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Girolamo DD, Benavente-Diaz M, Murolo M, Grimaldi A, Lopes PT, Evano B, Kuriki M, Gioftsidi S, Laville V, Tinevez JY, Letort G, Mella S, Tajbakhsh S, Comai G. Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures. Development 2024; 151:dev202144. [PMID: 38240380 DOI: 10.1242/dev.202144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/27/2023] [Indexed: 02/22/2024]
Abstract
Skeletal muscle stem cells (MuSCs) are recognised as functionally heterogeneous. Cranial MuSCs are reported to have greater proliferative and regenerative capacity when compared with those in the limb. A comprehensive understanding of the mechanisms underlying this functional heterogeneity is lacking. Here, we have used clonal analysis, live imaging and single cell transcriptomic analysis to identify crucial features that distinguish extraocular muscle (EOM) from limb muscle stem cell populations. A MyogeninntdTom reporter showed that the increased proliferation capacity of EOM MuSCs correlates with deferred differentiation and lower expression of the myogenic commitment gene Myod. Unexpectedly, EOM MuSCs activated in vitro expressed a large array of extracellular matrix components typical of mesenchymal non-muscle cells. Computational analysis underscored a distinct co-regulatory module, which is absent in limb MuSCs, as driver of these features. The EOM transcription factor network, with Foxc1 as key player, appears to be hardwired to EOM identity as it persists during growth, disease and in vitro after several passages. Our findings shed light on how high-performing MuSCs regulate myogenic commitment by remodelling their local environment and adopting properties not generally associated with myogenic cells.
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Affiliation(s)
- Daniela Di Girolamo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Maria Benavente-Diaz
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Melania Murolo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Alexandre Grimaldi
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Priscilla Thomas Lopes
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Brendan Evano
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Mao Kuriki
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Stamatia Gioftsidi
- Université Paris-Est, 77420 Champs-sur- Marne, France
- Freie Universität Berlin, 14195 Berlin, Germany
- Inserm, IMRB U955-E10, 94000 Créteil, France
| | - Vincent Laville
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015 Paris, France
| | - Gaëlle Letort
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Sebastian Mella
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Glenda Comai
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
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Evano B, Sarde L, Tajbakhsh S. Temporal static and dynamic imaging of skeletal muscle in vivo. Exp Cell Res 2023; 424:113484. [PMID: 36693490 DOI: 10.1016/j.yexcr.2023.113484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
A major challenge in the study of living systems is understanding how tissues and organs are established, maintained during homeostasis, reconstituted following injury or deteriorated during disease. Most of the studies that interrogate in vivo cell biological properties of cell populations within tissues are obtained through static imaging approaches. However, in vertebrates, little is known about which, when, and how extracellular and intracellular signals are dynamically integrated to regulate cell behaviour and fates, due largely to technical challenges. Intravital imaging of cellular dynamics in mammalian models has exposed surprising properties that have been missed by conventional static imaging approaches. Here we highlight some selected examples of intravital imaging in mouse intestinal stem cells, hematopoietic stem cells, hair follicle stem cells, and neural stem cells in the brain, each of which have distinct features from an anatomical and niche-architecture perspective. Intravital imaging of mouse skeletal muscles is comparatively less advanced due to several technical constraints that will be discussed, yet this approach holds great promise as a complementary investigative method to validate findings obtained by static imaging, as well as a method for discovery.
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Affiliation(s)
- Brendan Evano
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, 75015, France; CNRS UMR 3738, Institut Pasteur, Paris, 75015, France
| | - Liza Sarde
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, 75015, France; CNRS UMR 3738, Institut Pasteur, Paris, 75015, France; Sorbonne Université, Complexité Du Vivant, F-75005, Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, 75015, France; CNRS UMR 3738, Institut Pasteur, Paris, 75015, France.
