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Guo H, Zhang Y, Xiang X, Tang N, Gao W, Cui X. Single-cell RNA sequencing analysis provides novel insights into the role of apoptosis-related genes in muscle aging. Arch Gerontol Geriatr 2024; 125:105499. [PMID: 38852373 DOI: 10.1016/j.archger.2024.105499] [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: 04/05/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE This study employed a comprehensive single-cell analysis approach to explore the role of cell apoptosis-related genes in muscle aging. METHODS The single-cell RNA sequencing data from the GSE143704 dataset were used to identify distinct cell clusters and assess gene expression patterns related to apoptosis activation. The "limma" package was used to identify hub genes, after which we performed Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to identify relevant pathways. Additionally, Gene Set Enrichment Analysis(GSEA) and Gene Set Variation Analysis (GSVA) were used to uncover relevant biological pathways. The Receiver Operating Characteristic Curve (ROC) was used to evaluate the diagnostic value of the hub genes. Single-sample Gene Set Enrichment Analysis (ssGSEA) was used to analyze the immune cell infiltration levels. RESULTS Single-cell sequencing data from muscle aging patients allowed the identification of various cell types, including epithelial cells, adipocytes, and tissue-resident macrophages. By conducting a differential expression analysis that intersected active and nonactive apoptosis, as well as comparing elderly and young samples, a total of 22 hub genes were identified (p < 0.05). The 22 hub genes have discriminative ability as potential biomarkers for diagnosing muscle aging. The enrichment analysis indicated that these genes were closely associated with diverse pathways, including "response to UV-B" and "extracellular matrix organization" (p < 0.05). Furthermore, GSEA and GSVA indicated that multiple pathways emerged-for example, the "complement and coagulation cascades", "proteasome", "insulin signaling pathway", and "MAPK signaling pathway". Additionally, the analysis of immune cell infiltration revealed positive correlations between most of the hub genes and immune cells. CONCLUSION Our study identified 22 apoptosis-related genes involved in muscle aging and indicated their potential diagnostic value. These findings offer a novel perspective on the pathogenesis of muscle aging and present potential targets for therapeutic interventions.
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Affiliation(s)
- Hua Guo
- Department of General Medicine and Sleep Medicine Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University; Wuxi Medical Center, Nanjing Medical University Wuxi People's Hospital, Wuxi, Jiangsu Province, China
| | - Yunyun Zhang
- Department of General Medicine and Sleep Medicine Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University; Wuxi Medical Center, Nanjing Medical University Wuxi People's Hospital, Wuxi, Jiangsu Province, China
| | - Xin Xiang
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Na Tang
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Gao
- Department of Geriatrics, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China.
| | - Xiaochuan Cui
- Department of General Medicine and Sleep Medicine Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University; Wuxi Medical Center, Nanjing Medical University Wuxi People's Hospital, Wuxi, Jiangsu Province, China.
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2
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Redd PS, Merting AD, Klement JD, Poschel DB, Yang D, Liu K. In vitro antibody-mediated SARS-CoV-2 infection suppression through human ACE2 receptor blockade. Immunol Lett 2024; 268:106887. [PMID: 38925442 PMCID: PMC11256821 DOI: 10.1016/j.imlet.2024.106887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/23/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Vaccines and antibodies that specifically target or neutralize components of the SARS-CoV-2 virus are effective in prevention and treatment of human patients with SARS-CoV-2 infection. However, vaccines and SARS-CoV-2 neutralization antibodies target a subset of epitopes of viral proteins, and the fast evolution of the SARS-CoV-2 virus and the continuing emergence of SARS-CoV-2 variants confer SARS-CoV-2 immune escape from these therapies. ACE2 is the human cell receptor that serves as the entry point for SARS-CoV-2 into human cells and thus is the gatekeeper for SARS-CoV-2 infection of humans. We report here the development of 4G8C11, an anti-human ACE2 receptor monoclonal antibody that recognizes ACE2 on human cell surfaces. We determined that 4G8C11 blocks SARS-CoV-2 and variant infection of ACE2+ human cells. Furthermore, 4G8C11 has minimal effects on ACE2 receptor activity. 4G8C11 is therefore a monoclonal antibody for ACE2 receptor detection and potentially an effective immunotherapeutic agent for SARS-CoV-2 and variants.
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Affiliation(s)
- Priscilla S Redd
- CheMedImmune Inc., Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA.
| | - Alyssa D Merting
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - John D Klement
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Dakota B Poschel
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Dafeng Yang
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia. Augusta, GA 30912, USA; Georgia Cancer Center, Augusta, GA 30912, USA; Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
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Mozin E, Massouridès E, Mournetas V, Lièvre C, Bourdon A, Jackson DL, Packer JS, Seong J, Trapnell C, Le Guiner C, Adjali O, Pinset C, Mack DL, Dupont JB. Dystrophin deficiency impairs cell junction formation during embryonic myogenesis from pluripotent stem cells. iScience 2024; 27:110242. [PMID: 39040067 PMCID: PMC11261405 DOI: 10.1016/j.isci.2024.110242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/02/2024] [Accepted: 06/07/2024] [Indexed: 07/24/2024] Open
Abstract
Mutations in the DMD gene lead to Duchenne muscular dystrophy (DMD), a severe neuromuscular disorder affecting young boys as they acquire motor functions. DMD is typically diagnosed at 2-4 years of age, but the absence of dystrophin has negative impacts on skeletal muscles before overt symptoms appear in patients, which poses a serious challenge in current standards of care. Here, we investigated the consequences of dystrophin deficiency during skeletal muscle development. We used single-cell transcriptome profiling to characterize the myogenic trajectory of human pluripotent stem cells and showed that DMD cells bifurcate to an alternative branch when they reach the somite stage. Dystrophin deficiency was linked to marked dysregulations of cell junction proteins involved in the cell state transitions characteristic of embryonic somitogenesis. Altogether, this work demonstrates that in vitro, dystrophin deficiency has deleterious effects on cell-cell communication during myogenic development, which should be considered in future therapeutic strategies for DMD.
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Affiliation(s)
- Elise Mozin
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | | | | | - Clémence Lièvre
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Audrey Bourdon
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Dana L. Jackson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Jonathan S. Packer
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Juyoung Seong
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | | | - Oumeya Adjali
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Christian Pinset
- Centre d’Etude des Cellules Souches, I-Stem, AFM, F-91100 Corbeil-Essonnes, France
| | - David L. Mack
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
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Dai Q, Wan C, Xu Y, Fei K, Olivere LA, Garrett B, Akers L, Peters D, Otto J, Kontos CD, Ji Z, Diao Y, Southerland KW. Vcam1+ Fibro-adipogenic Progenitors Mark Fatty Infiltration in Chronic Limb Threatening Ischemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602430. [PMID: 39026697 PMCID: PMC11257459 DOI: 10.1101/2024.07.08.602430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Skeletal muscle health and function is a critical determinant of clinical outcomes in patients with peripheral arterial disease (PAD). Herein, we identify fatty infiltration, the ectopic deposition of adipocytes in skeletal muscle, as a histological hallmark of end-stage PAD, also known as chronic limb threatening ischemia (CLTI). Leveraging single cell transcriptome mapping in mouse models of PAD, we identify a pro-adipogenic mesenchymal stromal cell population marked by expression of Vcam1 (termed Vcam1+ FAPs) that expands in the ischemic limb. Mechanistically, we identify Sfrp1 and Nr3c1 as regulators of Vcam1+ FAP adipogenic differentiation. Loss of Sfrp1 and Nr3c1 impair Vcam1+ FAP differentiation into adipocytes in vitro. Finally, we show that Vcam1+ FAPs are enriched in human CLTI patients. Collectively, our results identify a pro-adipogenic FAP subpopulation in CLTI patients and provide a potential therapeutic target for muscle regeneration in PAD.
