages, or limbs. In amniotes, this process requires a signaling cascade including the transcription factor paired box 3 (Pax3). RESULTS In this study, we found that, unlike in mammals, pax3a/3b double mutant zebrafish develop near to normal appendicular muscle. By analyzing numerous mutant combinations of pax3a, pax3b and pax7a, and pax7b, we determined that there is a feedback system and a compensatory mechanism between Pax3 and Pax7 in this developmental process, even though Pax7 alone is not required for appendicular myogenesis. pax3a/3b/7a/7b quadruple mutant developed muscle-less pectoral fins. CONCLUSIONS We found that Pax3 and Pax7 are redundantly required during appendicular myogenesis in zebrafish, where Pax7 is able to activate the same developmental programs as Pax3 in the premigratory progenitor cells.
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Affiliation(s)
- Hanna Nord
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Abraha Kahsay
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Nils Dennhag
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Fatima Pedrosa Domellöf
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden.,Department of Clinical Science, Ophthalmology, Umeå University, Umeå, Sweden
| | - Jonas von Hofsten
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
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35
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Tiu GC, Kerr CH, Forester CM, Krishnarao PS, Rosenblatt HD, Raj N, Lantz TC, Zhulyn O, Bowen ME, Shokat L, Attardi LD, Ruggero D, Barna M. A p53-dependent translational program directs tissue-selective phenotypes in a model of ribosomopathies. Dev Cell 2021; 56:2089-2102.e11. [PMID: 34242585 PMCID: PMC8319123 DOI: 10.1016/j.devcel.2021.06.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/26/2021] [Accepted: 06/11/2021] [Indexed: 12/13/2022]
Abstract
In ribosomopathies, perturbed expression of ribosome components leads to tissue-specific phenotypes. What accounts for such tissue-selective manifestations as a result of mutations in the ribosome, a ubiquitous cellular machine, has remained a mystery. Combining mouse genetics and in vivo ribosome profiling, we observe limb-patterning phenotypes in ribosomal protein (RP) haploinsufficient embryos, and we uncover selective translational changes of transcripts that controlling limb development. Surprisingly, both loss of p53, which is activated by RP haploinsufficiency, and augmented protein synthesis rescue these phenotypes. These findings are explained by the finding that p53 functions as a master regulator of protein synthesis, at least in part, through transcriptional activation of 4E-BP1. 4E-BP1, a key translational regulator, in turn, facilitates selective changes in the translatome downstream of p53, and this thereby explains how RP haploinsufficiency may elicit specificity to gene expression. These results provide an integrative model to help understand how in vivo tissue-specific phenotypes emerge in ribosomopathies.
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Affiliation(s)
- Gerald C Tiu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Stanford Medical Scientist Training Program, Stanford University, Stanford, CA 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Craig M Forester
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Division of Pediatric Allergy, Immunology and Bone Marrow Transplantation, University of California, San Francisco, San Francisco, CA 94143, USA; Children's Hospital Colorado, Division of Pediatric Hematology/Oncology/Bone Marrow Transplant, Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Pallavi S Krishnarao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Hannah D Rosenblatt
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Nitin Raj
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Travis C Lantz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olena Zhulyn
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Margot E Bowen
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leila Shokat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Laura D Attardi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
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36
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Feregrino C, Tschopp P. Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Dev Dyn 2021; 251:1472-1489. [PMID: 34114716 PMCID: PMC9545966 DOI: 10.1002/dvdy.384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built—largely—by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear. Results Here, we developed a user‐friendly bioinformatics workflow to detect gene co‐expression modules and test for their conservation across developmental stages and species boundaries. Using a paradigm of morphological diversification, the tetrapod limb, and single‐cell RNA‐sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. With mouse limb data as reference, we identified 19 gene co‐expression modules with varying tissue or cell type‐restricted activities. Testing for co‐expression conservation revealed modules with high evolutionary turnover, while others seemed maintained—to different degrees, in module make‐up, density or connectivity—over developmental and evolutionary timescales. Conclusions We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data. We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data.
