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Yi L, Li Q, Zhu J, Cheng W, Xie Y, Huang Y, Zhao H, Hao M, Wei H, Zhao S. Single-nucleus RNA sequencing and lipidomics reveal characteristics of transcriptional and lipid composition in porcine longissimus dorsi muscle. BMC Genomics 2024; 25:622. [PMID: 38902599 PMCID: PMC11188186 DOI: 10.1186/s12864-024-10488-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Global per capita meat consumption continues to rise, especially pork. Meat quality is influenced by the content of intramuscular fat (IMF) as a key factor. The longissimus dorsi muscle of Dahe pigs (DHM, IMF: 7.98% ± 1.96%) and Dahe black pigs (DHBM, IMF: 3.30% ± 0.64%) was studied to explore cellular heterogeneity and differentially expressed genes (DEGs) associated with IMF deposition using single-nucleus RNA sequencing (snRNA-seq). The lipid composition was then analyzed using non-targeted lipidomics. RESULTS A total of seven cell subpopulations were identified, including myocytes, fibroblast/fibro/adipogenic progenitors (FAPs), satellite cells, endothelial cells, macrophages, pericytes, and adipocytes. Among them, FAPs and adipocytes were more focused because they could be associated with lipid deposition. 1623 DEGs in the FAPs subpopulation of DHBM were up-regulated compared with DHM, while 1535 were down-regulated. These DEGs enriched in the glycolysis/gluconeogenesis pathway. 109 DEGs were up-regulated and 806 were down-regulated in the adipocyte subpopulation of DHBM compared with DHM, which were mainly enriched in the PPAR signaling pathway and fatty acid (FA) biosynthesis. The expression level of PPARG, ABP4, LEP, and ACSL1 genes in DHM was higher than that in DHBM. Lipidomics reveals porcine lipid composition characteristics of muscle tissue. A total of 41 lipid classes and 2699 lipid species were identified in DHM and DHBM groups. The top ten relative peak areas of lipid classes in DHM and DHBM were triglyceride (TG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), diglyceride (DG), cardiolipin (CL), ceramides (Cer), Simple Glc series (Hex1Cer), sphingomyelin (phSM), and phosphatidylinositol (PI). The relative peak areas of 35 lipid species in DHM were lower than DHBM, and 28 lipid species that were higher. There was a significant increase in the TG fatty acyl chains C6:0, C17:0, and C11:4, and a significant decrease in C16:0, C18:1, C18:2, and C22:4 in DHBM (p < 0.05). CONCLUSIONS C16:0 FA may downregulate the expression level of PPARG gene, which leads to the downregulation of fat metabolism-related genes such as ACSL, PLIN2, and FABP4 in DHBM compared with DHM. This may be the reason that the lipid deposition ability of Dahe pigs is stronger than that of Dahe black pigs, which need further investigation.
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Affiliation(s)
- Lanlan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Qiuyan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Junhong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenjie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yuxiao Xie
- College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi, 563006, China
| | - Ying Huang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Hongye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Meilin Hao
- College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi, 563006, China
| | - Hongjiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
| | - Sumei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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2
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Kuriki M, Korb A, Comai G, Tajbakhsh S. Interplay between Pitx2 and Pax7 temporally governs specification of extraocular muscle stem cells. PLoS Genet 2024; 20:e1010935. [PMID: 38875306 PMCID: PMC11178213 DOI: 10.1371/journal.pgen.1010935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/05/2024] [Indexed: 06/16/2024] Open
Abstract
Gene regulatory networks that act upstream of skeletal muscle fate determinants are distinct in different anatomical locations. Despite recent efforts, a clear understanding of the cascade of events underlying the emergence and maintenance of the stem cell pool in specific muscle groups remains unresolved and debated. Here, we invalidated Pitx2 with multiple Cre-driver mice prenatally, postnatally, and during lineage progression. We showed that this gene becomes progressively dispensable for specification and maintenance of the muscle stem (MuSC) cell pool in extraocular muscles (EOMs) despite being, together with Myf5, a major upstream regulator during early development. Moreover, constitutive inactivation of Pax7 postnatally led to a greater loss of MuSCs in the EOMs compared to the limb. Thus, we propose a relay between Pitx2, Myf5 and Pax7 for EOM stem cell maintenance. We demonstrate also that MuSCs in the EOMs adopt a quiescent state earlier that those in limb muscles and do not spontaneously proliferate in the adult, yet EOMs have a significantly higher content of Pax7+ MuSCs per area pre- and post-natally. Finally, while limb MuSCs proliferate in the mdx mouse model for Duchenne muscular dystrophy, significantly less MuSCs were present in the EOMs of the mdx mouse model compared to controls, and they were not proliferative. Overall, our study provides a comprehensive in vivo characterisation of MuSC heterogeneity along the body axis and brings further insights into the unusual sparing of EOMs during muscular dystrophy.
