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Calamari ZT, Flynn JJ. Gene expression supports a single origin of horns and antlers in hoofed mammals. Commun Biol 2024; 7:509. [PMID: 38769090 PMCID: PMC11106249 DOI: 10.1038/s42003-024-06134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/02/2024] [Indexed: 05/22/2024] Open
Abstract
Horns, antlers, and other bony cranial appendages of even-toed hoofed mammals (ruminant artiodactyls) challenge traditional morphological homology assessments. Cranial appendages all share a permanent bone portion with family-specific integument coverings, but homology determination depends on whether the integument covering is an essential component or a secondary elaboration of each structure. To enhance morphological homology assessments, we tested whether juvenile cattle horn bud transcriptomes share homologous gene expression patterns with deer antlers relative to pig outgroup tissues, treating the integument covering as a secondary elaboration. We uncovered differentially expressed genes that support horn and antler homology, potentially distinguish them from non-cranial-appendage bone and other tissues, and highlight the importance of phylogenetic outgroups in homology assessments. Furthermore, we found differentially expressed genes that could support a shared cranial neural crest origin for horns and antlers and expression patterns that refine our understanding of the timing of horn and antler differentiation.
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Affiliation(s)
- Zachary T Calamari
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA.
- Department of Natural Sciences, Baruch College, City University of New York, 17 Lexington Avenue, Box A-920, New York, NY, 10010, USA.
| | - John J Flynn
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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2
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Sohail A, Bendall AJ. DLX gene expression in the developing chick pharyngeal arches and relationship to endothelin signaling and avian jaw patterning. Dev Dyn 2024; 253:255-271. [PMID: 37706631 DOI: 10.1002/dvdy.653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/09/2023] [Accepted: 08/20/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND A hinged jaw that articulates with the skull base is a striking feature of the vertebrate head and has been greatly modified between, and within, vertebrate classes. Genes belonging to the DLX homeobox family are conserved mediators of local signaling pathways that distinguish the dorsal and ventral aspects of the first pharyngeal arch. Specifically, a subset of DLX genes are expressed in the cranial neural crest-derived mandibular ectomesenchyme in response to ventral endothelin signaling, an important step that confers the first arch with maxillary and mandibular identities. Downstream targets of DLX genes then execute the morphogenetic processes that lead to functional jaws. Identifying lineage-specific variations in DLX gene expression and the regulatory networks downstream of DLX action is necessary to understand how different kinds of jaws evolved. RESULTS Here, we describe and compare the expression of all six DLX genes in the chick pharyngeal arches, focusing on the period of active patterning in the first arch. Disruption of endothelin signaling results in the down-regulation of ventral-specific DLX genes and confirms their functional role in avian jaw patterning. CONCLUSIONS This expression resource will be important for comparative embryology and for identifying synexpression groups of DLX-regulated genes in the chick.
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Affiliation(s)
- Afshan Sohail
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Andrew J Bendall
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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3
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Nguyen JKB, Gómez-Picos P, Liu Y, Ovens K, Eames BF. Common features of cartilage maturation are not conserved in an amphibian model. Dev Dyn 2023; 252:1375-1390. [PMID: 37083105 DOI: 10.1002/dvdy.594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/04/2023] [Accepted: 04/09/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Mouse, chick, and zebrafish undergo a highly conserved program of cartilage maturation during endochondral ossification (bone formation via a cartilage template). Standard histological and molecular features of cartilage maturation are chondrocyte hypertrophy, downregulation of the chondrogenic markers Sox9 and Col2a1, and upregulation of Col10a1. We tested whether cartilage maturation is conserved in an amphibian, the western clawed frog Xenopus tropicalis, using in situ hybridization for standard markers and a novel laser-capture microdissection RNAseq data set. We also functionally tested whether thyroid hormone drives cartilage maturation in X tropicalis, as it does in other vertebrates. RESULTS The developing frog humerus mostly followed the standard progression of cartilage maturation. Chondrocytes gradually became hypertrophic as col2a1 and sox9 were eventually down-regulated, but col10a1 was not up-regulated. However, the expression levels of several genes associated with the early formation of cartilage, such as acan, sox5, and col9a2, remained highly expressed even as humeral chondrocytes matured. Greater deviances were observed in head cartilages, including the ceratohyal, which underwent hypertrophy within hours of becoming cartilaginous, maintained relatively high levels of col2a1 and sox9, and lacked col10a1 expression. Interestingly, treating frog larvae with thyroid hormone antagonists did not specifically reduce head cartilage hypertrophy, resulting rather in a global developmental delay. CONCLUSION These data reveal that basic cartilage maturation features in the head, and to a lesser extent in the limb, are not conserved in X tropicalis. Future work revealing how frogs deviate from the standard cartilage maturation program might shed light on both evolutionary and health studies.
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Affiliation(s)
- Jason K B Nguyen
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Patsy Gómez-Picos
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yiwen Liu
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Katie Ovens
- Department of Computer Science, University of Calgary, Calgary, Alberta, Canada
| | - B Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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4
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Graham A, Hikspoors JPJM, Lamers WH, Anderson RH, Bamforth SD. Morphogenetic processes in the development and evolution of the arteries of the pharyngeal arches: their relations to congenital cardiovascular malformations. Front Cell Dev Biol 2023; 11:1259175. [PMID: 37900278 PMCID: PMC10602722 DOI: 10.3389/fcell.2023.1259175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
The heart and aortic arch arteries in amniotes form a double circulation, taking oxygenated blood from the heart to the body and deoxygenated blood to the lungs. These major vessels are formed in embryonic development from a series of paired and symmetrical arteries that undergo a complex remodelling process to form the asymmetric arch arteries in the adult. These embryonic arteries form in the pharyngeal arches, which are symmetrical bulges on the lateral surface of the head. The pharyngeal arches, and their associated arteries, are found in all classes of vertebrates, but the number varies, typically with the number of arches reducing through evolution. For example, jawed vertebrates have six pairs of pharyngeal arch arteries but amniotes, a clade of tetrapod vertebrates, have five pairs. This had led to the unusual numbering system attributed to each of the pharyngeal arch arteries in amniotes (1, 2, 3, 4, and 6). We, therefore, propose that these instead be given names to reflect the vessel: mandibular (1st), hyoid (2nd), carotid (3rd), aortic (4th) and pulmonary (most caudal). Aberrant arch artery formation or remodelling leads to life-threatening congenital cardiovascular malformations, such as interruption of the aortic arch, cervical origin of arteries, and vascular rings. We discuss why an alleged fifth arch artery has erroneously been used to interpret congenital cardiac lesions, which are better explained as abnormal collateral channels, or remodelling of the aortic sac.