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Affiliation(s)
- Christian Feregrino
- DUW Zoology, University of Basel, Basel, Switzerland.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Hannoversche Str. 28, Berlin, Germany
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37
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Tissières V, Geier F, Kessler B, Wolf E, Zeller R, Lopez-Rios J. Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits. Cell Rep 2021; 31:107490. [PMID: 32268095 PMCID: PMC7166081 DOI: 10.1016/j.celrep.2020.03.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 08/19/2019] [Accepted: 03/16/2020] [Indexed: 10/28/2022] Open
Abstract
Digit loss/reductions are evolutionary adaptations in cursorial mammals such as pigs. To gain mechanistic insight into these processes, we performed a comparative molecular analysis of limb development in mouse and pig embryos, which revealed a loss of anterior-posterior polarity during distal progression of pig limb bud development. These alterations in pig limb buds are paralleled by changes in the mesenchymal response to Sonic hedgehog (SHH) signaling, which is altered upstream of the reduction and loss of Fgf8 expression in the ectoderm that overlaps the reduced and vestigial digit rudiments of the pig handplate, respectively. Furthermore, genome-wide open chromatin profiling using equivalent developmental stages of mouse and pig limb buds reveals the functional divergence of about one-third of the regulatory genome. This study uncovers widespread alterations in the regulatory landscapes of genes essential for limb development that likely contributed to the morphological diversion of artiodactyl limbs from the pentadactyl archetype of tetrapods.
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Affiliation(s)
- Virginie Tissières
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain
| | - Florian Geier
- Bioinformatics Core Facility, Department of Biomedicine, University of Basel and University Hospital, 4053 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Barbara Kessler
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, 41013 Seville, Spain.
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38
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Bortoluzzi C, Megens HJ, Bosse M, Derks MFL, Dibbits B, Laport K, Weigend S, Groenen MAM, Crooijmans RPMA. Parallel Genetic Origin of Foot Feathering in Birds. Mol Biol Evol 2021; 37:2465-2476. [PMID: 32344429 PMCID: PMC7475038 DOI: 10.1093/molbev/msaa092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.
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Affiliation(s)
- Chiara Bortoluzzi
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Kimberly Laport
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Steffen Weigend
- Friedrich-Loeffler-Institut (FLI), Institute of Farm Animal Genetics, Neustadt, Germany
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
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Onimaru K, Tatsumi K, Tanegashima C, Kadota M, Nishimura O, Kuraku S. Developmental hourglass and heterochronic shifts in fin and limb development. eLife 2021; 10:62865. [PMID: 33560225 PMCID: PMC7932699 DOI: 10.7554/elife.62865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here, we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open-chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls. Animals come in all shapes and sizes. This diversity arose through genetic mutations during evolution, but it is unclear exactly how these variations led to the formation of new shapes. There is increasing evidence to suggest that not all shapes are possible and that variability between animals is limited by a phenomenon known as “developmental constraint”. These limitations direct parts of the body towards a specific shape as they develop in the embryo. Therefore, understanding the mechanisms underlying these developmental constraints could help explain how different body shapes evolved. The limbs of humans and other mammals evolved from the fins of fish, and this transition is often used to study the role developmental constraints play in evolution. This is an ideal model as there is already a detailed fossil record mapping this evolutionary event, and data pinpointing some of the genes involved in the development of limbs and fins. But this data is incomplete, and a full comparison between the genes activated in the fin and the limb during embryonic development had not been achieved. This is because most fish used for research have undergone recent genetic changes, making it hard to spot which genetic differences are linked to the evolution of the limb. To overcome this barrier, Onimaru et al. compared genetic data from the developing limbs of mice to the developing fins of the brown-banded bamboo shark, which evolves much slower than other fish. This revealed that although many genes commonly played a role in the development of the fin and the limb in the embryo, the activity of these shared genes was not the same. For example, genes that switched on in the late stages of limb development, switched off in the late stages of fin development. But in the middle of development, those differences were relatively small and both species activated very similar sets of genes. Many of these genes were pleiotropic, which means they have important roles in other tissues and therefore mutate less often. This suggests that the mid-stage of limb development is under the strongest level of constraint. Darwin’s theory of natural selection explains that mutations drive evolution. But the theory cannot predict what kinds of new body shapes new mutations will produce. Understanding how the activity levels of different genes affect development could help to fill this knowledge gap. This has potential medical applications, for example, understanding why some genetic changes cause more serious problems than others. This work suggests that mutations in genes that are active during the mid-stage of limb development may have the most serious impact.
