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Grau-Bové X, Subirana L, Meister L, Soubigou A, Neto A, Elek A, Naranjo S, Fornas O, Gomez-Skarmeta JL, Tena JJ, Irimia M, Bertrand S, Sebé-Pedrós A, Escriva H. An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm. Nat Commun 2024; 15:4550. [PMID: 38811547 PMCID: PMC11136973 DOI: 10.1038/s41467-024-48774-4] [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: 06/22/2023] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Anaël Soubigou
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France
| | - Ana Neto
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Oscar Fornas
- Flow Cytometry Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France.
- Institut universitaire de France (IUF), Paris, France.
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650, Banyuls-sur-Mer, France.
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Vaché C, Cubedo N, Mansard L, Sarniguet J, Baux D, Faugère V, Baudoin C, Moclyn M, Touraine R, Lina-Granade G, Cossée M, Bergougnoux A, Kalatzis V, Rossel M, Roux AF. Identification and in vivo functional investigation of a HOMER2 nonstop variant causing hearing loss. Eur J Hum Genet 2023; 31:834-840. [PMID: 37173411 PMCID: PMC10326047 DOI: 10.1038/s41431-023-01374-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
DFNA68 is a rare subtype of autosomal dominant nonsyndromic hearing impairment caused by heterozygous alterations in the HOMER2 gene. To date, only 5 pathogenic or likely pathogenic coding variants, including two missense substitutions (c.188 C > T and c.587 G > C), a single base pair duplication (c.840dupC) and two short deletions (c.592_597delACCACA and c.832_836delCCTCA) have been described in 5 families. In this study, we report a novel HOMER2 variation, identified by massively parallel sequencing, in a Sicilian family suffering from progressive dominant hearing loss over 3 generations. This novel alteration is a nonstop substitution (c.1064 A > G) that converts the translational termination codon (TAG) of the gene into a tryptophan codon (TGG) and is predicted to extend the HOMER2 protein by 10 amino acids. RNA analyses from the proband suggested that HOMER2 transcripts carrying the nonstop variant escaped the non-stop decay pathway. Finally, in vivo studies using a zebrafish animal model and behavioral tests clearly established the deleterious impact of this novel HOMER2 alteration on hearing function. This study identifies the fourth causal variation responsible for DFNA68 and describes a simple in vivo approach to assess the pathogenicity of candidate HOMER2 variants.
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Affiliation(s)
- Christel Vaché
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France.
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France.
| | - Nicolas Cubedo
- MMDN, Univ Montpellier, EPHE, INSERM, Montpellier, France
| | - Luke Mansard
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | | | - David Baux
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
| | - Valérie Faugère
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Corinne Baudoin
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Melody Moclyn
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Renaud Touraine
- Department of Genetics, CHU Hopital Nord, Saint-Etienne, France
| | - Geneviève Lina-Granade
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon University Hospital, Lyon, France
| | - Mireille Cossée
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- PhyMedExp, Univ Montpellier, INSERM, CNRS, Montpellier, France
| | - Anne Bergougnoux
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- PhyMedExp, Univ Montpellier, INSERM, CNRS, Montpellier, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
| | | | - Anne-Françoise Roux
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
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Meister L, Escriva H, Bertrand S. Functions of the FGF signalling pathway in cephalochordates provide insight into the evolution of the prechordal plate. Development 2022; 149:275365. [PMID: 35575387 PMCID: PMC9188755 DOI: 10.1242/dev.200252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
The fibroblast growth factor (FGF) signalling pathway plays various roles during vertebrate embryogenesis, from mesoderm formation to brain patterning. This diversity of functions relies on the fact that vertebrates possess the largest FGF gene complement among metazoans. In the cephalochordate amphioxus, which belongs to the chordate clade together with vertebrates and tunicates, we have previously shown that the main role of FGF during early development is the control of rostral somite formation. Inhibition of this signalling pathway induces the loss of these structures, resulting in an embryo without anterior segmented mesoderm, as in the vertebrate head. Here, by combining several approaches, we show that the anterior presumptive paraxial mesoderm cells acquire an anterior axial fate when FGF signal is inhibited and that they are later incorporated in the anterior notochord. Our analysis of notochord formation in wild type and in embryos in which FGF signalling is inhibited also reveals that amphioxus anterior notochord presents transient prechordal plate features. Altogether, our results give insight into how changes in FGF functions during chordate evolution might have participated to the emergence of the complex vertebrate head. Summary: FGF signalling inhibition in cephalochordates induces a loss of anteriormost somites. After FGFR inhibition, the presomitic anterior region cells are incorporated in the anterior notochord which transiently present prechordal plate features.