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Affiliation(s)
- Anthony Graham
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | | | - Wouter H. Lamers
- Department of Anatomy and Embryology, Maastricht University, Maastricht, Netherlands
| | - Robert H. Anderson
- Centre for Life, Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon D. Bamforth
- Centre for Life, Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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5
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Root ZD, Jandzik D, Gould C, Allen C, Brewer M, Medeiros DM. Cartilage diversification and modularity drove the evolution of the ancestral vertebrate head skeleton. EvoDevo 2023; 14:8. [PMID: 37147719 PMCID: PMC10161429 DOI: 10.1186/s13227-023-00211-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/04/2023] [Indexed: 05/07/2023] Open
Abstract
The vertebrate head skeleton has evolved a myriad of forms since their divergence from invertebrate chordates. The connection between novel gene expression and cell types is therefore of importance in this process. The transformation of the jawed vertebrate (gnathostome) head skeleton from oral cirri to jointed jaw elements required a diversity of cartilages as well as changes in the patterning of these tissues. Although lampreys are a sister clade to gnathostomes, they display skeletal diversity with distinct gene expression and histologies, a useful model for addressing joint evolution. Specifically, the lamprey tissue known as mucocartilage has noted similarities with the jointed elements of the mandibular arch in jawed vertebrates. We thus asked whether the cells in lamprey mucocartilage and gnathostome joint tissue could be considered homologous. To do this, we characterized new genes that are involved in gnathostome joint formation and characterized the histochemical properties of lamprey skeletal types. We find that most of these genes are minimally found in mucocartilage and are likely later innovations, but we do identify new activity for gdf5/6/7b in both hyaline and mucocartilage, supporting its role as a chondrogenic regulator. Contrary to previous works, our histological assays do not find any perichondrial fibroblasts surrounding mucocartilage, suggesting that mucocartilage is non-skeletogenic tissue that is partially chondrified. Interestingly, we also identify new histochemical features of the lamprey otic capsule that diverge from normal hyaline. Paired with our new insights into lamprey mucocartilage, we propose a broader framework for skeletal evolution in which an ancestral soxD/E and gdf5/6/7 network directs mesenchyme along a spectrum of cartilage-like features.
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Affiliation(s)
- Zachary D. Root
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
- Department of Zoology, Comenius University in Bratislava, Bratislava, 84215 Slovakia
| | - Claire Gould
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Cara Allen
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Margaux Brewer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Daniel M. Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
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6
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Rose CS. The cellular basis of cartilage growth and shape change in larval and metamorphosing Xenopus frogs. PLoS One 2023; 18:e0277110. [PMID: 36634116 PMCID: PMC9836273 DOI: 10.1371/journal.pone.0277110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/19/2022] [Indexed: 01/13/2023] Open
Abstract
As the first and sometimes only skeletal tissue to appear, cartilage plays a fundamental role in the development and evolution of vertebrate body shapes. This is especially true for amphibians whose largely cartilaginous feeding skeleton exhibits unparalleled ontogenetic and phylogenetic diversification as a consequence of metamorphosis. Fully understanding the evolutionary history, evolvability and regenerative potential of cartilage requires in-depth analysis of how chondrocytes drive growth and shape change. This study is a cell-level description of the larval growth and postembryonic shape change of major cartilages of the feeding skeleton of a metamorphosing amphibian. Histology and immunohistochemistry are used to describe and quantify patterns and trends in chondrocyte size, shape, division, death, and arrangement, and in percent matrix from hatchling to froglet for the lower jaw, hyoid and branchial arch cartilages of Xenopus laevis. The results are interpreted and integrated into programs of cell behaviors that account for the larval growth and histology, and metamorphic remodeling of each element. These programs provide a baseline for investigating hormone-mediated remodeling, cartilage regeneration, and intrinsic shape regulating mechanisms. These programs also contain four features not previously described in vertebrates: hypertrophied chondrocytes being rejuvenated by rapid cell cycling to a prechondrogenic size and shape; chondrocytes dividing and rearranging to reshape a cartilage; cartilage that lacks a perichondrium and grows at single-cell dimensions; and an adult cartilage forming de novo in the center of a resorbing larval one. Also, the unexpected superimposition of cell behaviors for shape change onto ones for larval growth and the unprecedented exploitation of very large and small cell sizes provide new directions for investigating the development and evolution of skeletal shape and metamorphic ontogenies.
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Affiliation(s)
- Christopher S. Rose
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
- * E-mail:
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7
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Rapid induction and long-term self-renewal of neural crest-derived ectodermal chondrogenic cells from hPSCs. NPJ Regen Med 2022; 7:69. [PMID: 36477591 PMCID: PMC9729200 DOI: 10.1038/s41536-022-00265-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Articular cartilage is highly specific and has limited capacity for regeneration if damaged. Human pluripotent stem cells (hPSCs) have the potential to generate any cell type in the body. Here, we report the dual-phase induction of ectodermal chondrogenic cells (ECCs) from hPSCs through the neural crest (NC). ECCs were able to self-renew long-term (over numerous passages) in a cocktail of growth factors and small molecules. The cells stably expressed cranial neural crest-derived mandibular condylar cartilage markers, such as MSX1, FOXC1 and FOXC2. Compared with chondroprogenitors from iPSCs via the paraxial mesoderm, ECCs had single-cell transcriptome profiles similar to condylar chondrocytes. After the removal of the cocktail sustaining self-renewal, the cells stopped proliferating and differentiated into a homogenous chondrocyte population. Remarkably, after transplantation, this cell lineage was able to form cartilage-like structures resembling mandibular condylar cartilage in vivo. This finding provides a framework to generate self-renewing cranial chondrogenic progenitors, which could be useful for developing cell-based therapy for cranial cartilage injury.