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Affiliation(s)
- Mao Kuriki
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, Institut Pasteur, Paris, France
| | - Amaury Korb
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, Institut Pasteur, Paris, France
| | - Glenda Comai
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, Institut Pasteur, Paris, France
| | - Shahragim Tajbakhsh
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, Institut Pasteur, Paris, France
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3
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Zhi Y, Wang Q, Zi M, Zhang S, Ge J, Liu K, Lu L, Fan C, Yan Q, Shi L, Chen P, Fan S, Liao Q, Guo C, Wang F, Gong Z, Xiong W, Zeng Z. Spatial Transcriptomic and Metabolomic Landscapes of Oral Submucous Fibrosis-Derived Oral Squamous Cell Carcinoma and its Tumor Microenvironment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306515. [PMID: 38229179 DOI: 10.1002/advs.202306515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/19/2023] [Indexed: 01/18/2024]
Abstract
In South and Southeast Asia, the habit of chewing betel nuts is prevalent, which leads to oral submucous fibrosis (OSF). OSF is a well-established precancerous lesion, and a portion of OSF cases eventually progress to oral squamous cell carcinoma (OSCC). However, the specific molecular mechanisms underlying the malignant transformation of OSCC from OSF are poorly understood. In this study, the leading-edge techniques of Spatial Transcriptomics (ST) and Spatial Metabolomics (SM) are integrated to obtain spatial location information of cancer cells, fibroblasts, and immune cells, as well as the transcriptomic and metabolomic landscapes in OSF-derived OSCC tissues. This work reveals for the first time that some OSF-derived OSCC cells undergo partial epithelial-mesenchymal transition (pEMT) within the in situ carcinoma (ISC) region, eventually acquiring fibroblast-like phenotypes and participating in collagen deposition. Complex interactions among epithelial cells, fibroblasts, and immune cells in the tumor microenvironment are demonstrated. Most importantly, significant metabolic reprogramming in OSF-derived OSCC, including abnormal polyamine metabolism, potentially playing a pivotal role in promoting tumorigenesis and immune evasion is discovered. The ST and SM data in this study shed new light on deciphering the mechanisms of OSF-derived OSCC. The work also offers invaluable clues for the prevention and treatment of OSCC.
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Affiliation(s)
- Yuan Zhi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Qian Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Moxin Zi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Junshang Ge
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Keyue Liu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Linsong Lu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Qijia Yan
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Pan Chen
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Songqing Fan
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, 410078, China
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4
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Robertson R, Li S, Filippelli RL, Chang NC. Muscle stem cell dysfunction in rhabdomyosarcoma and muscular dystrophy. Curr Top Dev Biol 2024; 158:83-121. [PMID: 38670717 DOI: 10.1016/bs.ctdb.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Muscle stem cells (MuSCs) are crucial to the repair and homeostasis of mature skeletal muscle. MuSC dysfunction and dysregulation of the myogenic program can contribute to the development of pathology ranging from cancers like rhabdomyosarcoma (RMS) or muscle degenerative diseases such as Duchenne muscular dystrophy (DMD). Both diseases exhibit dysregulation at nearly all steps of myogenesis. For instance, MuSC self-renewal processes are altered. In RMS, this leads to the creation of tumor propagating cells. In DMD, impaired asymmetric stem cell division creates a bias towards producing self-renewing stem cells instead of committing to differentiation. Hyperproliferation of these cells contribute to tumorigenesis in RMS and symmetric expansion of the self-renewing MuSC population in DMD. Both diseases also exhibit a repression of factors involved in terminal differentiation, halting RMS cells in the proliferative stage and thus driving tumor growth. Conversely, the MuSCs in DMD exhibit impaired differentiation and fuse prematurely, affecting myonuclei maturation and the integrity of the dystrophic muscle fiber. Finally, both disease states cause alterations to the MuSC niche. Various elements of the niche such as inflammatory and migratory signaling that impact MuSC behavior are dysregulated. Here we show how these seemingly distantly related diseases indeed have similarities in MuSC dysfunction, underlying the importance of considering MuSCs when studying the pathophysiology of muscle diseases.