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Affiliation(s)
- Qunsheng Dai
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Changxin Wan
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Yueyuan Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Kaileen Fei
- Duke University School of Medicine, Duke University, Durham, NC, USA
| | - Lindsey A Olivere
- Division of Vascular Surgery, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Brianna Garrett
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Leo Akers
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Derek Peters
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - James Otto
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Christopher D Kontos
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Zhiceng Ji
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Kevin W Southerland
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, USA
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Fernández-Simón E, Piñol-Jurado P, Gokul-Nath R, Unsworth A, Alonso-Pérez J, Schiava M, Nascimento A, Tasca G, Queen R, Cox D, Suarez-Calvet X, Díaz-Manera J. Single cell RNA sequencing of human FAPs reveals different functional stages in Duchenne muscular dystrophy. Front Cell Dev Biol 2024; 12:1399319. [PMID: 39045456 PMCID: PMC11264872 DOI: 10.3389/fcell.2024.1399319] [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: 03/11/2024] [Accepted: 06/03/2024] [Indexed: 07/25/2024] Open
Abstract
Background: Duchenne muscular dystrophy is a genetic disease produced by mutations in the dystrophin gene characterized by early onset muscle weakness leading to severe and irreversible disability. Muscle degeneration involves a complex interplay between multiple cell lineages spatially located within areas of damage, termed the degenerative niche, including inflammatory cells, satellite cells (SCs) and fibro-adipogenic precursor cells (FAPs). FAPs are mesenchymal stem cell which have a pivotal role in muscle homeostasis as they can either promote muscle regeneration or contribute to muscle degeneration by expanding fibrotic and fatty tissue. Although it has been described that FAPs could have a different behavior in DMD patients than in healthy controls, the molecular pathways regulating their function as well as their gene expression profile are unknown. Methods: We used single-cell RNA sequencing (scRNAseq) with 10X Genomics and Illumina technology to elucidate the differences in the transcriptional profile of isolated FAPs from healthy and DMD patients. Results: Gene signatures in FAPs from both groups revealed transcriptional differences. Seurat analysis categorized cell clusters as proliferative FAPs, regulatory FAPs, inflammatory FAPs, and myofibroblasts. Differentially expressed genes (DEGs) between healthy and DMD FAPs included upregulated genes CHI3L1, EFEMP1, MFAP5, and TGFBR2 in DMD. Functional analysis highlighted distinctions in system development, wound healing, and cytoskeletal organization in control FAPs, while extracellular organization, degradation, and collagen degradation were upregulated in DMD FAPs. Validation of DEGs in additional samples (n = 9) using qPCR reinforced the specific impact of pathological settings on FAP heterogeneity, reflecting their distinct contribution to fibro or fatty degeneration in vivo. Conclusion: Using the single-cell RNA seq from human samples provide new opportunities to study cellular coordination to further understand the regulation of muscle homeostasis and degeneration that occurs in muscular dystrophies.
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Affiliation(s)
- Esther Fernández-Simón
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Patricia Piñol-Jurado
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Rasya Gokul-Nath
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Adrienne Unsworth
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Jorge Alonso-Pérez
- Bioinformatics Unit, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Marianela Schiava
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Andres Nascimento
- Neuromuscular Disorders Unit, Neurology Department, Hospital Sant Joan de Deu, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain
| | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Rachel Queen
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Dan Cox
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
| | - Xavier Suarez-Calvet
- Neuromuscular Disorders Unit, Neurology Department, Insitut de Recerca de l’Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
- Neuromuscular Disease Unit, Neurology Department, Hospital Universitario Nuestra Señora de Candelaria, Fundación Canaria Instituto de Investigación Sanitaria de Canarias (FIISC), Tenerife, Spain
| | - Jordi Díaz-Manera
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, NE1 3BZ, Newcastle Upon Tyne, United Kingdom
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Disorders Unit, Neurology Department, Insitut de Recerca de l’Hospital de la Santa Creu I Sant Pau, Barcelona, Spain
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Engquist EN, Greco A, Joosten LA, van Engelen BG, Banerji CR, Zammit PS. Transcriptomic gene signatures measure satellite cell activity in muscular dystrophies. iScience 2024; 27:109947. [PMID: 38840844 PMCID: PMC11150970 DOI: 10.1016/j.isci.2024.109947] [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: 12/12/2023] [Revised: 03/20/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
The routine need for myonuclear turnover in skeletal muscle, together with more sporadic demands for hypertrophy and repair, are performed by resident muscle stem cells called satellite cells. Muscular dystrophies are characterized by muscle wasting, stimulating chronic repair/regeneration by satellite cells. Here, we derived and validated transcriptomic signatures for satellite cells, myoblasts/myocytes, and myonuclei using publicly available murine single cell RNA-Sequencing data. Our signatures distinguished disease from control in transcriptomic data from several muscular dystrophies including facioscapulohumeral muscular dystrophy (FSHD), Duchenne muscular dystrophy, and myotonic dystrophy type I. For FSHD, the expression of our gene signatures correlated with direct counts of satellite cells on muscle sections, as well as with increasing clinical and pathological severity. Thus, our gene signatures enable the investigation of myogenesis in bulk transcriptomic data from muscle biopsies. They also facilitate study of muscle regeneration in transcriptomic data from human muscle across health and disease.
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Affiliation(s)
- Elise N. Engquist
- King’s College London, Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK
| | - Anna Greco
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, The Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University if Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Baziel G.M. van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Christopher R.S. Banerji
- King’s College London, Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK
- The Alan Turing Institute, The British Library, 96 Euston Road, London NW1 2DB, UK
- University College London Hospitals, NHS Foundation Trust, London NW1 2BU, UK
| | - Peter S. Zammit
- King’s College London, Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK
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Ozturk T, Mignot J, Gattazzo F, Gervais M, Relaix F, Rouard H, Didier N. Dual inhibition of P38 MAPK and JNK pathways preserves stemness markers and alleviates premature activation of muscle stem cells during isolation. Stem Cell Res Ther 2024; 15:179. [PMID: 38902774 PMCID: PMC11191274 DOI: 10.1186/s13287-024-03795-0] [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: 04/03/2024] [Accepted: 06/08/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Adult skeletal muscle contains resident muscle stem cells (MuSC) with high myogenic and engraftment potentials, making them suitable for cell therapy and regenerative medicine approaches. However, purification process of MuSC remains a major hurdle to their use in the clinic. Indeed, muscle tissue enzymatic dissociation triggers a massive activation of stress signaling pathways, among which P38 and JNK MAPK, associated with a premature loss of MuSC quiescence. While the role of these pathways in the myogenic progression of MuSC is well established, the extent to which their dissociation-induced activation affects the functionality of these cells remains unexplored. METHODS We assessed the effect of P38 and JNK MAPK induction on stemness marker expression and MuSC activation state during isolation by pharmacological approaches. MuSC functionality was evaluated by in vitro assays and in vivo transplantation experiments. We performed a comparative analysis of the transcriptome of human MuSC purified with pharmacological inhibitors of P38 and JNK MAPK (SB202190 and SP600125, respectively) versus available RNAseq resources. RESULTS We monitored PAX7 protein levels in murine MuSC during muscle dissociation and demonstrated a two-step decline partly dependent on P38 and JNK MAPK activities. We showed that simultaneous inhibition of these pathways throughout the MuSC isolation process preserves the expression of stemness markers and limits their premature activation, leading to improved survival and amplification in vitro as well as increased engraftment in vivo. Through a comparative RNAseq analysis of freshly isolated human MuSC, we provide evidence that our findings in murine MuSC could be relevant to human MuSC. Based on these findings, we implemented a purification strategy, significantly improving the recovery yields of human MuSC. CONCLUSION Our study highlights the pharmacological limitation of P38 and JNK MAPK activities as a suitable strategy to qualitatively and quantitatively ameliorate human MuSC purification process, which could be of great interest for cell-based therapies.