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8
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Leyhr J, Waldmann L, Filipek-Górniok B, Zhang H, Allalou A, Haitina T. A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint. eLife 2022; 11:e75749. [PMID: 36377467 PMCID: PMC9665848 DOI: 10.7554/elife.75749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of nkx3.2 and leads to a transient jaw joint deformation and partial fusion. Emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.
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Affiliation(s)
- Jake Leyhr
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala UniversityUppsalaSweden
| | - Laura Waldmann
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala UniversityUppsalaSweden
| | - Beata Filipek-Górniok
- Science for Life Laboratory Genome Engineering Zebrafish Facility, Department of Organismal Biology, Uppsala UniversityUppsalaSweden
| | - Hanqing Zhang
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala UniversityUppsalaSweden
- Science for Life Laboratory BioImage Informatics FacilityUppsalaSweden
| | - Amin Allalou
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala UniversityUppsalaSweden
- Science for Life Laboratory BioImage Informatics FacilityUppsalaSweden
| | - Tatjana Haitina
- Subdepartment of Evolution and Development, Department of Organismal Biology, Uppsala UniversityUppsalaSweden
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9
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Keer S, Cousin H, Jourdeuil K, Neilson KM, Tavares ALP, Alfandari D, Moody SA. Mcrs1 is required for branchial arch and cranial cartilage development. Dev Biol 2022; 489:62-75. [PMID: 35697116 PMCID: PMC10426812 DOI: 10.1016/j.ydbio.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022]
Abstract
Mcrs1 is a multifunctional protein that is critical for many cellular processes in a wide range of cell types. Previously, we showed that Mcrs1 binds to the Six1 transcription factor and reduces the ability of the Six1-Eya1 complex to upregulate transcription, and that Mcrs1 loss-of-function leads to the expansion of several neural plate genes, reduction of neural border and pre-placodal ectoderm (PPR) genes, and pleiotropic effects on various neural crest (NC) genes. Because the affected embryonic structures give rise to several of the cranial tissues affected in Branchio-otic/Branchio-oto-renal (BOR) syndrome, herein we tested whether these gene expression changes subsequently alter the development of the proximate precursors of BOR affected structures - the otic vesicles (OV) and branchial arches (BA). We found that Mcrs1 is required for the expression of several OV genes involved in inner ear formation, patterning and otic capsule cartilage formation. Mcrs1 knockdown also reduced the expression domains of many genes expressed in the larval BA, derived from either NC or PPR, except for emx2, which was expanded. Reduced Mcrs1 also diminished the length of the expression domain of tbx1 in BA1 and BA2 and interfered with cranial NC migration from the dorsal neural tube; this subsequently resulted in defects in the morphology of lower jaw cartilages derived from BA1 and BA2, including the infrarostral, Meckel's, and ceratohyal as well as the otic capsule. These results demonstrate that Mcrs1 plays an important role in processes that lead to the formation of craniofacial cartilages and its loss results in phenotypes consistent with reduced Six1 activity associated with BOR.
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Affiliation(s)
- Stephanie Keer
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, 2300 I (eye) Street, NW, Washington, DC, 20037, USA
| | - Helene Cousin
- Department of Animal Science, University of Massachusetts Amherst, Integrated Science Building, 661 N. Pleasant Street, Amherst, MA, 01003, USA
| | - Karyn Jourdeuil
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, 2300 I (eye) Street, NW, Washington, DC, 20037, USA
| | - Karen M Neilson
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, 2300 I (eye) Street, NW, Washington, DC, 20037, USA
| | - Andre L P Tavares
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, 2300 I (eye) Street, NW, Washington, DC, 20037, USA
| | - Dominique Alfandari
- Department of Animal Science, University of Massachusetts Amherst, Integrated Science Building, 661 N. Pleasant Street, Amherst, MA, 01003, USA
| | - Sally A Moody
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, 2300 I (eye) Street, NW, Washington, DC, 20037, USA.
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10
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Zahn N, James-Zorn C, Ponferrada VG, Adams DS, Grzymkowski J, Buchholz DR, Nascone-Yoder NM, Horb M, Moody SA, Vize PD, Zorn AM. Normal Table of Xenopus development: a new graphical resource. Development 2022; 149:dev200356. [PMID: 35833709 PMCID: PMC9445888 DOI: 10.1242/dev.200356] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/17/2022] [Indexed: 12/26/2022]
Abstract
Normal tables of development are essential for studies of embryogenesis, serving as an important resource for model organisms, including the frog Xenopus laevis. Xenopus has long been used to study developmental and cell biology, and is an increasingly important model for human birth defects and disease, genomics, proteomics and toxicology. Scientists utilize Nieuwkoop and Faber's classic 'Normal Table of Xenopus laevis (Daudin)' and accompanying illustrations to enable experimental reproducibility and reuse the illustrations in new publications and teaching. However, it is no longer possible to obtain permission for these copyrighted illustrations. We present 133 new, high-quality illustrations of X. laevis development from fertilization to metamorphosis, with additional views that were not available in the original collection. All the images are available on Xenbase, the Xenopus knowledgebase (http://www.xenbase.org/entry/zahn.do), for download and reuse under an attributable, non-commercial creative commons license. Additionally, we have compiled a 'Landmarks Table' of key morphological features and marker gene expression that can be used to distinguish stages quickly and reliably (https://www.xenbase.org/entry/landmarks-table.do). This new open-access resource will facilitate Xenopus research and teaching in the decades to come.