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Affiliation(s)
- Rebecca Robertson
- Department of Biochemistry, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Shulei Li
- Department of Biochemistry, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC, Canada
| | - Romina L Filippelli
- Department of Biochemistry, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada
| | - Natasha C Chang
- Department of Biochemistry, Faculty of Medicine and Health Sciences, McGill University, Montréal, QC, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montréal, QC, Canada.
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5
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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] [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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6
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Theret M, Chazaud B. Skeletal muscle niche, at the crossroad of cell/cell communications. Curr Top Dev Biol 2024; 158:203-220. [PMID: 38670706 DOI: 10.1016/bs.ctdb.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Skeletal muscle is composed of a variety of tissue and non-tissue resident cells that participate in homeostasis. In particular, the muscle stem cell niche is a dynamic system, requiring direct and indirect communications between cells, involving local and remote cues. Interactions within the niche must happen in a timely manner for the maintenance or recovery of the homeostatic niche. For instance, after an injury, pro-myogenic cues delivered too early will impact on muscle stem cell proliferation, delaying the repair process. Within the niche, myofibers, endothelial cells, perivascular cells (pericytes, smooth muscle cells), fibro-adipogenic progenitors, fibroblasts, and immune cells are in close proximity with each other. Each cell behavior, membrane profile, and secretome can interfere with muscle stem cell fate and skeletal muscle regeneration. On top of that, the muscle stem cell niche can also be modified by extra-muscle (remote) cues, as other tissues may act on muscle regeneration via the production of circulating factors or the delivery of cells. In this review, we highlight recent publications evidencing both local and remote effectors of the muscle stem cell niche.
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Affiliation(s)
- Marine Theret
- School of Biomedical Engineering and Department of Medical Genetics University of British Columbia, Vancouver, BC, Canada
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, Inserm U1315, CNRS UMR 5261, Lyon, France.
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7
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Careccia G, Mangiavini L, Cirillo F. Regulation of Satellite Cells Functions during Skeletal Muscle Regeneration: A Critical Step in Physiological and Pathological Conditions. Int J Mol Sci 2023; 25:512. [PMID: 38203683 PMCID: PMC10778731 DOI: 10.3390/ijms25010512] [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: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Skeletal muscle regeneration is a complex process involving the generation of new myofibers after trauma, competitive physical activity, or disease. In this context, adult skeletal muscle stem cells, also known as satellite cells (SCs), play a crucial role in regulating muscle tissue homeostasis and activating regeneration. Alterations in their number or function have been associated with various pathological conditions. The main factors involved in the dysregulation of SCs' activity are inflammation, oxidative stress, and fibrosis. This review critically summarizes the current knowledge on the role of SCs in skeletal muscle regeneration. It examines the changes in the activity of SCs in three of the most common and severe muscle disorders: sarcopenia, muscular dystrophy, and cancer cachexia. Understanding the molecular mechanisms involved in their dysregulations is essential for improving current treatments, such as exercise, and developing personalized approaches to reactivate SCs.
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Affiliation(s)
- Giorgia Careccia
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Laura Mangiavini
- IRCCS Istituto Ortopedico Galeazzi, 20161 Milan, Italy;
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Federica Cirillo
- IRCCS Policlinico San Donato, 20097 San Donato Milanese, Italy
- Institute for Molecular and Translational Cardiology (IMTC), 20097 San Donato Milanese, Italy
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8
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Guardiola O, Iavarone F, Nicoletti C, Ventre M, Rodríguez C, Pisapia L, Andolfi G, Saccone V, Patriarca EJ, Puri PL, Minchiotti G. CRIPTO-based micro-heterogeneity of mouse muscle satellite cells enables adaptive response to regenerative microenvironment. Dev Cell 2023; 58:2896-2913.e6. [PMID: 38056454 PMCID: PMC10855569 DOI: 10.1016/j.devcel.2023.11.009] [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: 08/24/2022] [Revised: 07/01/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
Skeletal muscle repair relies on heterogeneous populations of satellite cells (SCs). The mechanisms that regulate SC homeostasis and state transition during activation are currently unknown. Here, we investigated the emerging role of non-genetic micro-heterogeneity, i.e., intrinsic cell-to-cell variability of a population, in this process. We demonstrate that micro-heterogeneity of the membrane protein CRIPTO in mouse-activated SCs (ASCs) identifies metastable cell states that allow a rapid response of the population to environmental changes. Mechanistically, CRIPTO micro-heterogeneity is generated and maintained through a process of intracellular trafficking coupled with active shedding of CRIPTO from the plasma membrane. Irreversible perturbation of CRIPTO micro-heterogeneity affects the balance of proliferation, self-renewal, and myogenic commitment in ASCs, resulting in increased self-renewal in vivo. Our findings demonstrate that CRIPTO micro-heterogeneity regulates the adaptative response of ASCs to microenvironmental changes, providing insights into the role of intrinsic heterogeneity in preserving stem cell population diversity during tissue repair.