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Affiliation(s)
- Teoman Ozturk
- Univ Paris Est Creteil, INSERM, EFS, IMRB, 94010, Creteil, France
| | - Julien Mignot
- Univ Paris Est Creteil, INSERM, EFS, IMRB, 94010, Creteil, France
| | | | - Marianne Gervais
- Univ Paris Est Creteil, INSERM, EFS, IMRB, 94010, Creteil, France
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EFS, IMRB, 94010, Creteil, France
- EnvA, IMRB, 94700, Maisons-Alfort, France
- AP-HP, Hopital Mondor, Service d'histologie, 94010, Creteil, France
| | - Hélène Rouard
- Univ Paris Est Creteil, INSERM, EFS, IMRB, 94010, Creteil, France
- AP-HP, Hopital Mondor, Service d'histologie, 94010, Creteil, France
| | - Nathalie Didier
- Univ Paris Est Creteil, INSERM, EFS, IMRB, 94010, Creteil, France.
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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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Flores-Opazo M, Kopinke D, Helmbacher F, Fernández-Verdejo R, Tuñón-Suárez M, Lynch GS, Contreras O. Fibro-adipogenic progenitors in physiological adipogenesis and intermuscular adipose tissue remodeling. Mol Aspects Med 2024; 97:101277. [PMID: 38788527 DOI: 10.1016/j.mam.2024.101277] [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: 02/01/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Excessive accumulation of intermuscular adipose tissue (IMAT) is a common pathological feature in various metabolic and health conditions and can cause muscle atrophy, reduced function, inflammation, insulin resistance, cardiovascular issues, and unhealthy aging. Although IMAT results from fat accumulation in muscle, the mechanisms underlying its onset, development, cellular components, and functions remain unclear. IMAT levels are influenced by several factors, such as changes in the tissue environment, muscle type and origin, extent and duration of trauma, and persistent activation of fibro-adipogenic progenitors (FAPs). FAPs are a diverse and transcriptionally heterogeneous population of stromal cells essential for tissue maintenance, neuromuscular stability, and tissue regeneration. However, in cases of chronic inflammation and pathological conditions, FAPs expand and differentiate into adipocytes, resulting in the development of abnormal and ectopic IMAT. This review discusses the role of FAPs in adipogenesis and how they remodel IMAT. It highlights evidence supporting FAPs and FAP-derived adipocytes as constituents of IMAT, emphasizing their significance in adipose tissue maintenance and development, as well as their involvement in metabolic disorders, chronic pathologies and diseases. We also investigated the intricate molecular pathways and cell interactions governing FAP behavior, adipogenesis, and IMAT accumulation in chronic diseases and muscle deconditioning. Finally, we hypothesize that impaired cellular metabolic flexibility in dysfunctional muscles impacts FAPs, leading to IMAT. A deeper understanding of the biology of IMAT accumulation and the mechanisms regulating FAP behavior and fate are essential for the development of new therapeutic strategies for several debilitating conditions.
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Affiliation(s)
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, 32610, FL, USA; Myology Institute, University of Florida College of Medicine, Gainesville, FL, USA.
| | | | - Rodrigo Fernández-Verdejo
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, USA; Laboratorio de Fisiología Del Ejercicio y Metabolismo (LABFEM), Escuela de Kinesiología, Facultad de Medicina, Universidad Finis Terrae, Chile.
| | - Mauro Tuñón-Suárez
- Laboratorio de Fisiología Del Ejercicio y Metabolismo (LABFEM), Escuela de Kinesiología, Facultad de Medicina, Universidad Finis Terrae, Chile.
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Parkville 3010, Australia.
| | - Osvaldo Contreras
- Developmental and Regenerative Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia.
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10
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Li Y, Wang W, Kong C, Chen X, Li C, Lu S. Identifying the miRNA-gene networks contributes to exploring paravertebral muscle degeneration's underlying pathogenesis and therapy strategy. Heliyon 2024; 10:e30517. [PMID: 38765163 PMCID: PMC11098802 DOI: 10.1016/j.heliyon.2024.e30517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
Low back pain (LBP) is a worldwide problem with public health. Paravertebral muscle degeneration (PMD) is believed to be associated with LBP. Increasing evidence has demonstrated that microRNA (miRNA)-mRNA signaling networks have been implicated in the pathophysiology of diseases. Research suggests that cell death, oxidative stress, inflammatory and immune response, and extracellular matrix (ECM) metabolism are the pathogenesis of PMD; however, the miRNA-mRNA mediated the pathological process of PMD remains elusive. RNA sequencing (RNA-seq) and single cell RNA-seq (scRNA-seq) are invaluable tools for uncovering the functional biology underlying these miRNA and gene expression changes. Using scRNA-seq, we show that multiple immunocytes are presented during PMD, revealing that they may have been implicated with PMD. Additionally, using RNA-seq, we identified 76 differentially expressed genes (DEGs) and 106 differentially expressed miRNAs (DEMs), among which IL-24 and CCDC63 were the top upregulated and downregulated genes in PMD. Comprehensive bioinformatics analyses, including Venn diagrams, differential expression, functional enrichment, and protein-protein interaction analysis, were then conducted to identify six ferroptosis-related DEGs, two oxidative stress-related DEGs, eleven immunity-related DEGs, five ECM-related DEGs, among which AKR1C2/AKR1C3/SIRT1/ALB/IL-24 belong to inflammatory genes. Furthermore, 67 DEMs were predicted to be upstream miRNAs of 25 key DEGs by merging RNA-seq, TargetScan, and mirDIP databases. Finally, a miRNA-gene network was constructed using Cytoscape software and an alluvial plot. ROC curve analysis unveiled multiple key DEGs with the high clinical diagnostic value, providing novel approaches for diagnosing and treating PMD diseases.
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Affiliation(s)
- Yongjin Li
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
- Spine Center, Department of Orthopaedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No.17, Lujiang Road, Hefei, Anhui, 230001, China
| | - Wei Wang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
| | - Chao Kong
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
| | - Xiaolong Chen
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
| | - Chaoyi Li
- Department of Joint Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | - Shibao Lu
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
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11
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Kilpiö T, Skarp S, Perjés Á, Swan J, Kaikkonen L, Saarimäki S, Szokodi I, Penninger JM, Szabó Z, Magga J, Kerkelä R. Apelin regulates skeletal muscle adaptation to exercise in a high-intensity interval training model. Am J Physiol Cell Physiol 2024; 326:C1437-C1450. [PMID: 38525542 DOI: 10.1152/ajpcell.00427.2023] [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: 09/05/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024]
Abstract
Plasma apelin levels are reduced in aging and muscle wasting conditions. We aimed to investigate the significance of apelin signaling in cardiac and skeletal muscle responses to physiological stress. Apelin knockout (KO) and wild-type (WT) mice were subjected to high-intensity interval training (HIIT) by treadmill running. The effects of apelin on energy metabolism were studied in primary mouse skeletal muscle myotubes and cardiomyocytes. Apelin increased mitochondrial ATP production and mitochondrial coupling efficiency in myotubes and promoted the expression of mitochondrial genes both in primary myotubes and cardiomyocytes. HIIT induced mild concentric cardiac hypertrophy in WT mice, whereas eccentric growth was observed in the left ventricles of apelin KO mice. HIIT did not affect myofiber size in skeletal muscles of WT mice but decreased the myofiber size in apelin KO mice. The decrease in myofiber size resulted from a fiber type switch toward smaller slow-twitch type I fibers. The increased proportion of slow-twitch type I fibers in apelin KO mice was associated with upregulation of myosin heavy chain slow isoform expression, accompanied with upregulated expression of genes related to fatty acid transport and downregulated expression of genes related to glucose metabolism. Mechanistically, skeletal muscles of apelin KO mice showed defective induction of insulin-like growth factor-1 signaling in response to HIIT. In conclusion, apelin is required for proper skeletal and cardiac muscle adaptation to high-intensity exercise. Promoting apelinergic signaling may have benefits in aging- or disease-related muscle wasting conditions.NEW & NOTEWORTHY Apelin levels decline with age. This study demonstrates that in trained mice, apelin deficiency results in a switch from fast type II myofibers to slow oxidative type I myofibers. This is associated with a concomitant change in gene expression profile toward fatty acid utilization, indicating an aged-muscle phenotype in exercised apelin-deficient mice. These data are of importance in the design of exercise programs for aging individuals and could offer therapeutic target to maintain muscle mass.