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Affiliation(s)
| | - Christina James-Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Virgilio G. Ponferrada
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Ave, Cincinnati, OH 45229, USA
| | - Dany S. Adams
- Lucell Diagnostics Inc, 16 Stearns Street, Cambridge, MA 02138, USA
| | - Julia Grzymkowski
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695, USA
| | - Daniel R. Buchholz
- Department of Biology Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Nanette M. Nascone-Yoder
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695, USA
| | - Marko Horb
- National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, George Washington University Medical Center, Washington, DC 20037, USA
| | - Peter D. Vize
- Xenbase, Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Aaron M. Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Ave, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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11
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Gomez-Picos P, Ovens K, Eames BF. Limb Mesoderm and Head Ectomesenchyme Both Express a Core Transcriptional Program During Chondrocyte Differentiation. Front Cell Dev Biol 2022; 10:876825. [PMID: 35784462 PMCID: PMC9247276 DOI: 10.3389/fcell.2022.876825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
To explain how cartilage appeared in different parts of the vertebrate body at discrete times during evolution, we hypothesize that different embryonic populations co-opted expression of a core gene regulatory network (GRN) driving chondrocyte differentiation. To test this hypothesis, laser-capture microdissection coupled with RNA-seq was used to reveal chondrocyte transcriptomes in the developing chick humerus and ceratobranchial, which are mesoderm- and neural crest-derived, respectively. During endochondral ossification, two general types of chondrocytes differentiate. Immature chondrocytes (IMM) represent the early stages of cartilage differentiation, while mature chondrocytes (MAT) undergo additional stages of differentiation, including hypertrophy and stimulating matrix mineralization and degradation. Venn diagram analyses generally revealed a high degree of conservation between chondrocyte transcriptomes of the limb and head, including SOX9, COL2A1, and ACAN expression. Typical maturation genes, such as COL10A1, IBSP, and SPP1, were upregulated in MAT compared to IMM in both limb and head chondrocytes. Gene co-expression network (GCN) analyses of limb and head chondrocyte transcriptomes estimated the core GRN governing cartilage differentiation. Two discrete portions of the GCN contained genes that were differentially expressed in limb or head chondrocytes, but these genes were enriched for biological processes related to limb/forelimb morphogenesis or neural crest-dependent processes, respectively, perhaps simply reflecting the embryonic origin of the cells. A core GRN driving cartilage differentiation in limb and head was revealed that included typical chondrocyte differentiation and maturation markers, as well as putative novel "chondrocyte" genes. Conservation of a core transcriptional program during chondrocyte differentiation in both the limb and head suggest that the same core GRN was co-opted when cartilage appeared in different regions of the skeleton during vertebrate evolution.
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Affiliation(s)
- Patsy Gomez-Picos
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Katie Ovens
- Department of Computer Science, University of Calgary, Calgary, AB, Canada
| | - B. Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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12
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Dickinson AJG, Turner SD, Wahl S, Kennedy AE, Wyatt BH, Howton DA. E-liquids and vanillin flavoring disrupts retinoic acid signaling and causes craniofacial defects in Xenopus embryos. Dev Biol 2022; 481:14-29. [PMID: 34543654 PMCID: PMC8665092 DOI: 10.1016/j.ydbio.2021.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/03/2023]
Abstract
Environmental teratogens such as smoking are known risk factors for developmental disorders such as cleft palate. While smoking rates have declined, a new type of smoking, called vaping is on the rise. Vaping is the use of e-cigarettes to vaporize and inhale an e-liquid containing nicotine and food-like flavors. There is the potential that, like smoking, vaping could also pose a danger to the developing human. Rather than waiting for epidemiological and mammalian studies, we have turned to an aquatic developmental model, Xenopus laevis, to more quickly assess whether e-liquids contain teratogens that could lead to craniofacial malformations. Xenopus, like zebrafish, has the benefit of being a well-established developmental model and has also been effective in predicting whether a chemical could be a teratogen. We have determined that embryonic exposure to dessert flavored e-liquids can cause craniofacial abnormalities, including an orofacial cleft in Xenopus. To better understand the underlying mechanisms contributing to these defects, transcriptomic analysis of the facial tissues of embryos exposed to a representative dessert flavored e-liquid vapor extract was performed. Analysis of differentially expressed genes in these embryos revealed several genes associated with retinoic acid metabolism or the signaling pathway. Consistently, retinoic acid receptor inhibition phenocopied the craniofacial defects as those embryos exposed to the vapor extract of the e-liquid. Such malformations also correlated with a group of common differentially expressed genes, two of which are associated with midface birth defects in humans. Further, e-liquid exposure sensitized embryos to forming craniofacial malformations when they already had depressed retinoic acid signaling. Moreover, 13-cis-retinoic acid treatment could significantly reduce the e-liquid induced malformation in the midface. Such results suggest the possibility of an interaction between retinoic acid signaling and e-liquid exposure. One of the most popular and concentrated flavoring chemicals in dessert flavored e-liquids is vanillin. Xenopus embryos exposed to this chemical closely resembled embryos exposed to dessert-like e-liquids and a retinoic acid receptor antagonist. In summary, we determined that e-liquid chemicals, in particular vanillin, can cause craniofacial defects potentially by dysregulating retinoic acid signaling. This work warrants the evaluation of vanillin and other such flavoring additives in e-liquids on mammalian development.
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Affiliation(s)
| | - Stephen D Turner
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA; Signature Science LLC, Charlottesville, VA, USA
| | - Stacey Wahl
- Research and Education Department, Tompkins-McCaw Library for the Health Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Allyson E Kennedy
- Directorate for Computer and Information Science and Engineering, National Science Foundation, Alexandria, VA, USA
| | - Brent H Wyatt
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27607, USA
| | - Deborah A Howton
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
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13
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Waldmann L, Leyhr J, Zhang H, Öhman-Mägi C, Allalou A, Haitina T. The broad role of Nkx3.2 in the development of the zebrafish axial skeleton. PLoS One 2021; 16:e0255953. [PMID: 34411150 PMCID: PMC8376051 DOI: 10.1371/journal.pone.0255953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
The transcription factor Nkx3.2 (Bapx1) is an important chondrocyte maturation inhibitor. Previous Nkx3.2 knockdown and overexpression studies in non-mammalian gnathostomes have focused on its role in primary jaw joint development, while the function of this gene in broader skeletal development is not fully described. We generated a mutant allele of nkx3.2 in zebrafish with CRISPR/Cas9 and applied a range of techniques to characterize skeletal phenotypes at developmental stages from larva to adult, revealing loss of the jaw joint, fusions in bones of the occiput, morphological changes in the Weberian apparatus, and the loss or deformation of bony elements derived from basiventral cartilages of the vertebrae. Axial phenotypes are reminiscent of Nkx3.2 knockout in mammals, suggesting that the function of this gene in axial skeletal development is ancestral to osteichthyans. Our results highlight the broad role of nkx3.2 in zebrafish skeletal development and its context-specific functions in different skeletal elements.