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Affiliation(s)
- Ombretta Guardiola
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy.
| | - Francescopaolo Iavarone
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy
| | - Chiara Nicoletti
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Maurizio Ventre
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples "Federico II", Naples 80125, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia, Naples 80125, Italy
| | - Cristina Rodríguez
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy
| | - Laura Pisapia
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy
| | - Gennaro Andolfi
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy
| | - Valentina Saccone
- IRCCS Fondazione Santa Lucia, Rome 00143, Italy; Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Rome 00168, Italy
| | - Eduardo J Patriarca
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, Naples 80131, Italy.
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9
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Bencze M, Periou B, Punzón I, Barthélémy I, Taglietti V, Hou C, Zaidan L, Kefi K, Blot S, Agbulut O, Gervais M, Derumeaux G, Authier F, Tiret L, Relaix F. Receptor interacting protein kinase-3 mediates both myopathy and cardiomyopathy in preclinical animal models of Duchenne muscular dystrophy. J Cachexia Sarcopenia Muscle 2023; 14:2520-2531. [PMID: 37909859 PMCID: PMC10751447 DOI: 10.1002/jcsm.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is a progressive muscle degenerative disorder, culminating in a complete loss of ambulation, hypertrophic cardiomyopathy and a fatal cardiorespiratory failure. Necroptosis is the form of necrosis that is dependent upon the receptor-interacting protein kinase (RIPK) 3; it is involved in several inflammatory and neurodegenerative conditions. We previously identified RIPK3 as a key player in the acute myonecrosis affecting the hindlimb muscles of the mdx dystrophic mouse model. Whether necroptosis also mediates respiratory and heart disorders in DMD is currently unknown. METHODS Evidence of activation of the necroptotic axis was examined in dystrophic tissues from Golden retriever muscular dystrophy (GRMD) dogs and R-DMDdel52 rats. A functional assessment of the involvement of necroptosis in dystrophic animals was performed on mdx mice that were genetically depleted for RIPK3. Dystrophic mice aged from 12 to 18 months were analysed by histology and molecular biology to compare the phenotype of muscles from mdxRipk3+/+ and mdxRipk3-/- mice. Heart function was also examined by echocardiography in 40-week-old mice. RESULTS RIPK3 expression in sartorius and biceps femoris muscles from GRMD dogs positively correlated to myonecrosis levels (r = 0.81; P = 0.0076). RIPK3 was also found elevated in the diaphragm (P ≤ 0.05). In the slow-progressing heart phenotype of GRMD dogs, the phosphorylated form of RIPK1 at the Serine 161 site was dramatically increased in cardiomyocytes. A similar p-RIPK1 upregulation characterized the cardiomyocytes of the severe DMDdel52 rat model, associated with a marked overexpression of Ripk1 (P = 0.007) and Ripk3 (P = 0.008), indicating primed activation of the necroptotic pathway in the dystrophic heart. MdxRipk3-/- mice displayed decreased compensatory hypertrophy of the heart (P = 0.014), and echocardiography showed a 19% increase in the relative wall thickness (P < 0.05) and 29% reduction in the left ventricle mass (P = 0.0144). Besides, mdxRipk3-/- mice presented no evidence of a regenerative default or sarcopenia in skeletal muscles, moreover around 50% less affected by fibrosis (P < 0.05). CONCLUSIONS Our data highlight molecular and histological evidence that the necroptotic pathway is activated in degenerative tissues from dystrophic animal models, including the diaphragm and the heart. We also provide the genetic proof of concept that selective inhibition of necroptosis in dystrophic condition improves both histological features of muscles and cardiac function, suggesting that prevention of necroptosis is susceptible to providing multiorgan beneficial effects for DMD.