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Affiliation(s)
- Teemu Kilpiö
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Sini Skarp
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Ábel Perjés
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Julia Swan
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Leena Kaikkonen
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Samu Saarimäki
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - István Szokodi
- Heart Institute, Medical School, and Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zoltán Szabó
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Johanna Magga
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Risto Kerkelä
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
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12
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Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V, Pett JP, Li T, Lawrence JEG, Perera S, Prete M, Huang N, Guo Q, Zeng X, Yang L, Polański K, Chipampe NJ, Dabrowska M, Li X, Bayraktar OA, Patel M, Kumasaka N, Mahbubani KT, Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. Human skeletal muscle aging atlas. NATURE AGING 2024; 4:727-744. [PMID: 38622407 PMCID: PMC11108788 DOI: 10.1038/s43587-024-00613-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Skeletal muscle aging is a key contributor to age-related frailty and sarcopenia with substantial implications for global health. Here we profiled 90,902 single cells and 92,259 single nuclei from 17 donors to map the aging process in the adult human intercostal muscle, identifying cellular changes in each muscle compartment. We found that distinct subsets of muscle stem cells exhibit decreased ribosome biogenesis genes and increased CCL2 expression, causing different aging phenotypes. Our atlas also highlights an expansion of nuclei associated with the neuromuscular junction, which may reflect re-innervation, and outlines how the loss of fast-twitch myofibers is mitigated through regeneration and upregulation of fast-type markers in slow-twitch myofibers with age. Furthermore, we document the function of aging muscle microenvironment in immune cell attraction. Overall, we present a comprehensive human skeletal muscle aging resource ( https://www.muscleageingcellatlas.org/ ) together with an in-house mouse muscle atlas to study common features of muscle aging across species.
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Affiliation(s)
- Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Tianliang Liu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Qin Guo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xinrui Zeng
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Omer Ali Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Collaborative Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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13
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Zhong H, Sian V, Johari M, Katayama S, Oghabian A, Jonson PH, Hackman P, Savarese M, Udd B. Revealing myopathy spectrum: integrating transcriptional and clinical features of human skeletal muscles with varying health conditions. Commun Biol 2024; 7:438. [PMID: 38600180 PMCID: PMC11006663 DOI: 10.1038/s42003-024-06143-3] [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: 08/22/2023] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Myopathy refers to a large group of heterogeneous, rare muscle diseases. Bulk RNA-sequencing has been utilized for the diagnosis and research of these diseases for many years. However, the existing valuable sequencing data often lack integration and clinical interpretation. In this study, we integrated bulk RNA-sequencing data from 1221 human skeletal muscles (292 with myopathies, 929 controls) from both databases and our local samples. By applying a method similar to single-cell analysis, we revealed a general spectrum of muscle diseases, ranging from healthy to mild disease, moderate muscle wasting, and severe muscle disease. This spectrum was further partly validated in three specific myopathies (97 muscles) through clinical features including trinucleotide repeat expansion, magnetic resonance imaging fat fraction, pathology, and clinical severity scores. This spectrum helped us identify 234 genuinely healthy muscles as unprecedented controls, providing a new perspective for deciphering the hallmark genes and pathways among different myopathies. The newly identified featured genes of general myopathy, inclusion body myositis, and titinopathy were highly expressed in our local muscles, as validated by quantitative polymerase chain reaction.
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Affiliation(s)
- Huahua Zhong
- Department of Neurology, Huashan Rare Disease Center, Huashan Hospital, Fudan University, Shanghai, China.
| | - Veronica Sian
- Department of Precision Medicine, "Luigi Vanvitelli" University of Campania, Via L. De Crecchio 7, Naples, Italy
| | - Mridul Johari
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Shintaro Katayama
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ali Oghabian
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per Harald Jonson
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Marco Savarese
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Department of Medical and Clinical Genetics, Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
- Tampere Neuromuscular Center, University Hospital, Tampere, Finland
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14
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Mozin E, Massouridès E, Mournetas V, Lièvre C, Bourdon A, Jackson DL, Packer JS, Seong J, Trapnell C, Le Guiner C, Adjali O, Pinset C, Mack DL, Dupont JB. Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.569919. [PMID: 38106055 PMCID: PMC10723310 DOI: 10.1101/2023.12.05.569919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mutations in the DMD gene lead to Duchenne muscular dystrophy, a severe X-linked neuromuscular disorder that manifests itself as young boys acquire motor functions. DMD is typically diagnosed at 2 to 4 years of age, but the absence of dystrophin negatively impacts muscle structure and function before overt symptoms appear in patients, which poses a serious challenge in the optimization of standards of care. In this report, we investigated the early consequences of dystrophin deficiency during skeletal muscle development. We used single-cell transcriptome profiling to characterize the myogenic trajectory of human pluripotent stem cells and showed that DMD cells bifurcate to an alternative branch when they reach the somite stage. Here, dystrophin deficiency was linked to marked dysregulations of cell junction protein families involved in the cell state transitions characteristic of embryonic somitogenesis. Altogether, this work demonstrates that in vitro, dystrophin deficiency has deleterious effects on cell-cell communication during myogenic development, which should be considered in future therapeutic strategies for DMD.
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Affiliation(s)
- Elise Mozin
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | | | | | - Clémence Lièvre
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Audrey Bourdon
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Jonathan S Packer
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Juyoung Seong
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | | | - Oumeya Adjali
- Nantes Université, CHU Nantes, INSERM, TARGET, F-44000 Nantes, France
| | - Christian Pinset
- Centre d’Etude des Cellules Souches, I-Stem, AFM, F-91100 Corbeil-Essonnes, France
| | - David L Mack
- Institute for Stem Cell and Regenerative Medicine, Department of Rehabilitation Medicine, University of Washington, Seattle, WA 98109, USA
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15
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Mejias Rivera L, Shore EM, Mourkioti F. Cellular and Molecular Mechanisms of Heterotopic Ossification in Fibrodysplasia Ossificans Progressiva. Biomedicines 2024; 12:779. [PMID: 38672135 PMCID: PMC11048698 DOI: 10.3390/biomedicines12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Fibrodysplasia ossificans progressiva (FOP) is a debilitating genetic disorder characterized by recurrent episodes of heterotopic ossification (HO) formation in muscles, tendons, and ligaments. FOP is caused by a missense mutation in the ACVR1 gene (activin A receptor type I), an important signaling receptor involved in endochondral ossification. The ACVR1R206H mutation induces increased downstream canonical SMAD-signaling and drives tissue-resident progenitor cells with osteogenic potential to participate in endochondral HO formation. In this article, we review aberrant ACVR1R206H signaling and the cells that give rise to HO in FOP. FOP mouse models and lineage tracing analyses have been used to provide strong evidence for tissue-resident mesenchymal cells as cellular contributors to HO. We assess how the underlying mutation in FOP disrupts muscle-specific dynamics during homeostasis and repair, with a focus on muscle-resident mesenchymal cells known as fibro-adipogenic progenitors (FAPs). Accumulating research points to FAPs as a prominent HO progenitor population, with ACVR1R206H FAPs not only aberrantly differentiating into chondro-osteogenic lineages but creating a permissive environment for bone formation at the expense of muscle regeneration. We will further discuss the emerging role of ACVR1R206H FAPs in muscle regeneration and therapeutic targeting of these cells to reduce HO formation in FOP.
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Affiliation(s)
- Loreilys Mejias Rivera
- Cell and Molecular Biology, Genetics and Epigenetics Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104, USA
- Center for Research in FOP and Related Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eileen M. Shore
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104, USA
- Center for Research in FOP and Related Disorders, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, 3450 Hamilton Walk, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Musculoskeletal Program, Penn Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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16
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Ma N, Mourkioti F. Ex vivo two-photon imaging of whole-mount skeletal muscles to visualize stem cell behavior. STAR Protoc 2024; 5:102772. [PMID: 38085638 PMCID: PMC10733746 DOI: 10.1016/j.xpro.2023.102772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Quiescent skeletal muscle stem cells (MuSCs) are morphologically and functionally heterogeneous and exhibit different lengths of cellular extensions, which we call protrusions. Here, we present a protocol for ex vivo two-photon imaging of MuSCs in their native environment. We describe steps for muscle dissection, fixation, embedding, imaging, and analysis of datasets. This protocol allows the examination of MuSC morphology and protrusions at the single-cell level as well as stem cell numbers. For complete details on the use and execution of this protocol, please refer to Ma et al. (2022).1.