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Affiliation(s)
- Laura Waldmann
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Jake Leyhr
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hanqing Zhang
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory BioImage Informatics Facility, Uppsala, Sweden
| | - Caroline Öhman-Mägi
- Department of Materials Science and Engineering, Uppsala University, Uppsala, Sweden
| | - Amin Allalou
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory BioImage Informatics Facility, Uppsala, Sweden
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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14
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Waldmann L, Leyhr J, Zhang H, Allalou A, Öhman-Mägi C, Haitina T. The role of Gdf5 in the development of the zebrafish fin endoskeleton. Dev Dyn 2021; 251:1535-1549. [PMID: 34242444 DOI: 10.1002/dvdy.399] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/22/2021] [Accepted: 07/08/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The development of the vertebrate limb skeleton requires a complex interaction of multiple factors to facilitate the correct shaping and positioning of bones and joints. Growth and differentiation factor 5 (Gdf5) is involved in patterning appendicular skeletal elements including joints. Expression of gdf5 in zebrafish has been detected in fin mesenchyme condensations and segmentation zones as well as the jaw joint, however, little is known about the functional role of Gdf5 outside of Amniota. RESULTS We generated CRISPR/Cas9 knockout of gdf5 in zebrafish and analyzed the resulting phenotype at different developmental stages. Homozygous gdf5 mutant zebrafish displayed changes in segmentation of the endoskeletal disc and, as a consequence, loss of posterior radials in the pectoral fins. Mutant fish also displayed disorganization and reduced length of endoskeletal elements in the median fins, while joints and mineralization seemed unaffected. CONCLUSIONS Our study demonstrates the importance of Gdf5 in the development of the zebrafish pectoral and median fin endoskeleton and reveals that the severity of the effect increases from anterior to posterior elements. Our findings are consistent with phenotypes observed in the human and mouse appendicular skeleton in response to Gdf5 knockout, suggesting a broadly conserved role for Gdf5 in Osteichthyes.
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Affiliation(s)
- Laura Waldmann
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Jake Leyhr
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hanqing Zhang
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory BioImage Informatics Facility, Uppsala, Sweden
| | - Amin Allalou
- Division of Visual Information and Interaction, Department of Information Technology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory BioImage Informatics Facility, Uppsala, Sweden
| | - Caroline Öhman-Mägi
- Department of Materials Science and Engineering, Uppsala University, Uppsala, Sweden
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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15
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A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nat Commun 2021; 12:2217. [PMID: 33850120 PMCID: PMC8044108 DOI: 10.1038/s41467-021-22448-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research.
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16
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Khor JM, Ettensohn CA. Transcription Factors of the Alx Family: Evolutionarily Conserved Regulators of Deuterostome Skeletogenesis. Front Genet 2020; 11:569314. [PMID: 33329706 PMCID: PMC7719703 DOI: 10.3389/fgene.2020.569314] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Members of the alx gene family encode transcription factors that contain a highly conserved Paired-class, DNA-binding homeodomain, and a C-terminal OAR/Aristaless domain. Phylogenetic and comparative genomic studies have revealed complex patterns of alx gene duplications during deuterostome evolution. Remarkably, alx genes have been implicated in skeletogenesis in both echinoderms and vertebrates. In this review, we provide an overview of current knowledge concerning alx genes in deuterostomes. We highlight their evolutionarily conserved role in skeletogenesis and draw parallels and distinctions between the skeletogenic gene regulatory circuitries of diverse groups within the superphylum.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
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17
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Barske L, Fabian P, Hirschberger C, Jandzik D, Square T, Xu P, Nelson N, Yu HV, Medeiros DM, Gillis JA, Crump JG. Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer. Proc Natl Acad Sci U S A 2020; 117:24876-24884. [PMID: 32958671 PMCID: PMC7547273 DOI: 10.1073/pnas.2011531117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Whereas the gill chambers of jawless vertebrates open directly into the environment, jawed vertebrates evolved skeletal appendages that drive oxygenated water unidirectionally over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single large gill cover in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here, we find that these divergent patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs. We identify a deeply conserved Pou3f3 arch enhancer present in humans through sharks but undetectable in jawless fish. Minor differences between the bony and cartilaginous fish enhancers account for their restricted versus pan-arch expression patterns. In zebrafish, mutation of Pou3f3 or the conserved enhancer disrupts gill cover formation, whereas ectopic pan-arch Pou3f3b expression generates ectopic skeletal elements resembling the multimeric covers of cartilaginous fishes. Emergence of this Pou3f3 arch enhancer >430 Mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution.