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Affiliation(s)
- Maximilien Bencze
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Baptiste Periou
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Isabel Punzón
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Inès Barthélémy
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Valentina Taglietti
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Cyrielle Hou
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Louai Zaidan
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Kaouthar Kefi
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Stéphane Blot
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Onnik Agbulut
- Institut de Biologie Paris‐Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, Biological Adaptation and AgeingSorbonne UniversitéParisFrance
| | - Marianne Gervais
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Geneviève Derumeaux
- Team Derumeaux, Department of Physiology, Henri Mondor Hospital, FHU‐SENEC, AP‐HPU955‐IMRB, Université Paris‐Est Créteil (UPEC)CréteilFrance
| | - François‐Jérôme Authier
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Laurent Tiret
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
| | - Fréderic Relaix
- Team Relaix, Biology of the Neuromuscular SystemU955‐IMRB, Inserm, UPEC, ENVA, EFSCréteilFrance
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10
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Cardone N, Taglietti V, Baratto S, Kefi K, Periou B, Gitiaux C, Barnerias C, Lafuste P, Pharm FL, Pharm JN, Panicucci C, Desguerre I, Bruno C, Authier FJ, Fiorillo C, Relaix F, Malfatti E. Myopathologic trajectory in Duchenne muscular dystrophy (DMD) reveals lack of regeneration due to senescence in satellite cells. Acta Neuropathol Commun 2023; 11:167. [PMID: 37858263 PMCID: PMC10585739 DOI: 10.1186/s40478-023-01657-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a devastating X-linked muscular disease, caused by mutations in the DMD gene encoding Dystrophin and affecting 1:5000 boys worldwide. Lack of Dystrophin leads to progressive muscle wasting and degeneration resulting in cardiorespiratory failure. Despite the absence of a definitive cure, innovative therapeutic avenues are emerging. Myopathologic studies are important to further understand the biological mechanisms of the disease and to identify histopathologic benchmarks for clinical evaluations. We conducted a myopathologic analysis on twenty-four muscle biopsies from DMD patients, with particular emphasis on regeneration, fibro-adipogenic progenitors and muscle stem cells behavior. We describe an increase in content of fibro-adipogenic progenitors, central orchestrators of fibrotic progression and lipid deposition, concurrently with a decline in muscle regenerative capacity. This regenerative impairment strongly correlates with compromised activation and expansion of muscle stem cells. Furthermore, our study uncovers an early acquisition of a senescence phenotype by DMD-afflicted muscle stem cells. Here we describe the myopathologic trajectory intrinsic to DMD and establish muscle stem cell senescence as a pivotal readout for future therapeutic interventions.
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Affiliation(s)
| | | | - Serena Baratto
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Kaouthar Kefi
- Univ Paris Est Creteil, INSERM, IMRB, 94010, Creteil, France
| | - Baptiste Periou
- Univ Paris Est Creteil, INSERM, IMRB, 94010, Creteil, France
- APHP, Filnemus, EuroNMD, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Henri Mondor Hospital, Paris, France
| | - Ciryl Gitiaux
- Neurophysiologie clinique pédiatrique, Centre de référence des maladies neuromusculaires Hôpital universitaire Necker-Enfants Malades-Paris, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Henri Mondor Hospital, Université Paris Est, U955 INSERM, IMRB, APHP, Creteil, France
- Reference Center for Neuromuscular Disorders, Filnemus, EuroNMD, Assistance Publique-Hôpitaux de Paris (APHP) Necker Enfants Malades Hospital, Paris, France
| | - Christine Barnerias
- Reference Center for Neuromuscular Disorders, Filnemus, EuroNMD, Assistance Publique-Hôpitaux de Paris (APHP) Necker Enfants Malades Hospital, Paris, France
| | - Peggy Lafuste
- Univ Paris Est Creteil, INSERM, IMRB, 94010, Creteil, France
| | - France Leturcq Pharm
- Service de Médecine Génomique, Maladies de Système et d'Organe - Fédération de Génétique et de Médecine Génomique, DMU BioPhyGen, APHP Centre-Université Paris Cité - Hôpital Cochin, Paris, France
| | - Juliette Nectoux Pharm
- Service de Médecine Génomique, Maladies de Système et d'Organe - Fédération de Génétique et de Médecine Génomique, DMU BioPhyGen, APHP Centre-Université Paris Cité - Hôpital Cochin, Paris, France
| | - Chiara Panicucci
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Isabelle Desguerre
- Reference Center for Neuromuscular Disorders, Filnemus, EuroNMD, Assistance Publique-Hôpitaux de Paris (APHP) Necker Enfants Malades Hospital, Paris, France
| | - Claudio Bruno
- Centre of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health-DINOGMI, University of Genova, Genoa, Italy
| | - François-Jerome Authier
- Univ Paris Est Creteil, INSERM, IMRB, 94010, Creteil, France
- APHP, Filnemus, EuroNMD, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Henri Mondor Hospital, Paris, France
| | - Chiara Fiorillo
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health-DINOGMI, University of Genova, Genoa, Italy
- Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Frederic Relaix
- Univ Paris Est Creteil, INSERM, IMRB, 94010, Creteil, France.