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Affiliation(s)
- Nuoying Ma
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Bioengineering Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Regenerative Medicine, Musculoskeletal Regeneration Program, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Hoolachan JM, McCallion E, Sutton ER, Çetin Ö, Pacheco-Torres P, Dimitriadi M, Sari S, Miller GJ, Okoh M, Walter LM, Claus P, Wood MJA, Tonge DP, Bowerman M. A transcriptomics-based drug repositioning approach to identify drugs with similar activities for the treatment of muscle pathologies in spinal muscular atrophy (SMA) models. Hum Mol Genet 2024; 33:400-425. [PMID: 37947217 PMCID: PMC10877467 DOI: 10.1093/hmg/ddad192] [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: 07/13/2023] [Revised: 10/08/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a genetic neuromuscular disorder caused by the reduction of survival of motor neuron (SMN) protein levels. Although three SMN-augmentation therapies are clinically approved that significantly slow down disease progression, they are unfortunately not cures. Thus, complementary SMN-independent therapies that can target key SMA pathologies and that can support the clinically approved SMN-dependent drugs are the forefront of therapeutic development. We have previously demonstrated that prednisolone, a synthetic glucocorticoid (GC) improved muscle health and survival in severe Smn-/-;SMN2 and intermediate Smn2B/- SMA mice. However, long-term administration of prednisolone can promote myopathy. We thus wanted to identify genes and pathways targeted by prednisolone in skeletal muscle to discover clinically approved drugs that are predicted to emulate prednisolone's activities. Using an RNA-sequencing, bioinformatics, and drug repositioning pipeline on skeletal muscle from symptomatic prednisolone-treated and untreated Smn-/-; SMN2 SMA and Smn+/-; SMN2 healthy mice, we identified molecular targets linked to prednisolone's ameliorative effects and a list of 580 drug candidates with similar predicted activities. Two of these candidates, metformin and oxandrolone, were further investigated in SMA cellular and animal models, which highlighted that these compounds do not have the same ameliorative effects on SMA phenotypes as prednisolone; however, a number of other important drug targets remain. Overall, our work further supports the usefulness of prednisolone's potential as a second-generation therapy for SMA, identifies a list of potential SMA drug treatments and highlights improvements for future transcriptomic-based drug repositioning studies in SMA.
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Affiliation(s)
- Joseph M Hoolachan
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Eve McCallion
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Emma R Sutton
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Özge Çetin
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Paloma Pacheco-Torres
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Maria Dimitriadi
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, Hertfordshire, AL910 9AB, United Kingdom
| | - Suat Sari
- Department of Pharmaceutical Chemistry, Hacettepe University, Ankara, 06100, Turkey
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Gavin J Miller
- School of Chemical and Physical Sciences, Lennard-Jones Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Centre for Glycoscience, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Magnus Okoh
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Lisa M Walter
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Peter Claus
- SMATHERIA gGmbH – Non-Profit Biomedical Research Institute, Feodor-Lynen-Straße 31, 30625, Hannover, Germany
- Centre of Systems Neuroscience (ZSN), Hannover Medical School, Bünteweg 2, 30559, Hannover, Germany
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe, Headington Oxford, OX3 9DU, United Kingdom
| | - Daniel P Tonge
- School of Life Sciences, Huxley Building, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Melissa Bowerman
- School of Medicine, David Weatherall Building, Keele University, Staffordshire, ST5 5BG, United Kingdom
- Wolfson Centre for Inherited Neuromuscular Disease, RJAH Orthopaedic Hospital, Oswestry, SY10 7AG, United Kingdom
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18
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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19
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Punzon-Jimenez P, Machado-Lopez A, Perez-Moraga R, Llera-Oyola J, Grases D, Galvez-Viedma M, Sibai M, Satorres-Perez E, Lopez-Agullo S, Badenes R, Ferrer-Gomez C, Porta-Pardo E, Roson B, Simon C, Mas A. Effect of aging on the human myometrium at single-cell resolution. Nat Commun 2024; 15:945. [PMID: 38296945 PMCID: PMC10830479 DOI: 10.1038/s41467-024-45143-z] [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: 07/17/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Age-associated myometrial dysfunction can prompt complications during pregnancy and labor, which is one of the factors contributing to the 7.8-fold increase in maternal mortality in women over 40. Using single-cell/single-nucleus RNA sequencing and spatial transcriptomics, we have constructed a cellular atlas of the aging myometrium from 186,120 cells across twenty perimenopausal and postmenopausal women. We identify 23 myometrial cell subpopulations, including contractile and venous capillary cells as well as immune-modulated fibroblasts. Myometrial aging leads to fewer contractile capillary cells, a reduced level of ion channel expression in smooth muscle cells, and impaired gene expression in endothelial, smooth muscle, fibroblast, perivascular, and immune cells. We observe altered myometrial cell-to-cell communication as an aging hallmark, which associated with the loss of 25 signaling pathways, including those related to angiogenesis, tissue repair, contractility, immunity, and nervous system regulation. These insights may contribute to a better understanding of the complications faced by older individuals during pregnancy and labor.
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Affiliation(s)
- Paula Punzon-Jimenez
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain
| | - Alba Machado-Lopez
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Raul Perez-Moraga
- Carlos Simon Foundation, Valencia, Spain
- R&D Department, Igenomix, Valencia, Spain
| | | | - Daniela Grases
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | | | - Mustafa Sibai
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | | | | | - Rafael Badenes
- Department of Surgery, University of Valencia, Valencia, Spain
- Hospital Clinico Universitario, Valencia, Spain
| | | | | | - Beatriz Roson
- Carlos Simon Foundation, Valencia, Spain
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Carlos Simon
- Carlos Simon Foundation, Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, Valencia, Spain.
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA.
| | - Aymara Mas
- Carlos Simon Foundation, Valencia, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
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20
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Naraoka Y, Mabuchi Y, Kiuchi M, Kumagai K, Hisamatsu D, Yoneyama Y, Takebe T, Akazawa C. Quality Control of Stem Cell-Based Cultured Meat According to Specific Differentiation Abilities. Cells 2024; 13:135. [PMID: 38247826 PMCID: PMC10814720 DOI: 10.3390/cells13020135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
The demand for stem cell-based cultured meat as an alternative protein source is increasing in response to global food scarcity. However, the definition of quality controls, including appropriate growth factors and cell characteristics, remains incomplete. Cluster of differentiation (CD) 29 is ubiquitously expressed in bovine muscle tissue and is a marker of progenitor cells in cultured meat. However, CD29+ cells are naturally heterogeneous, and this quality control issue must be resolved. In this study, the aim was to identify the subpopulation of the CD29+ cell population with potential utility in cultured meat production. The CD29+ cell population exhibited heterogeneity, discernible through the CD44 and CD344 markers. CD29+CD44-CD344- cells displayed the ability for long-term culture, demonstrating high adipogenic potential and substantial lipid droplet accumulation, even within 3D cultures. Conversely, CD29+CD44+ cells exhibited rapid proliferation but were not viable for prolonged culture. Using cells suitable for adipocyte and muscle differentiation, we successfully designed meat buds, especially those rich in fat. Collectively, the identification and comprehension of distinct cell populations within bovine tissues contribute to quality control predictions in meat production. They also aid in establishing a stable and reliable cultured meat production technique.
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Grants
- JPMJMI18CB Japan Science and Technology Agency
- JP21H03328 Ministry of Education, Culture, Sports, Science and Technology
- JP19K19986 Ministry of Education, Culture, Sports, Science and Technology
- JP22K17699 Ministry of Education, Culture, Sports, Science and Technology
- no number Otsuka Holdings Co., Ltd.