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Affiliation(s)
- Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
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Aldea D, Subirana L, Keime C, Meister L, Maeso I, Marcellini S, Gomez-Skarmeta JL, Bertrand S, Escriva H. Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm. Nat Ecol Evol 2019; 3:1233-1240. [PMID: 31263232 DOI: 10.1038/s41559-019-0933-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 01/13/2023]
Abstract
The evolution of vertebrates from an ancestral chordate was accompanied by the acquisition of a predatory lifestyle closely associated to the origin of a novel anterior structure, the highly specialized head. While the vertebrate head mesoderm is unsegmented, the paraxial mesoderm of the earliest divergent chordate clade, the cephalochordates (amphioxus), is fully segmented in somites. We have previously shown that fibroblast growth factor signalling controls the formation of the most anterior somites in amphioxus; therefore, unravelling the fibroblast growth factor signalling downstream effectors is of crucial importance to shed light on the evolutionary origin of vertebrate head muscles. By using a comparative RNA sequencing approach and genetic functional analyses, we show that several transcription factors, such as Six1/2, Pax3/7 and Zic, act in combination to ensure the formation of three different somite populations. Interestingly, these proteins are orthologous to key regulators of trunk, and not head, muscle formation in vertebrates. Contrary to prevailing thinking, our results suggest that the vertebrate head mesoderm is of visceral and not paraxial origin and support a multistep evolutionary scenario for the appearance of the unsegmented mesoderm of the vertebrates new 'head'.
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Affiliation(s)
- Daniel Aldea
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Celine Keime
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM, U1258, CNRS, UMR7104, Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Lydvina Meister
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Sylvain Marcellini
- Laboratory of Development and Evolution, Department of Cell Biology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France.
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls-sur-Mer, France.
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Yu H, Li H, Li Q, Xu R, Yue C, Du S. Targeted Gene Disruption in Pacific Oyster Based on CRISPR/Cas9 Ribonucleoprotein Complexes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:301-309. [PMID: 30810831 DOI: 10.1007/s10126-019-09885-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The Pacific oyster (Crassostrea gigas) is a representative bivalve mollusc that is widely cultured in the world. In recent years, it has become an important model species for ecological, evolutionary, and developmental studies because of its ability to survive in extreme environmental conditions as a sessile filter feeder and its classical mosaic pattern of development. Although the complete genome sequence of C. gigas is available and omics data have been rapidly generated for the past few years, the genetic tools for gene functional studies have thus far been limited to RNA interference technology. In this study, we developed a gene editing system for C. gigas based on CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 ribonucleoprotein complexes. Two candidate genes, myostatin (MSTN) and Twist, were selected as targets. After microinjecting CRISPR/Cas9 ribonucleoprotein complexes into fertilized eggs, CRISPR-induced indel mutations were detected in the target genes. The CRISPR/Cas9-induced mutations were predominantly small indel mutations ranging in size from 1 to 24 bp in these two target genes. These results demonstrate that CRISPR/Cas9 can be successfully used as an effective targeted gene editing system in C. gigas. The method reported here provides a powerful tool for gene functional studies in oysters and other marine bivalves, and potentially as a new technology for genetic engineering to improve oyster traits for aquaculture.
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Affiliation(s)
- Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Huijuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Rui Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chenyang Yue
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21202, USA
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Steventon B, Duarte F, Lagadec R, Mazan S, Nicolas JF, Hirsinger E. Species-specific contribution of volumetric growth and tissue convergence to posterior body elongation in vertebrates. Development 2016; 143:1732-41. [PMID: 26989170 DOI: 10.1242/dev.126375] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 03/09/2016] [Indexed: 01/04/2023]
Abstract
Posterior body elongation is a widespread mechanism propelling the generation of the metazoan body plan. The posterior growth model predicts that a posterior growth zone generates sufficient tissue volume to elongate the posterior body. However, there are energy supply-related differences between vertebrates in the degree to which growth occurs concomitantly with embryogenesis. By applying a multi-scalar morphometric analysis in zebrafish embryos, we show that posterior body elongation is generated by an influx of cells from lateral regions, by convergence-extension of cells as they exit the tailbud, and finally by a late volumetric growth in the spinal cord and notochord. Importantly, the unsegmented region does not generate additional tissue volume. Fibroblast growth factor inhibition blocks tissue convergence rather than volumetric growth, showing that a conserved molecular mechanism can control convergent morphogenesis through different cell behaviours. Finally, via a comparative morphometric analysis in lamprey, dogfish, zebrafish and mouse, we propose that elongation via posterior volumetric growth is linked to increased energy supply and is associated with an overall increase in volumetric growth and elongation.
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Affiliation(s)
- Ben Steventon
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 25 rue du Docteur Roux, Paris cedex 15 75724, France
| | - Fernando Duarte
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 25 rue du Docteur Roux, Paris cedex 15 75724, France
| | - Ronan Lagadec
- Development and Evolution of Vertebrates, CNRS-UPMC-UMR 7150, Station Biologique, Roscoff 29680, France CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, Banyuls 66650, France
| | - Sylvie Mazan
- Development and Evolution of Vertebrates, CNRS-UPMC-UMR 7150, Station Biologique, Roscoff 29680, France CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, Banyuls 66650, France
| | - Jean-François Nicolas
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 25 rue du Docteur Roux, Paris cedex 15 75724, France
| | - Estelle Hirsinger
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 25 rue du Docteur Roux, Paris cedex 15 75724, France
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