| | - Edoardo Malfatti
- Univ Paris Est Creteil, INSERM, IMRB, 94010, Creteil, France.
- APHP, Filnemus, EuroNMD, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Henri Mondor Hospital, Paris, France.
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11
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Qabrati X, Kim I, Ghosh A, Bundschuh N, Noé F, Palmer AS, Bar-Nur O. Transgene-free direct conversion of murine fibroblasts into functional muscle stem cells. NPJ Regen Med 2023; 8:43. [PMID: 37553383 PMCID: PMC10409758 DOI: 10.1038/s41536-023-00317-z] [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: 07/21/2022] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Transcription factor-based cellular reprogramming provides an attractive approach to produce desired cell types for regenerative medicine purposes. Such cellular conversions are widely dependent on viral vectors to efficiently deliver and express defined factors in target cells. However, use of viral vectors is associated with unfavorable genomic integrations that can trigger deleterious molecular consequences, rendering this method a potential impediment to clinical applications. Here, we report on a highly efficient transgene-free approach to directly convert mouse fibroblasts into induced myogenic progenitor cells (iMPCs) by overexpression of synthetic MyoD-mRNA in concert with an enhanced small molecule cocktail. First, we performed a candidate compound screen and identified two molecules that enhance fibroblast reprogramming into iMPCs by suppression of the JNK and JAK/STAT pathways. Simultaneously, we developed an optimal transfection protocol to transiently overexpress synthetic MyoD-mRNA in fibroblasts. Combining these two techniques enabled robust and rapid reprogramming of fibroblasts into Pax7 positive iMPCs in as little as 10 days. Nascent transgene-free iMPCs proliferated extensively in vitro, expressed a suite of myogenic stem cell markers, and could differentiate into highly multinucleated and contractile myotubes. Furthermore, using global and single-cell transcriptome assays, we delineated gene expression changes associated with JNK and JAK/STAT pathway inhibition during reprogramming, and identified in iMPCs a Pax7+ stem cell subpopulation resembling satellite cells. Last, transgene-free iMPCs robustly engrafted skeletal muscles of a Duchenne muscular dystrophy mouse model, restoring dystrophin expression in hundreds of myofibers. In summary, this study reports on an improved and clinically safer approach to convert fibroblasts into myogenic stem cells that can efficiently contribute to muscle regeneration in vivo.
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Affiliation(s)
- Xhem Qabrati
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Inseon Kim
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Adhideb Ghosh
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Nicola Bundschuh
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
| | - Falko Noé
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Andrew S Palmer
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland
- Institute for Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Ori Bar-Nur
- Laboratory of Regenerative and Movement Biology, Department of Health Sciences and Technology, ETH Zurich, Schwerzenbach, Switzerland.