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Affiliation(s)
- Yuna Naraoka
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; (Y.N.); (Y.M.); (M.K.); (K.K.); (D.H.)
| | - Yo Mabuchi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; (Y.N.); (Y.M.); (M.K.); (K.K.); (D.H.)
- Department of Clinical Regenerative Medicine, Fujita Medical Innovation Center, Fujita Health University, 1-1-4, Hanedakuko, Ota-ku, Tokyo 144-0041, Japan
| | - Mai Kiuchi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; (Y.N.); (Y.M.); (M.K.); (K.K.); (D.H.)
| | - Kyoko Kumagai
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; (Y.N.); (Y.M.); (M.K.); (K.K.); (D.H.)
| | - Daisuke Hisamatsu
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; (Y.N.); (Y.M.); (M.K.); (K.K.); (D.H.)
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; (Y.Y.); (T.T.)
| | - Takanori Takebe
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; (Y.Y.); (T.T.)
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children Hospital Medical Center, Cincinnati, OH 45229-3039, USA
- Division of Developmental Biology, Cincinnati Children Hospital Medical Center, Cincinnati, OH 45229-3039, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children Hospital Medical Center, Cincinnati, OH 45229-3039, USA
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chihiro Akazawa
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; (Y.N.); (Y.M.); (M.K.); (K.K.); (D.H.)
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21
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Garcia SM, Lau J, Diaz A, Chi H, Lizarraga M, Wague A, Montenegro C, Davies MR, Liu X, Feeley BT. Distinct human stem cell subpopulations drive adipogenesis and fibrosis in musculoskeletal injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.28.551038. [PMID: 38260367 PMCID: PMC10802239 DOI: 10.1101/2023.07.28.551038] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Fibroadipogenic progenitors (FAPs) maintain healthy skeletal muscle in homeostasis but drive muscle degeneration in chronic injuries by promoting adipogenesis and fibrosis. To uncover how these stem cells switch from a pro-regenerative to pro-degenerative role we perform single-cell mRNA sequencing of human FAPs from healthy and injured human muscles across a spectrum of injury, focusing on rotator cuff tears. We identify multiple subpopulations with progenitor, adipogenic, or fibrogenic gene signatures. We utilize full spectrum flow cytometry to identify distinct FAP subpopulations based on highly multiplexed protein expression. Injury severity increases adipogenic commitment of FAP subpopulations and is driven by the downregulation of DLK1. Treatment of FAPs both in vitro and in vivo with DLK1 reduces adipogenesis and fatty infiltration, suggesting that during injury, reduced DLK1 within a subpopulation of FAPs may drive degeneration. This work highlights how stem cells perform varied functions depending on tissue context, by dynamically regulating subpopulation fate commitment, which can be targeted improve patient outcomes after injury.
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22
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Cervone DT, Moreno-Justicia R, Quesada JP, Deshmukh AS. Mass spectrometry-based proteomics approaches to interrogate skeletal muscle adaptations to exercise. Scand J Med Sci Sports 2024; 34:e14334. [PMID: 36973869 DOI: 10.1111/sms.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
Acute exercise and chronic exercise training elicit beneficial whole-body changes in physiology that ultimately depend on profound alterations to the dynamics of tissue-specific proteins. Since the work accomplished during exercise owes predominantly to skeletal muscle, it has received the majority of interest from exercise scientists that attempt to unravel adaptive mechanisms accounting for salutary metabolic effects and performance improvements that arise from training. Contemporary scientists are also beginning to use mass spectrometry-based proteomics, which is emerging as a powerful approach to interrogate the muscle protein signature in a more comprehensive manner. Collectively, these technologies facilitate the analysis of skeletal muscle protein dynamics from several viewpoints, including changes to intracellular proteins (expression proteomics), secreted proteins (secretomics), post-translational modifications as well as fiber-, cell-, and organelle-specific changes. This review aims to highlight recent literature that has leveraged new workflows and advances in mass spectrometry-based proteomics to further our understanding of training-related changes in skeletal muscle. We call attention to untapped areas in skeletal muscle proteomics research relating to exercise training and metabolism, as well as basic points of contention when applying mass spectrometry-based analyses, particularly in the study of human biology. We further encourage researchers to couple the hypothesis-generating and descriptive nature of omics data with functional analyses that propel our understanding of the complex adaptive responses in skeletal muscle that occur with acute and chronic exercise.
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Affiliation(s)
- Daniel T Cervone
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Roger Moreno-Justicia
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Júlia Prats Quesada
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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23
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Varshney A, Manickam N, Orchard P, Tovar A, Zhang Z, Feng F, Erdos MR, Narisu N, Ventresca C, Nishino K, Rai V, Stringham HM, Jackson AU, Tamsen T, Gao C, Yang M, Koues OI, Welch JD, Burant CF, Williams LK, Jenkinson C, DeFronzo RA, Norton L, Saramies J, Lakka TA, Laakso M, Tuomilehto J, Mohlke KL, Kitzman JO, Koistinen HA, Liu J, Boehnke M, Collins FS, Scott LJ, Parker SCJ. Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571696. [PMID: 38168419 PMCID: PMC10760134 DOI: 10.1101/2023.12.15.571696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Skeletal muscle, the largest human organ by weight, is relevant to several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing the relevant cell types, regulatory elements, target genes, and causal variants. Here, we used genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing 456,880 nuclei. We identified 13 cell types that collectively represented 983,155 ATAC summits. We integrated genetic variation to discover 6,866 expression quantitative trait loci (eQTL) and 100,928 chromatin accessibility QTL (caQTL) (5% FDR) across the five most abundant cell types, cataloging caQTL peaks that atlas-level snATAC maps often miss. We identified 1,973 eGenes colocalized with caQTL and used mediation analyses to construct causal directional maps for chromatin accessibility and gene expression. 3,378 genome-wide association study (GWAS) signals across 43 relevant traits colocalized with sn-e/caQTL, 52% in a cell-specific manner. 77% of GWAS signals colocalized with caQTL and not eQTL, highlighting the critical importance of population-scale chromatin profiling for GWAS functional studies. GWAS-caQTL colocalization showed distinct cell-specific regulatory paradigms. For example, a C2CD4A/B T2D GWAS signal colocalized with caQTL in muscle fibers and multiple chromatin loop models nominated VPS13C, a glucose uptake gene. Sequence of the caQTL peak overlapping caSNP rs7163757 showed allelic regulatory activity differences in a human myocyte cell line massively parallel reporter assay. These results illuminate the genetic regulatory architecture of human skeletal muscle at high-resolution epigenomic, transcriptomic, and cell state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.