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Affiliation(s)
- Lindsey Barske
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033;
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Peter Fabian
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | | | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
- Department of Zoology, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Pengfei Xu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Nellie Nelson
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Haoze Vincent Yu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - J Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
- Marine Biological Laboratory, Woods Hole, MA 02543
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033;
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18
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Square TA, Jandzik D, Massey JL, Romášek M, Stein HP, Hansen AW, Purkayastha A, Cattell MV, Medeiros DM. Evolution of the endothelin pathway drove neural crest cell diversification. Nature 2020; 585:563-568. [PMID: 32939088 DOI: 10.1038/s41586-020-2720-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Neural crest cells (NCCs) are migratory, multipotent embryonic cells that are unique to vertebrates and form an array of clade-defining adult features. The evolution of NCCs has been linked to various genomic events, including the evolution of new gene-regulatory networks1,2, the de novo evolution of genes3 and the proliferation of paralogous genes during genome-wide duplication events4. However, conclusive functional evidence linking new and/or duplicated genes to NCC evolution is lacking. Endothelin ligands (Edns) and endothelin receptors (Ednrs) are unique to vertebrates3,5,6, and regulate multiple aspects of NCC development in jawed vertebrates7-10. Here, to test whether the evolution of Edn signalling was a driver of NCC evolution, we used CRISPR-Cas9 mutagenesis11 to disrupt edn, ednr and dlx genes in the sea lamprey, Petromyzon marinus. Lampreys are jawless fishes that last shared a common ancestor with modern jawed vertebrates around 500 million years ago12. Thus, comparisons between lampreys and gnathostomes can identify deeply conserved and evolutionarily flexible features of vertebrate development. Using the frog Xenopus laevis to expand gnathostome phylogenetic representation and facilitate side-by-side analyses, we identify ancient and lineage-specific roles for Edn signalling. These findings suggest that Edn signalling was activated in NCCs before duplication of the vertebrate genome. Then, after one or more genome-wide duplications in the vertebrate stem, paralogous Edn pathways functionally diverged, resulting in NCC subpopulations with different Edn signalling requirements. We posit that this new developmental modularity facilitated the independent evolution of NCC derivatives in stem vertebrates. Consistent with this, differences in Edn pathway targets are associated with differences in the oropharyngeal skeleton and autonomic nervous system of lampreys and modern gnathostomes. In summary, our work provides functional genetic evidence linking the origin and duplication of new vertebrate genes with the stepwise evolution of a defining vertebrate novelty.
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Affiliation(s)
- Tyler A Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA. .,Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA.
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA. .,Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia. .,Department of Zoology, Charles University in Prague, Prague, Czech Republic.
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Marek Romášek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Gymnázium Jiřího Wolkera, Prostějov, Czech Republic
| | - Haley P Stein
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Andrew W Hansen
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Amrita Purkayastha
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Maria V Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Department of Biology, Metropolitan State University, Denver, CO, USA
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
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19
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Stundl J, Pospisilova A, Matějková T, Psenicka M, Bronner ME, Cerny R. Migratory patterns and evolutionary plasticity of cranial neural crest cells in ray-finned fishes. Dev Biol 2020; 467:14-29. [PMID: 32835652 DOI: 10.1016/j.ydbio.2020.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
The cranial neural crest (CNC) arises within the developing central nervous system, but then migrates away from the neural tube in three consecutive streams termed mandibular, hyoid and branchial, respectively, according to the order along the anteroposterior axis. While the process of neural crest emigration generally follows a conserved anterior to posterior sequence across vertebrates, we find that ray-finned fishes (bichir, sterlet, gar, and pike) exhibit several heterochronies in the timing and order of CNC emergence that influences their subsequent migratory patterns. First, emigration of the cranial neural crest in these fishes occurs prematurely compared to other vertebrates, already initiating during early neurulation and well before neural tube closure. Second, delamination of the hyoid stream occurs prior to the more anterior mandibular stream; this is associated with early morphogenesis of key hyoid structures like external gills (bichir), a large opercular flap (gar) or first forming cartilage (pike). In sterlet, the hyoid and branchial CNC cells form a single hyobranchial sheet, which later segregates in concert with second pharyngeal pouch morphogenesis. Taken together, the results show that despite generally conserved migratory patterns, heterochronic alterations in the timing of emigration and pattern of migration of CNC cells accompanies morphological diversity of ray-finned fishes.
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Affiliation(s)
- Jan Stundl
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic.
| | - Anna Pospisilova
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Tereza Matějková
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Martin Psenicka
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Robert Cerny
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.
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20
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Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
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21
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Song EK, Jeon J, Jang DG, Kim HE, Sim HJ, Kwon KY, Medina-Ruiz S, Jang HJ, Lee AR, Rho JG, Lee HS, Kim SJ, Park CY, Myung K, Kim W, Kwon T, Yang S, Park TJ. ITGBL1 modulates integrin activity to promote cartilage formation and protect against arthritis. Sci Transl Med 2019; 10:10/462/eaam7486. [PMID: 30305454 DOI: 10.1126/scitranslmed.aam7486] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 09/20/2018] [Indexed: 11/02/2022]
Abstract
Developing and mature chondrocytes constantly interact with and remodel the surrounding extracellular matrix (ECM). Recent research indicates that integrin-ECM interaction is differentially regulated during cartilage formation (chondrogenesis). Integrin signaling is also a key source of the catabolic reactions responsible for joint destruction in both rheumatoid arthritis and osteoarthritis. However, we do not understand how chondrocytes dynamically regulate integrin signaling in such an ECM-rich environment. Here, we found that developing chondrocytes express integrin-β-like 1 (Itgbl1) at specific stages, inhibiting integrin signaling and promoting chondrogenesis. Unlike cytosolic integrin inhibitors, ITGBL1 is secreted and physically interacts with integrins to down-regulate activity. We observed that Itgbl1 expression was strongly reduced in the damaged articular cartilage of patients with osteoarthritis (OA). Ectopic expression of Itgbl1 protected joint cartilage against OA development in the destabilization of the medial meniscus-induced OA mouse model. Our results reveal ITGBL1 signaling as an underlying mechanism of protection against destructive cartilage disorders and suggest the potential therapeutic utility of targeting ITGBL1 to modulate integrin signaling in human disease.