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Affiliation(s)
- Koh Onimaru
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,Laboratory for Bioinformatics Research, RIKEN BDR, Wako City, Japan.,Molecular Oncology Laboratory, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
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40
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Berenguer M, Duester G. Role of Retinoic Acid Signaling, FGF Signaling and Meis Genes in Control of Limb Development. Biomolecules 2021; 11:80. [PMID: 33435477 DOI: 10.3390/biom11010080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022] Open
Abstract
The function of retinoic acid (RA) during limb development is still debated, as loss and gain of function studies led to opposite conclusions. With regard to limb initiation, genetic studies demonstrated that activation of FGF10 signaling is required for the emergence of limb buds from the trunk, with Tbx5 and RA signaling acting upstream in the forelimb field, whereas Tbx4 and Pitx1 act upstream in the hindlimb field. Early studies in chick embryos suggested that RA as well as Meis1 and Meis2 (Meis1/2) are required for subsequent proximodistal patterning of both forelimbs and hindlimbs, with RA diffusing from the trunk, functioning to activate Meis1/2 specifically in the proximal limb bud mesoderm. However, genetic loss of RA signaling does not result in loss of limb Meis1/2 expression and limb patterning is normal, although Meis1/2 expression is reduced in trunk somitic mesoderm. More recent studies demonstrated that global genetic loss of Meis1/2 results in a somite defect and failure of limb bud initiation. Other new studies reported that conditional genetic loss of Meis1/2 in the limb results in proximodistal patterning defects, and distal FGF8 signaling represses Meis1/2 to constrain its expression to the proximal limb. In this review, we hypothesize that RA and Meis1/2 both function in the trunk to initiate forelimb bud initiation, but that limb Meis1/2 expression is activated proximally by a factor other than RA and repressed distally by FGF8 to generate proximodistal patterning.
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Yin Z, Lin J, Yan R, Liu R, Liu M, Zhou B, Zhou W, An C, Chen Y, Hu Y, Fan C, Zhao K, Wu B, Zou X, Zhang J, El‐Hashash AH, Chen X, Ouyang H. Atlas of Musculoskeletal Stem Cells with the Soft and Hard Tissue Differentiation Architecture. Adv Sci (Weinh) 2020; 7:2000938. [PMID: 33304744 PMCID: PMC7710003 DOI: 10.1002/advs.202000938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Although being of utmost importance for human health and mobility, stem cell identity and hierarchical organization of musculoskeletal progenitors remain largely unexplored. Here, cells from E10.5, E12.5, and E15.5 murine limbs are analyzed by high throughput single-cell RNA sequencing to illustrate the cellular architecture during limb development. Single-cell transcriptional profiling demonstrates the identity and differentiation architecture of musculoskeletal stem cells (MSSC), soft and hard tissue progenitors through expression pattern of musculoskeletal markers (scleraxis [Scx], Hoxd13, Sox9, and Col1a1). This is confirmed by genetic in vivo lineage tracing. Moreover, single-cell analyses of Scx knockout mice tissues illustrates that Scx regulates MSSC self-renewal and proliferation potential. A high-throughput and low-cost multi-tissues RNA sequencing strategy further provides evidence that musculoskeletal system tissues, including muscle, bone, meniscus, and cartilage, are all abnormally developed in Scx knockout mice. These results establish the presence of an indispensable limb Scx+Hoxd13+ MSSC population and their differentiation into soft tissue progenitors (Scx+Col1a1+) and hard tissue progenitors (Scx+Sox9+). Collectively, this study paves the way for systematically decoding the complex molecular mechanisms and cellular programs of musculoskeletal tissues morphogenesis in limb development and regeneration.