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Affiliation(s)
- Arushi Varshney
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Nandini Manickam
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Orchard
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adelaide Tovar
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Zhenhao Zhang
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fan Feng
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Erdos
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Narisu Narisu
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christa Ventresca
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Dept. of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Kirsten Nishino
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Vivek Rai
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Heather M Stringham
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Anne U Jackson
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Tricia Tamsen
- Biomedical Research Core Facilities Advanced Genomics Core, University of Michigan, Ann Arbor, MI, USA
| | - Chao Gao
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mao Yang
- Department of Internal Medicine, Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI, USA
| | - Olivia I Koues
- Biomedical Research Core Facilities Advanced Genomics Core, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D Welch
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - L Keoki Williams
- Department of Internal Medicine, Center for Individualized and Genomic Medicine Research, Henry Ford Hospital, Detroit, MI, USA
| | - Chris Jenkinson
- South Texas Diabetes and Obesity Research Institute, School of Medicine, University of Texas, Rio Grande Valley, TX, USA
| | - Ralph A DeFronzo
- Department of Medicine/Diabetes Division, University of Texas Health, San Antonio, TX, USA
| | - Luke Norton
- Department of Medicine/Diabetes Division, University of Texas Health, San Antonio, TX, USA
| | - Jouko Saramies
- Savitaipale Health Center, South Karelia Central Hospital, Lappeenranta, Finland
| | - Timo A Lakka
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Tuomilehto
- Dept. of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Dept. of Public Health, University of Helsinki, Helsinki, Finland
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Karen L Mohlke
- Dept. of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Jacob O Kitzman
- Dept. of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Heikki A Koistinen
- Dept. of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jie Liu
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Francis S Collins
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura J Scott
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephen C J Parker
- Dept. of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Dept. of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
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24
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Southerland KW, Xu Y, Peters DT, Lin X, Wei X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y. Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. Genome Med 2023; 15:95. [PMID: 37950327 PMCID: PMC10636829 DOI: 10.1186/s13073-023-01250-y] [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: 04/11/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Chronic limb-threatening ischemia (CLTI), a severe manifestation of peripheral arterial disease (PAD), is associated with a 1-year limb amputation rate of approximately 15-20% and substantial mortality. A key feature of CLTI is the compromised regenerative ability of skeletal muscle; however, the mechanisms responsible for this impairment are not yet fully understood. In this study, we aim to delineate pathological changes at both the cellular and transcriptomic levels, as well as in cell-cell signaling pathways, associated with compromised muscle regeneration in limb ischemia in both human tissue samples and murine models of CLTI. METHODS We performed single-cell transcriptome analysis of ischemic and non-ischemic muscle from the same CLTI patients and from a murine model of CLTI. In both datasets, we analyzed gene expression changes in macrophage and muscle satellite cell (MuSC) populations as well as differential cell-cell signaling interactions and differentiation trajectories. RESULTS Single-cell transcriptomic profiling and immunofluorescence analysis of CLTI patient skeletal muscle demonstrated that ischemic-damaged tissue displays a pro-inflammatory macrophage signature. Comparable results were observed in a murine CLTI model. Moreover, integrated analyses of both human and murine datasets revealed premature differentiation of MuSCs to be a key feature of failed muscle regeneration in the ischemic limb. Furthermore, in silico inferences of intercellular communication and in vitro assays highlight the importance of macrophage-MuSC signaling in ischemia induced muscle injuries. CONCLUSIONS Collectively, our research provides the first single-cell transcriptome atlases of skeletal muscle from CLTI patients and a murine CLTI model, emphasizing the crucial role of macrophages and inflammation in regulating muscle regeneration in CLTI through interactions with MuSCs.
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Affiliation(s)
- Kevin W Southerland
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Yueyuan Xu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Derek T Peters
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Xin Lin
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Xiaolin Wei
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Yu Xiang
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA
| | - Kaileen Fei
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Duke University School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Lindsey A Olivere
- Division of Vascular Surgery, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15217, USA
| | - Jeremy M Morowitz
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA
- Development and Stem Cell Biology Program, Duke University, Durham, NC, 27710, USA
| | - James Otto
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Qunsheng Dai
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Christopher D Kontos
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yarui Diao
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 27710, USA.
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, 27710, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, 27708, USA.
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA.
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25
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Mathieu M, Girousse A, Sengenès C. [What if the origin of FAPs was contributing to their heterogeneity in muscle?]. Med Sci (Paris) 2023; 39 Hors série n° 1:15-21. [PMID: 37975765 DOI: 10.1051/medsci/2023129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Fibro-adipogenic progenitors (FAPs) are resident mesenchymal stromal cells (MSCs) of skeletal muscle. They play a crucial role in muscle homeostasis and regeneration through their paracrine activity. Recent technological advances in single-cell RNA sequencing have allowed the characterization of the heterogeneity within this cell population. In this article, we will present the different subpopulations of FAPs under basal, injury, or degenerative conditions, as well as their associated functions in mice and humans. We will then discuss the potential extramuscular origin of a post-injury FAP population. Indeed, our recent work demonstrates that MSCs from adipose tissue, infiltrating the muscle, could contribute to FAP heterogeneity.
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Affiliation(s)
- Maxime Mathieu
- Institut RESTORE, UMR Inserm 1301 / CNRS 5070, Toulouse, France
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26
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Baldwin M, Buckley CD, Guilak F, Hulley P, Cribbs AP, Snelling S. A roadmap for delivering a human musculoskeletal cell atlas. Nat Rev Rheumatol 2023; 19:738-752. [PMID: 37798481 DOI: 10.1038/s41584-023-01031-2] [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] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
Advances in single-cell technologies have transformed the ability to identify the individual cell types present within tissues and organs. The musculoskeletal bionetwork, part of the wider Human Cell Atlas project, aims to create a detailed map of the healthy musculoskeletal system at a single-cell resolution throughout tissue development and across the human lifespan, with complementary generation of data from diseased tissues. Given the prevalence of musculoskeletal disorders, this detailed reference dataset will be critical to understanding normal musculoskeletal function in growth, homeostasis and ageing. The endeavour will also help to identify the cellular basis for disease and lay the foundations for novel therapeutic approaches to treating diseases of the joints, soft tissues and bone. Here, we present a Roadmap delineating the critical steps required to construct the first draft of a human musculoskeletal cell atlas. We describe the key challenges involved in mapping the extracellular matrix-rich, but cell-poor, tissues of the musculoskeletal system, outline early milestones that have been achieved and describe the vision and directions for a comprehensive musculoskeletal cell atlas. By embracing cutting-edge technologies, integrating diverse datasets and fostering international collaborations, this endeavour has the potential to drive transformative changes in musculoskeletal medicine.
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Affiliation(s)
- Mathew Baldwin
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Christopher D Buckley
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Farshid Guilak
- Department of Orthopaedic Surgery, Washington University in St. Louis, St. Louis, MO, USA
- Shriners Hospitals for Children, St. Louis, MO, USA
| | - Philippa Hulley
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Sarah Snelling
- The Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK.
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27
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Nelke C, Schroeter CB, Theissen L, Preusse C, Pawlitzki M, Räuber S, Dobelmann V, Cengiz D, Kleefeld F, Roos A, Schoser B, Brunn A, Neuen-Jacob E, Zschüntzsch J, Meuth SG, Stenzel W, Ruck T. Senescent fibro-adipogenic progenitors are potential drivers of pathology in inclusion body myositis. Acta Neuropathol 2023; 146:725-745. [PMID: 37773216 PMCID: PMC10564677 DOI: 10.1007/s00401-023-02637-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023]
Abstract
Inclusion body myositis (IBM) is unique across the spectrum of idiopathic inflammatory myopathies (IIM) due to its distinct clinical presentation and refractoriness to current treatment approaches. One explanation for this resistance may be the engagement of cell-autonomous mechanisms that sustain or promote disease progression of IBM independent of inflammatory activity. In this study, we focused on senescence of tissue-resident cells as potential driver of disease. For this purpose, we compared IBM patients to non-diseased controls and immune-mediated necrotizing myopathy patients. Histopathological analysis suggested that cellular senescence is a prominent feature of IBM, primarily affecting non-myogenic cells. In-depth analysis by single nuclei RNA sequencing allowed for the deconvolution and study of muscle-resident cell populations. Among these, we identified a specific cluster of fibro-adipogenic progenitors (FAPs) that demonstrated key hallmarks of senescence, including a pro-inflammatory secretome, expression of p21, increased β-galactosidase activity, and engagement of senescence pathways. FAP function is required for muscle cell health with changes to their phenotype potentially proving detrimental. In this respect, the transcriptomic landscape of IBM was also characterized by changes to the myogenic compartment demonstrating a pronounced loss of type 2A myofibers and a rarefication of acetylcholine receptor expressing myofibers. IBM muscle cells also engaged a specific pro-inflammatory phenotype defined by intracellular complement activity and the expression of immunogenic surface molecules. Skeletal muscle cell dysfunction may be linked to FAP senescence by a change in the collagen composition of the latter. Senescent FAPs lose collagen type XV expression, which is required to support myofibers' structural integrity and neuromuscular junction formation in vitro. Taken together, this study demonstrates an altered phenotypical landscape of muscle-resident cells and that FAPs, and not myofibers, are the primary senescent cell type in IBM.