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Affiliation(s)
- Eun Kyung Song
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jimin Jeon
- Department of Pharmacology, Ajou University School of Medicine, Suwon 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Republic of Korea.,CIRNO, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dong Gil Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ha Eun Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyo Jung Sim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Keun Yeong Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Hyun-Jun Jang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ah Reum Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun Gi Rho
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Hyun-Shik Lee
- KNU-Center for Nonlinear Dynamics, CMRI, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seok Jung Kim
- Department of Orthopaedic Surgery, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Chan Young Park
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Taejoon Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Siyoung Yang
- Department of Pharmacology, Ajou University School of Medicine, Suwon 16499, Republic of Korea. .,Department of Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Republic of Korea.,CIRNO, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Tae Joo Park
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea. .,Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
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22
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Poopalasundaram S, Richardson J, Scott A, Donovan A, Liu K, Graham A. Diminution of pharyngeal segmentation and the evolution of the amniotes. ZOOLOGICAL LETTERS 2019; 5:6. [PMID: 30788138 PMCID: PMC6369561 DOI: 10.1186/s40851-019-0123-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/05/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND The pharyngeal arches are a series of bulges found on the lateral surface of the head of vertebrate embryos, and it is within these segments that components of the later anatomy are laid down. In most vertebrates, the post-otic pharyngeal arches will form the branchial apparatus, while in amniotes these segments are believed to generate the larynx. It has been unclear how the development of these segments has been altered with the emergence of the amniotes. RESULTS In this study, we examined the development of pharyngeal arches in amniotes and show that the post-otic pharyngeal arches in this clade are greatly diminished. We find that the post-otic segments do not undergo myogenesis or skeletogenesis, but are remodelled before these processes occur. We also find that nested DLX expression, which is a feature of all the pharyngeal arches in anamniotes, is associated with the anterior segments but less so with the posterior arches in amniotes. We further show that the posterior arches of the mouse embryo fail to properly delineate, which demonstrates the lack of function of these posterior segments in later development. CONCLUSION In amniotes, there has been a loss of the ancestral "branchial" developmental programme that is a general feature of gnathostomes; myogenesis and skeletogenesis This is likely to have facilitated the emergence of the larynx as a new structure not constrained by the segmental organisation of the posterior pharyngeal region.
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Affiliation(s)
| | - Jo Richardson
- Centre for Developmental Neurobiology, King’s College London, London, UK
| | - Annabelle Scott
- Centre for Developmental Neurobiology, King’s College London, London, UK
| | - Alex Donovan
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, SE1 1UL UK
| | - Karen Liu
- Centre for Craniofacial and Regenerative Biology, King’s College London, London, SE1 1UL UK
| | - Anthony Graham
- Centre for Developmental Neurobiology, King’s College London, London, UK
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Pinet K, Deolankar M, Leung B, McLaughlin KA. Adaptive correction of craniofacial defects in pre-metamorphic Xenopus laevis tadpoles involves thyroid hormone-independent tissue remodeling. Development 2019; 146:dev.175893. [DOI: 10.1242/dev.175893] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022]
Abstract
While it is well-established that some organisms can regenerate lost structures, the ability to remodel existing malformed structures has been less well studied. Thus, in this study we examined the ability of pre-metamorphic Xenopus laevis tadpoles to self-correct malformed craniofacial tissues and found that tadpoles can adaptively improve and normalize abnormal craniofacial morphology caused by numerous developmental perturbations. We then investigated the tissue-level and molecular mechanisms that mediate the self-correction of craniofacial defects in pre-metamorphic X. laevis tadpoles. Our studies revealed that this adaptive response involves morphological changes and the remodeling of cartilage tissue, prior to metamorphosis. RT-qPCR and RNA-Seq analysis of gene expression suggests a thyroid hormone-independent endocrine signaling pathway as the potential mechanism responsible for triggering the adaptive and corrective remodeling response in these larvae that involves mmp1 and mmp13 upregulation. Thus, investigating how malformed craniofacial tissues are naturally corrected in X. laevis tadpoles has led us to valuable insights regarding the maintenance and manipulation of craniofacial morphology in a vertebrate system. These insights may help in the development of novel therapies for developmental craniofacial anomalies in humans.
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Affiliation(s)
- Kaylinnette Pinet
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
| | - Manas Deolankar
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
| | - Brian Leung
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
| | - Kelly A. McLaughlin
- Allen Discovery Center at Tufts University, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155-4243, USA
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Lukas P, Olsson L. Bapx1
is required for jaw joint development in amphibians. Evol Dev 2018; 20:192-206. [DOI: 10.1111/ede.12267] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Paul Lukas
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst‐Haeckel‐Haus und BiologiedidaktikFriedrich‐Schiller‐Universität JenaJenaGermany
| | - Lennart Olsson
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst‐Haeckel‐Haus und BiologiedidaktikFriedrich‐Schiller‐Universität JenaJenaGermany
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25
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Lukas P, Olsson L. Bapx1 upregulation is associated with ectopic mandibular cartilage development in amphibians. ZOOLOGICAL LETTERS 2018; 4:16. [PMID: 29942645 PMCID: PMC5998585 DOI: 10.1186/s40851-018-0101-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The emergence of novel structures during evolution is crucial for creating variation among organisms, but the underlying processes which lead to the emergence of evolutionary novelties are poorly understood. The gnathostome jaw joint is such a novelty, and the incorporation of bapx1 expression into the intermediate first pharyngeal arch may have played a major role in the evolution of this joint. Knockdown experiments revealed that loss of bapx1 function leads to the loss of the jaw joint, because Meckel's cartilage and the palatoquadrate fuse during development. We used Xenopus laevis and Ambystoma mexicanum to further investigate the function of bapx1 in amphibians. Bapx1 expression levels were upregulated through the use of Ly-294,002 and we investigated the potential consequences of the enhanced bapx1 expression in amphibians to test the hypothesized joint inducing function of bapx1. RESULTS We show that Ly-294,002 upregulates bapx1 expression in vivo. Additionally, ectopic mandibular arch derived cartilages develop after Ly-294,002 treatment. These ectopic cartilages are dorsoventrally oriented rods situated lateral to the palatoquadrate. The development of these additional cartilages did not change the muscular arrangement of mandibular arch-derived muscles. CONCLUSIONS Development of additional mandibular cartilages is not unusual in larval anurans. Therefore, changes in the bapx1 expression during evolution may have been the reason for the development of several additional cartilages in the larval anuran jaw. Furthermore, our observations imply a joint-promoting function of bapx1, which further substantiates its hypothetical role in the evolution of the gnathostome jaw joint.