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Affiliation(s)
- Zi Yin
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- China Orthopedic Regenerative Medicine (CORMed)Hangzhou310058China
| | - Junxin Lin
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Ruojin Yan
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Richun Liu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Mengfei Liu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Bo Zhou
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Wenyan Zhou
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
- Zhejiang University‐University of Edinburgh Institute & School of Basic MedicineZhejiang University School of MedicineHangzhou310058China
| | - Chengrui An
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Yangwu Chen
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Yejun Hu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Chunmei Fan
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
| | - Kun Zhao
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Bingbing Wu
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
| | - Xiaohui Zou
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- Department of Gynecologythe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou310058China
| | - Jin Zhang
- The First Affiliated Hospital and Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical SciencesSchool of MedicineZhejiang UniversityHangzhou310058China
| | - Ahmed H. El‐Hashash
- Zhejiang University‐University of Edinburgh Institute & School of Basic MedicineZhejiang University School of MedicineHangzhou310058China
- Edinburgh Medical SchoolUniversity of EdinburghEdinburghEH16 4SBUK
| | - Xiao Chen
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- China Orthopedic Regenerative Medicine (CORMed)Hangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
- Department of Sports MedicineSchool of MedicineZhejiang UniversityHangzhou310058China
| | - Hongwei Ouyang
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang ProvinceZhejiang University School of MedicineHangzhou310058China
- China Orthopedic Regenerative Medicine (CORMed)Hangzhou310058China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of The Second Affiliated HospitalZhejiang University School of MedicineHangzhou310058China
- Zhejiang University‐University of Edinburgh Institute & School of Basic MedicineZhejiang University School of MedicineHangzhou310058China
- Department of Sports MedicineSchool of MedicineZhejiang UniversityHangzhou310058China
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42
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Metscher B. A simple nuclear contrast staining method for microCT-based 3D histology using lead(II) acetate. J Anat 2020; 238:1036-1041. [PMID: 33140846 PMCID: PMC7930760 DOI: 10.1111/joa.13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 10/29/2022] Open
Abstract
X-ray microtomography (microCT) enables histological-scale 3D imaging of many types of biological samples, but it has yet to rival traditional histology for differentiation of tissue types and cell components. This report presents prima facie results indicating that a simple lead(II) acetate staining solution can impart preferential X-ray contrast to cell nuclei. While not strictly selective for nuclei, the staining reflects local cell-density differences. It can be applied in a single overnight treatment and does not require hematoxylin staining or drying of the sample. The stain is removable with EDTA, and it may enhance early calcifications. A basic protocol is given as a guide for further testing and optimization.
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Affiliation(s)
- Brian Metscher
- Department of Evolutionary Biology, Theoretical Biology Unit, University of Vienna, Vienna, Austria
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43
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Monti P, Ciribilli Y, Foggetti G, Menichini P, Bisio A, Cappato S, Inga A, Divizia MT, Lerone M, Bocciardi R, Fronza G. P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Biosci Rep 2019; 39:BSR20192114. [PMID: 31789342 DOI: 10.1042/BSR20192114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
TP63 is a member of the TP53 gene family, sharing a common gene structure that produces two groups of mRNAs' encoding proteins with different N-terminal regions (ΔN and TA isoforms); both transcripts are also subjected to alternative splicing mechanisms at C-terminus, generating a variety of isoforms. p63 is a master regulator of epidermal development and homoeostasis as well as an important player in tumorigenesis and cancer progression with both oncogenic and tumour suppressive roles. A number of studies have aimed at the identification of p63 target genes, allowing the dissection of the molecular pathways orchestrated by the different isoforms. In the present study we investigated in more detail the p63 responsiveness of the WDFY2 (WD repeat and FYVE domain containing 2) gene, encoding for an endosomal protein identified as a binding partner of the PI-3K/AKT signalling pathway. We showed that overexpression of different p63 isoforms was able to induce WDFY2 expression in TP53-null cells. The p63-dependent transcriptional activation was associated with specific response elements (REs) that have been identified by a bioinformatics tool and validated by yeast- and mammal-based assays. Interestingly, to confirm that WDFY2 belongs to the p63 network of cancer regulation, we analysed the impact of WDFY2 alterations, by showing its frequent deletion in different types of tumours and suggesting its expression level as a prognostic biomarker. Lastly, we identified a chromosomal translocation involving the WDFY2 locus in a patient affected by a rare congenital limb anomaly, indicating WDFY2 as a possible susceptibility gene placed downstream p63 in the network of limb development.
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44
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Zimmerli D, Borrelli C, Jauregi-Miguel A, Söderholm S, Brütsch S, Doumpas N, Reichmuth J, Murphy-Seiler F, Aguet MI, Basler K, Moor AE, Cantù C. TBX3 acts as tissue-specific component of the Wnt/β-catenin transcriptional complex. eLife 2020; 9:58123. [PMID: 32808927 PMCID: PMC7434441 DOI: 10.7554/elife.58123] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
BCL9 and PYGO are β-catenin cofactors that enhance the transcription of Wnt target genes. They have been proposed as therapeutic targets to diminish Wnt signaling output in intestinal malignancies. Here we find that, in colorectal cancer cells and in developing mouse forelimbs, BCL9 proteins sustain the action of β-catenin in a largely PYGO-independent manner. Our genetic analyses implied that BCL9 necessitates other interaction partners in mediating its transcriptional output. We identified the transcription factor TBX3 as a candidate tissue-specific member of the β-catenin transcriptional complex. In developing forelimbs, both TBX3 and BCL9 occupy a large number of Wnt-responsive regulatory elements, genome-wide. Moreover, mutations in Bcl9 affect the expression of TBX3 targets in vivo, and modulation of TBX3 abundance impacts on Wnt target genes transcription in a β-catenin- and TCF/LEF-dependent manner. Finally, TBX3 overexpression exacerbates the metastatic potential of Wnt-dependent human colorectal cancer cells. Our work implicates TBX3 as context-dependent component of the Wnt/β-catenin-dependent transcriptional complex.