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Evano B, Gill D, Hernando-Herraez I, Comai G, Stubbs TM, Commere PH, Reik W, Tajbakhsh S. Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation. PLoS Genet 2020; 16:e1009022. [PMID: 33125370 PMCID: PMC7657492 DOI: 10.1371/journal.pgen.1009022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 11/11/2020] [Accepted: 08/02/2020] [Indexed: 12/14/2022] Open
Abstract
Adult skeletal muscles are maintained during homeostasis and regenerated upon injury by muscle stem cells (MuSCs). A heterogeneity in self-renewal, differentiation and regeneration properties has been reported for MuSCs based on their anatomical location. Although MuSCs derived from extraocular muscles (EOM) have a higher regenerative capacity than those derived from limb muscles, the molecular determinants that govern these differences remain undefined. Here we show that EOM and limb MuSCs have distinct DNA methylation signatures associated with enhancers of location-specific genes, and that the EOM transcriptome is reprogrammed following transplantation into a limb muscle environment. Notably, EOM MuSCs expressed host-site specific positional Hox codes after engraftment and self-renewal within the host muscle. However, about 10% of EOM-specific genes showed engraftment-resistant expression, pointing to cell-intrinsic molecular determinants of the higher engraftment potential of EOM MuSCs. Our results underscore the molecular diversity of distinct MuSC populations and molecularly define their plasticity in response to microenvironmental cues. These findings provide insights into strategies designed to improve the functional capacity of MuSCs in the context of regenerative medicine.
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Affiliation(s)
- Brendan Evano
- Stem Cells & Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr. Roux, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Diljeet Gill
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Glenda Comai
- Stem Cells & Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr. Roux, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Thomas M. Stubbs
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Pierre-Henri Commere
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, 28 rue du Dr. Roux, Paris, France
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Shahragim Tajbakhsh
- Stem Cells & Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25 rue du Dr. Roux, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
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Abstract
Ageing is a multi-factorial condition that results in a gradual decline in tissue and organ function. Systemic, local and intrinsic factors play major roles in this process that also results in a decline in stem cell number and function. In this issue of The EMBO Journal, Li et al (2019) show that a subpopulation of mouse muscle stem cells is depleted in aged mice through loss of niche-derived granulocyte colony-stimulating factor (G-CSF).
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Affiliation(s)
- Brendan Evano
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France.,CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
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Abstract
Investigations on developmental and regenerative myogenesis have led to major advances in decrypting stem cell properties and potential, as well as their interactions within the evolving niche. As a consequence, regenerative myogenesis has provided a forum to investigate intrinsic regulators of stem cell properties as well as extrinsic factors, including stromal cells, during normal growth and following injury and disease. Here we review some of the latest advances in the field that have exposed fundamental processes including regulation of stress following trauma and ageing, senescence, DNA damage control and modes of symmetric and asymmetric cell divisions. Recent studies have begun to explore the nature of the niche that is distinct in different muscle groups, and that is altered from prenatal to postnatal stages, and during ageing. We also discuss heterogeneities among muscle stem cells and how distinct properties within the quiescent and proliferating cell states might impact on homoeostasis and regeneration. Interestingly, cellular quiescence, which was thought to be a passive cell state, is regulated by multiple mechanisms, many of which are deregulated in various contexts including ageing. These and other factors including metabolic activity and genetic background can impact on the efficiency of muscle regeneration.
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Affiliation(s)
- Brendan Evano
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
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Baghdadi MB, Firmino J, Soni K, Evano B, Di Girolamo D, Mourikis P, Castel D, Tajbakhsh S. Notch-Induced miR-708 Antagonizes Satellite Cell Migration and Maintains Quiescence. Cell Stem Cell 2018; 23:859-868.e5. [PMID: 30416072 DOI: 10.1016/j.stem.2018.09.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 07/18/2018] [Accepted: 09/27/2018] [Indexed: 12/31/2022]
Abstract
Critical features of stem cells include anchoring within a niche and activation upon injury. Notch signaling maintains skeletal muscle satellite (stem) cell quiescence by inhibiting differentiation and inducing expression of extracellular components of the niche. However, the complete spectrum of how Notch safeguards quiescence is not well understood. Here, we perform Notch ChIP-sequencing and small RNA sequencing in satellite cells and identify the Notch-induced microRNA-708, which is a mirtron that is highly expressed in quiescent cells and sharply downregulated in activated cells. We employ in vivo and ex vivo functional studies, in addition to live imaging, to show that miR-708 regulates quiescence and self-renewal by antagonizing cell migration through targeting the transcripts of the focal-adhesion-associated protein Tensin3. Therefore, this study identifies a Notch-miR708-Tensin3 axis and suggests that Notch signaling can regulate satellite cell quiescence and transition to the activation state through dynamic regulation of the migratory machinery.