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Affiliation(s)
- Paul Lukas
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Erbertstr. 1, 07743 Jena, Germany
| | - Lennart Olsson
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Erbertstr. 1, 07743 Jena, Germany
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26
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Endo C, Johnson TA, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Yamasaki T, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Tsunemi Y, Kamatani N, Kawashima M. Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations. Sci Rep 2018; 8:8974. [PMID: 29895819 PMCID: PMC5997657 DOI: 10.1038/s41598-018-27145-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/25/2018] [Indexed: 12/27/2022] Open
Abstract
Skin trait variation impacts quality-of-life, especially for females from the viewpoint of beauty. To investigate genetic variation related to these traits, we conducted a GWAS of various skin phenotypes in 11,311 Japanese women and identified associations for age-spots, freckles, double eyelids, straight/curly hair, eyebrow thickness, hairiness, and sweating. In silico annotation with RoadMap Epigenomics epigenetic state maps and colocalization analysis of GWAS and GTEx Project eQTL signals provided information about tissue specificity, candidate causal variants, and functional target genes. Novel signals for skin-spot traits neighboured AKAP1/MSI2 (rs17833789; P = 2.2 × 10-9), BNC2 (rs10810635; P = 2.1 × 10-22), HSPA12A (rs12259842; P = 7.1 × 10-11), PPARGC1B (rs251468; P = 1.3 × 10-21), and RAB11FIP2 (rs10444039; P = 5.6 × 10-21). HSPA12A SNPs were the only protein-coding gene eQTLs identified across skin-spot loci. Double edged eyelid analysis identified that a signal around EMX2 (rs12570134; P = 8.2 × 10-15) was also associated with expression of EMX2 and the antisense-RNA gene EMX2OS in brain putamen basal ganglia tissue. A known hair morphology signal in EDAR was associated with both eyebrow thickness (rs3827760; P = 1.7 × 10-9) and straight/curly hair (rs260643; P = 1.6 × 10-103). Excessive hairiness signals' top SNPs were also eQTLs for TBX15 (rs984225; P = 1.6 × 10-8), BCL2 (rs7226979; P = 7.3 × 10-11), and GCC2 and LIMS1 (rs6542772; P = 2.2 × 10-9). For excessive sweating, top variants in two signals in chr2:28.82-29.05 Mb (rs56089836; P = 1.7 × 10-11) were eQTLs for either PPP1CB or PLB1, while a top chr16:48.26-48.45 Mb locus SNP was a known ABCC11 missense variant (rs6500380; P = 6.8 × 10-10). In total, we identified twelve loci containing sixteen association signals, of which fifteen were novel. These findings will help dermatologic researchers better understand the genetic underpinnings of skin-related phenotypic variation in human populations.
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Affiliation(s)
- Chihiro Endo
- Department of Dermatology, School of Medicine, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | | | - Ryoko Morino
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | | | | | | | - Tatsuya Yamasaki
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Azusa Kami
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Yuria Hoshi
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Asami Tada
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | - Maaya Hine
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Miki Kobayashi
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Nami Kurume
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Yuichiro Tsunemi
- Department of Dermatology, School of Medicine, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
| | | | - Makoto Kawashima
- Department of Dermatology, School of Medicine, Tokyo Women's Medical University, Shinjuku, Tokyo, 162-8666, Japan
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27
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El-Hodiri HM, Kelly LE. Visualization of Gene Expression Patterns by In Situ Hybridization on Early Stages of Development of Xenopus laevis. Methods Mol Biol 2018; 1797:325-335. [PMID: 29896701 DOI: 10.1007/978-1-4939-7883-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In situ hybridization performed using whole fixed embryos provides accurate and detailed visualization of gene expression patterns. These patterns are useful for investigating spatial patterns of gene expression in normally developing embryos but can also be useful in investigating the effects of genetic or environmental changes on expression of genetic markers characteristic of particular tissues, organs, or genetic pathways. Our lab's protocol for whole-mount in situ hybridization is presented.
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Affiliation(s)
- Heithem M El-Hodiri
- Center for Molecular and Human Genetics, Nationwide Children's Hospital Research Institute, Columbus, OH, USA.
| | - Lisa E Kelly
- Center for Molecular and Human Genetics, Nationwide Children's Hospital Research Institute, Columbus, OH, USA
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28
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Square T, Jandzik D, Romášek M, Cerny R, Medeiros DM. The origin and diversification of the developmental mechanisms that pattern the vertebrate head skeleton. Dev Biol 2017; 427:219-229. [DOI: 10.1016/j.ydbio.2016.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/06/2016] [Accepted: 11/20/2016] [Indexed: 01/30/2023]
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29
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Square T, Jandzik D, Cattell M, Hansen A, Medeiros DM. Embryonic expression of endothelins and their receptors in lamprey and frog reveals stem vertebrate origins of complex Endothelin signaling. Sci Rep 2016; 6:34282. [PMID: 27677704 PMCID: PMC5039696 DOI: 10.1038/srep34282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/09/2016] [Indexed: 12/19/2022] Open
Abstract
Neural crest cells (NCCs) are highly patterned embryonic cells that migrate along stereotyped routes to give rise to a diverse array of adult tissues and cell types. Modern NCCs are thought to have evolved from migratory neural precursors with limited developmental potential and patterning. How this occurred is poorly understood. Endothelin signaling regulates several aspects of NCC development, including their migration, differentiation, and patterning. In jawed vertebrates, Endothelin signaling involves multiple functionally distinct ligands (Edns) and receptors (Ednrs) expressed in various NCC subpopulations. To test the potential role of endothelin signaling diversification in the evolution of modern, highly patterned NCC, we analyzed the expression of the complete set of endothelin ligands and receptors in the jawless vertebrate, the sea lamprey (Petromyzon marinus). To better understand ancestral features of gnathostome edn and ednr expression, we also analyzed all known Endothelin signaling components in the African clawed frog (Xenopus laevis). We found that the sea lamprey has a gnathsotome-like complement of edn and ednr duplicates, and these genes are expressed in patterns highly reminiscent of their gnathostome counterparts. Our results suggest that the duplication and specialization of vertebrate Endothelin signaling coincided with the appearance of highly patterned and multipotent NCCs in stem vertebrates.
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Affiliation(s)
- Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 84215, Slovakia
| | - Maria Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Andrew Hansen
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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