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Affiliation(s)
- Dario Zimmerli
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Amaia Jauregi-Miguel
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences; Linköping University, Linköping, Sweden
| | - Simon Söderholm
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences; Linköping University, Linköping, Sweden
| | - Salome Brütsch
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Nikolaos Doumpas
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Jan Reichmuth
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Fabienne Murphy-Seiler
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Lausanne, Switzerland
| | - MIchel Aguet
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, Lausanne, Switzerland
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences; Linköping University, Linköping, Sweden
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45
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Durston AJ. A Tribute to Lewis Wolpert and His Ideas on the 50th Anniversary of the Publication of His Paper 'Positional Information and the Spatial Pattern of Differentiation'. Evidence for a Timing Mechanism for Setting Up the Vertebrate Anterior-Posterior (A-P) Axis. Int J Mol Sci 2020; 21:E2552. [PMID: 32272563 PMCID: PMC7177403 DOI: 10.3390/ijms21072552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 11/16/2022] Open
Abstract
This article is a tribute to Lewis Wolpert and his ideas on the occasion of the recent 50th anniversary of the publication of his article 'Positional Information and the Spatial Pattern of Differentiation'. This tribute relates to another one of his ideas: his early 'Progress Zone' timing model for limb development. Recent evidence is reviewed showing a mechanism sharing features with this model patterning the main body axis in early vertebrate development. This tribute celebrates the golden era of Developmental Biology.
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Affiliation(s)
- Antony J Durston
- Institute of Biology, University of Leiden, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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46
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Kvon EZ, Zhu Y, Kelman G, Novak CS, Plajzer-Frick I, Kato M, Garvin TH, Pham Q, Harrington AN, Hunter RD, Godoy J, Meky EM, Akiyama JA, Afzal V, Tran S, Escande F, Gilbert-Dussardier B, Jean-Marçais N, Hudaiberdiev S, Ovcharenko I, Dobbs MB, Gurnett CA, Manouvrier-Hanu S, Petit F, Visel A, Dickel DE, Pennacchio LA. Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants. Cell 2020; 180:1262-1271.e15. [PMID: 32169219 DOI: 10.1016/j.cell.2020.02.031] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 12/17/2022]
Abstract
Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.
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47
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Kashgari G, Meinecke L, Gordon W, Ruiz B, Yang J, Ma AL, Xie Y, Ho H, Plikus MV, Nie Q, Jester JV, Andersen B. Epithelial Migration and Non-adhesive Periderm Are Required for Digit Separation during Mammalian Development. Dev Cell 2020; 52:764-778.e4. [PMID: 32109382 DOI: 10.1016/j.devcel.2020.01.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/26/2019] [Accepted: 01/28/2020] [Indexed: 01/04/2023]
Abstract
The fusion of digits or toes, syndactyly, can be part of complex syndromes, including van der Woude syndrome. A subset of van der Woude cases is caused by dominant-negative mutations in the epithelial transcription factor Grainyhead like-3 (GRHL3), and Grhl3-/-mice have soft-tissue syndactyly. Although impaired interdigital cell death of mesenchymal cells causes syndactyly in multiple genetic mutants, Grhl3-/- embryos had normal interdigital cell death, suggesting alternative mechanisms for syndactyly. We found that in digit separation, the overlying epidermis forms a migrating interdigital epithelial tongue (IET) when the epithelium invaginates to separate the digits. Normally, the non-adhesive surface periderm allows the IET to bifurcate as the digits separate. In contrast, in Grhl3-/- embryos, the IET moves normally between the digits but fails to bifurcate because of abnormal adhesion of the periderm. Our study identifies epidermal developmental processes required for digit separation.