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12
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Shen Y, Kim IM, Tang Y. Decoding the Gene Regulatory Network of Muscle Stem Cells in Mouse Duchenne Muscular Dystrophy: Revelations from Single-Nuclei RNA Sequencing Analysis. Int J Mol Sci 2023; 24:12463. [PMID: 37569835 PMCID: PMC10419276 DOI: 10.3390/ijms241512463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The gene dystrophin is responsible for Duchenne muscular dystrophy (DMD), a grave X-linked recessive ailment that results in respiratory and cardiac failure. As the expression of dystrophin in muscle stem cells (MuSCs) is a topic of debate, there exists a limited understanding of its influence on the gene network of MuSCs. This study was conducted with the objective of investigating the effects of dystrophin on the regulatory network of genes in MuSCs. To comprehend the function of dystrophin in MuSCs from DMD, this investigation employed single-nuclei RNA sequencing (snRNA-seq) to appraise the transcriptomic profile of MuSCs obtained from the skeletal muscles of dystrophin mutant mice (DMDmut) and wild-type control mice. The study revealed that the dystrophin mutation caused the disruption of several long non-coding RNAs (lncRNAs), leading to the inhibition of MEG3 and NEAT1 and the upregulation of GM48099, GM19951, and GM15564. The Gene Ontology (GO) enrichment analysis of biological processes (BP) indicated that the dystrophin mutation activated the cell adhesion pathway in MuSCs, inhibited the circulatory system process, and affected the regulation of binding. The study also revealed that the metabolic pathway activity of MuSCs was altered. The metabolic activities of oxidative phosphorylation (OXPHOS) and glycolysis were elevated in MuSCs from DMDmut. In summary, this research offers novel insights into the disrupted gene regulatory program in MuSCs due to dystrophin mutation at the single-cell level.
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Affiliation(s)
- Yan Shen
- Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Il-Man Kim
- Anatomy, Cell Biology, and Physiology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
| | - Yaoliang Tang
- Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
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13
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Nieves-Rodriguez S, Barthélémy F, Woods JD, Douine ED, Wang RT, Scripture-Adams DD, Chesmore KN, Galasso F, Miceli MC, Nelson SF. Transcriptomic analysis of paired healthy human skeletal muscles to identify modulators of disease severity in DMD. Front Genet 2023; 14:1216066. [PMID: 37576554 PMCID: PMC10415210 DOI: 10.3389/fgene.2023.1216066] [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: 05/06/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
Muscle damage and fibro-fatty replacement of skeletal muscles is a main pathologic feature of Duchenne muscular dystrophy (DMD) with more proximal muscles affected earlier and more distal affected later in the disease course, suggesting that different skeletal muscle groups possess distinctive characteristics that influence their susceptibility to disease. To explore transcriptomic factors driving differential gene expression and modulating DMD skeletal muscle severity, we characterized the transcriptome of vastus lateralis (VL), a more proximal and susceptible muscle, relative to tibialis anterior (TA), a more distal and protected muscle, in 15 healthy individuals using bulk RNA sequencing to identify gene expression differences that may mediate their relative susceptibility to damage with loss of dystrophin. Matching single nuclei RNA sequencing data was generated for 3 of the healthy individuals, to infer cell composition in the bulk RNA sequencing dataset and to improve mapping of differentially expressed genes to their cell source of expression. A total of 3,410 differentially expressed genes were identified and mapped to cell type using single nuclei RNA sequencing of muscle, including long non-coding RNAs and protein coding genes. There was an enrichment of genes involved in calcium release from the sarcoplasmic reticulum, particularly in the myofibers and these myofiber genes were higher in the VL. There was an enrichment of genes in "Collagen-Containing Extracellular Matrix" expressed by fibroblasts, endothelial, smooth muscle and pericytes, with most genes higher in the TA, as well as genes in "Regulation Of Apoptotic Process" expressed across all cell types. Previously reported genetic modifiers were also enriched within the differentially expressed genes. We also identify 6 genes with differential isoform usage between the VL and TA. Lastly, we integrate our findings with DMD RNA sequencing data from the TA, and identify "Collagen-Containing Extracellular Matrix" and "Negative Regulation Of Apoptotic Process" as differentially expressed between DMD compared to healthy. Collectively, these findings propose novel candidate mechanisms that may mediate differential muscle susceptibility in muscular dystrophies and provide new insight into potential therapeutic targets.
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Affiliation(s)
- Shirley Nieves-Rodriguez
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Florian Barthélémy
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jeremy D. Woods
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Emilie D. Douine
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Richard T. Wang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Deirdre D. Scripture-Adams
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kevin N. Chesmore
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
| | - Francesca Galasso
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - M. Carrie Miceli
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Microbiology, David Geffen School of Medicine and College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Center for Duchenne Muscular Dystrophy at UCLA, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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