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Affiliation(s)
- Meryem B Baghdadi
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris 75015, France; CNRS UMR 3738, Institut Pasteur, Paris 75015, France; Sorbonne Universités, UPMC, University of Paris 06, IFD-ED 515, Paris 75252, France
| | - Joao Firmino
- Bioimaging and Optics platform (BIOP), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Kartik Soni
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris 75015, France; CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Brendan Evano
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris 75015, France; CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Daniela Di Girolamo
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris 75015, France; Dipartimento di Medicina Clinica e Chirurgica, Università degli Studi di Napoli Frederico II, 80131 Naples, Italy
| | | | - David Castel
- UMR8203 "Vectorologie et Thérapeutiques Anticancéreuses," CNRS, Gustave Roussy, Université Paris-Sud, Université Paris-Saclay, 94805 Villejuif, France; Département de Cancérologie de l'Enfant et de l'Adolescent, Gustave Roussy, Université Paris-Sud, Université Paris-Saclay, 94805 Villejuif, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris 75015, France; CNRS UMR 3738, Institut Pasteur, Paris 75015, France.
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Al Adhami H, Evano B, Le Digarcher A, Gueydan C, Dubois E, Parrinello H, Dantec C, Bouschet T, Varrault A, Journot L. A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. Genome Res 2015; 25:353-67. [PMID: 25614607 PMCID: PMC4352888 DOI: 10.1101/gr.175919.114] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/08/2014] [Indexed: 11/24/2022]
Abstract
Genomic imprinting is an epigenetic mechanism that restrains the expression of ∼ 100 eutherian genes in a parent-of-origin-specific manner. The reason for this selective targeting of genes with seemingly disparate molecular functions is unclear. In the present work, we show that imprinted genes are coexpressed in a network that is regulated at the transition from proliferation to quiescence and differentiation during fibroblast cell cycle withdrawal, adipogenesis in vitro, and muscle regeneration in vivo. Imprinted gene regulation is not linked to alteration of DNA methylation or to perturbation of monoallelic, parent-of-origin-dependent expression. Overexpression and knockdown of imprinted gene expression alters the sensitivity of preadipocytes to contact inhibition and adipogenic differentiation. In silico and in cellulo experiments showed that the imprinted gene network includes biallelically expressed, nonimprinted genes. These control the extracellular matrix composition, cell adhesion, cell junction, and extracellular matrix-activated and growth factor-activated signaling. These observations show that imprinted genes share a common biological process that may account for their seemingly diverse roles in embryonic development, obesity, diabetes, muscle physiology, and neoplasm.
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Affiliation(s)
- Hala Al Adhami
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Brendan Evano
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Anne Le Digarcher
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Charlotte Gueydan
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | | | | | | | - Tristan Bouschet
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Annie Varrault
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France
| | - Laurent Journot
- Institut de Genomique Fonctionnelle, Montpellier 34094, France; CNRS, UMR 5203, Montpellier 34094, France; INSERM, U661, Montpellier 34094, France; Faculté des Sciences, Université de Montpellier, Montpellier 34095, France; MGX-Montpellier GenomiX, Montpellier 34094, France
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Abstract
In recent years, our views on how DNA and genes are organised and regulated have evolved significantly. One example is provided by reports that single DNA strands in the double helix could carry distinct forms of information. That chromatids carrying old and nascently replicated DNA strands are recognised by the mitotic machinery, then segregated in a concerted way to distinct daughter cells after cell division is remarkable. Notably, this phenomenon in several cases has been associated with the cell fate choice of resulting daughter cells. Here, we review the evidence for asymmetric or template DNA strand segregation in mammals with a focus on skeletal muscle.
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Affiliation(s)
- Brendan Evano
- Institut Pasteur, Stem Cells & Development, Department of Developmental & Stem Cell Biology, CNRS URA 2578, 25 rue du Dr. Roux, Paris 75015, France
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