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Affiliation(s)
- Ghaidaa Kashgari
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Lina Meinecke
- Department of Mathematics, School of Physical Sciences, University of California, Irvine, Irvine, CA, USA; Department of Developmental & Cell Biology, School of the Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - William Gordon
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Bryan Ruiz
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Jady Yang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Amy Lan Ma
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yilu Xie
- The Gavin Herbert Eye Institute, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Hsiang Ho
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Maksim V Plikus
- Department of Developmental & Cell Biology, School of the Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - Qing Nie
- Department of Mathematics, School of Physical Sciences, University of California, Irvine, Irvine, CA, USA; Department of Developmental & Cell Biology, School of the Biological Sciences, University of California, Irvine, Irvine, CA, USA
| | - James V Jester
- The Gavin Herbert Eye Institute, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Bogi Andersen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA; Department of Medicine, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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48
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Bastida MF, Pérez-Gómez R, Trofka A, Zhu J, Rada-Iglesias A, Sheth R, Stadler HS, Mackem S, Ros MA. The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13. Proc Natl Acad Sci U S A 2020; 117:1090-6. [PMID: 31896583 DOI: 10.1073/pnas.1919470117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the Hoxa13 mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in Hoxd transcriptional regulation, the expression of Hoxd13 in Hoxa13 mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal Hox transcripts, a circumstance that can explain its agenesis. The loss of Hoxd13 expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a Hoxd negative regulator, resulting from increased Gli3 transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on Gli3 regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing Gli3 transcription and by enabling expansion of the 5'Hoxd second expression phase, thereby establishing anterior-posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for Hox and Gli3 gene regulation in the context of development and evolution.
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49
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Cunningham TJ, Lancman JJ, Berenguer M, Dong PDS, Duester G. Genomic Knockout of Two Presumed Forelimb Tbx5 Enhancers Reveals They Are Nonessential for Limb Development. Cell Rep 2018; 23:3146-51. [PMID: 29898387 DOI: 10.1016/j.celrep.2018.05.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/02/2018] [Accepted: 05/15/2018] [Indexed: 11/23/2022] Open
Abstract
A standard approach in the identification of transcriptional enhancers is the use of transgenic animals carrying DNA elements joined to reporter genes inserted randomly in the genome. We examined elements near Tbx5, a gene required for forelimb development in humans and other vertebrates. Previous transgenic studies reported a mammalian Tbx5 fore-limb enhancer located in intron 2 containing a putative retinoic acid response element and a zebrafish tbx5a forelimb (pectoral fin) enhancer located downstream that is conserved from fish to mammals. We used CRISPR/Cas9 gene editing to knockout the endogenous elements and unexpectedly found that deletion of the intron 2 and downstream elements, either singly or together in double knockouts, resulted in no effect on forelimb development. Our findings show that reporter transgenes may not identify endogenous enhancers and that in vivo genetic loss-of-function studies are required, such as CRISPR/Cas9, which is similar in effort to production of animals carrying reporter transgenes.
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50
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Fowler DA, Larsson HCE. The benefits differential equations bring to limb development. Wiley Interdiscip Rev Dev Biol 2019; 9:e364. [PMID: 31637866 DOI: 10.1002/wdev.364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/22/2019] [Accepted: 09/07/2019] [Indexed: 11/07/2022]
Abstract
Systems biology is a large field, offering a number of advantages to a variety of biological disciplines. In limb development, differential-equation based models can provide insightful hypotheses about the gene/protein interactions and tissue differentiation events that form the core of limb development research. Differential equations are like any other communicative tool, with misuse and limitations that can come along with their advantages. Every theory should be critically analyzed to best ascertain whether they reflect the reality in biology as well they claim. Differential equation-based models have consistent features which researchers have drawn upon to aid in more realistic descriptions and hypotheses. Nine features are described that highlight these trade-offs. The advantages range from more detailed descriptions of gene interactions and their consequence and the capacity to model robustness to the incorporation of tissue size and shape. The drawbacks come with the added complication that additional genes and signaling pathways that require additional terms within the mathematical model. They also come in the translation between the mathematical terms of the model, values and matrices, to the real world of genes, proteins, and tissues that constitute limb development. A critical analysis is necessary to ensure that these models effectively expand the understanding of the origins of a diversity of limb anatomy, from evolution to teratology. This article is categorized under: Vertebrate Organogenesis > Musculoskeletal and Vascular Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Establishment of Spatial and Temporal Patterns > Repeating Patterns and Lateral Inhibition.
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Affiliation(s)
- Donald A Fowler
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
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