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Affiliation(s)
- Christopher Nelke
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Christina B Schroeter
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Lukas Theissen
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Corinna Preusse
- Department of Neuropathology, Charité-University Medicine Berlin, Bonhoefferweg 3, 10117, Berlin, Germany
| | - Marc Pawlitzki
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Saskia Räuber
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Vera Dobelmann
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Derya Cengiz
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Felix Kleefeld
- Department of Neurology, Charité-University Medicine Berlin, Bonhoefferweg 3, 10117, Berlin, Germany
| | - Andreas Roos
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, Centre for Neuromuscular Disorders in Children, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Benedikt Schoser
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336, Munich, Germany
| | - Anna Brunn
- Institute of Neuropathology, Heinrich Heine University, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Eva Neuen-Jacob
- Institute of Neuropathology, Heinrich Heine University, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Jana Zschüntzsch
- Department of Neurology, University Medical Center Göttingen, Robert-Koch-Str. 40, Göttingen, Germany
| | - Sven G Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité-University Medicine Berlin, Bonhoefferweg 3, 10117, Berlin, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany.
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28
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Zhao Q, Jing Y, Ma S, Zhang W, Qu J, Wang S, Liu GH. An efficient protocol for studying human pluripotent stem cell-derived myotube senescence. BIOPHYSICS REPORTS 2023; 9:232-240. [PMID: 38516297 PMCID: PMC10951477 DOI: 10.52601/bpr.2023.230013] [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: 09/13/2023] [Accepted: 10/29/2023] [Indexed: 03/23/2024] Open
Abstract
Sarcopenia, an age-related skeletal muscle condition characterized by a progressive decline in muscle mass and function, is linked to increased vulnerability, a higher likelihood of falls, and higher mortality rates in older individuals. A comprehensive understanding of the intricate mechanisms driving skeletal muscle aging is of great significance in both scientific and clinical fields. Consequently, myotube models that facilitate studying regulatory mechanisms underlying skeletal muscle aging are important tools required to advance intervention strategies against skeletal muscle aging and associated disorders. Here, we provide a detailed protocol to generate human pluripotent stem cells-derived myotubes and describe their applications in aging studies, as well as a troubleshooting for potential problems. Overall, this protocol serves as a valuable methodological reference for exploring the role and mechanism of genes involved in skeletal muscle aging.
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Affiliation(s)
- Qian Zhao
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Ying Jing
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
- Sino-Danish Center for Education and Research, Beijing 101408, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
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29
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Pass CG, Palzkill V, Tan J, Kim K, Thome T, Yang Q, Fazzone B, Robinson ST, O’Malley KA, Yue F, Scali ST, Berceli SA, Ryan TE. Single-Nuclei RNA-Sequencing of the Gastrocnemius Muscle in Peripheral Artery Disease. Circ Res 2023; 133:791-809. [PMID: 37823262 PMCID: PMC10599805 DOI: 10.1161/circresaha.123.323161] [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: 06/05/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Lower extremity peripheral artery disease (PAD) is a growing epidemic with limited effective treatment options. Here, we provide a single-nuclei atlas of PAD limb muscle to facilitate a better understanding of the composition of cells and transcriptional differences that comprise the diseased limb muscle. METHODS We obtained gastrocnemius muscle specimens from 20 patients with PAD and 12 non-PAD controls. Nuclei were isolated and single-nuclei RNA-sequencing was performed. The composition of nuclei was characterized by iterative clustering via principal component analysis, differential expression analysis, and the use of known marker genes. Bioinformatics analysis was performed to determine differences in gene expression between PAD and non-PAD nuclei, as well as subsequent analysis of intercellular signaling networks. Additional histological analyses of muscle specimens accompany the single-nuclei RNA-sequencing atlas. RESULTS Single-nuclei RNA-sequencing analysis indicated a fiber type shift with patients with PAD having fewer type I (slow/oxidative) and more type II (fast/glycolytic) myonuclei compared with non-PAD, which was confirmed using immunostaining of muscle specimens. Myonuclei from PAD displayed global upregulation of genes involved in stress response, autophagy, hypoxia, and atrophy. Subclustering of myonuclei also identified populations that were unique to PAD muscle characterized by metabolic dysregulation. PAD muscles also displayed unique transcriptional profiles and increased diversity of transcriptomes in muscle stem cells, regenerating myonuclei, and fibro-adipogenic progenitor cells. Analysis of intercellular communication networks revealed fibro-adipogenic progenitors as a major signaling hub in PAD muscle, as well as deficiencies in angiogenic and bone morphogenetic protein signaling which may contribute to poor limb function in PAD. CONCLUSIONS This reference single-nuclei RNA-sequencing atlas provides a comprehensive analysis of the cell composition, transcriptional signature, and intercellular communication pathways that are altered in the PAD condition.
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Affiliation(s)
- Caroline G. Pass
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Victoria Palzkill
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Jianna Tan
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Kyoungrae Kim
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Trace Thome
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Qingping Yang
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Brian Fazzone
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Scott T. Robinson
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Kerri A. O’Malley
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Feng Yue
- Department of Animal Sciences (F.Y.), The University of Florida, Gainesville
- Myology Institute (F.Y., T.E.R.), The University of Florida, Gainesville
| | - Salvatore T. Scali
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Scott A. Berceli
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Terence E. Ryan
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
- Center for Exercise Science (T.E.R.), The University of Florida, Gainesville
- Myology Institute (F.Y., T.E.R.), The University of Florida, Gainesville
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30
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Rubenstein AB, Smith GR, Zhang Z, Chen X, Chambers TL, Ruf-Zamojski F, Mendelev N, Cheng WS, Zamojski M, Amper MAS, Nair VD, Marderstein AR, Montgomery SB, Troyanskaya OG, Zaslavsky E, Trappe T, Trappe S, Sealfon SC. Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.558914. [PMID: 37808658 PMCID: PMC10557702 DOI: 10.1101/2023.09.26.558914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Endurance exercise is an important health modifier. We studied cell-type specific adaptations of human skeletal muscle to acute endurance exercise using single-nucleus (sn) multiome sequencing in human vastus lateralis samples collected before and 3.5 hours after 40 min exercise at 70% VO2max in four subjects, as well as in matched time of day samples from two supine resting circadian controls. High quality same-cell RNA-seq and ATAC-seq data were obtained from 37,154 nuclei comprising 14 cell types. Among muscle fiber types, both shared and fiber-type specific regulatory programs were identified. Single-cell circuit analysis identified distinct adaptations in fast, slow and intermediate fibers as well as LUM-expressing FAP cells, involving a total of 328 transcription factors (TFs) acting at altered accessibility sites regulating 2,025 genes. These data and circuit mapping provide single-cell insight into the processes underlying tissue and metabolic remodeling responses to exercise.
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Affiliation(s)
- Aliza B. Rubenstein
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Gregory R. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Zidong Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Toby L. Chambers
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Frederique Ruf-Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalia Mendelev
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Wan Sze Cheng
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Michel Zamojski
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mary Anne S. Amper
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Andrew R. Marderstein
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
| | - Todd Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, IN 47306, USA
- Senior author
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai (ISMMS), New York, NY 10029, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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31
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Ford H, Liu Q, Fu X, Strieder-Barboza C. White Adipose Tissue Heterogeneity in the Single-Cell Era: From Mice and Humans to Cattle. BIOLOGY 2023; 12:1289. [PMID: 37886999 PMCID: PMC10604679 DOI: 10.3390/biology12101289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
Adipose tissue is a major modulator of metabolic function by regulating energy storage and by acting as an endocrine organ through the secretion of adipokines. With the advantage of next-generation sequencing-based single-cell technologies, adipose tissue has been studied at single-cell resolution, thus providing unbiased insight into its molecular composition. Recent single-cell RNA sequencing studies in human and mouse models have dissected the transcriptional cellular heterogeneity of subcutaneous (SAT), visceral (VAT), and intramuscular (IMAT) white adipose tissue depots and revealed unique populations of adipose tissue progenitor cells, mature adipocytes, immune cell, vascular cells, and mesothelial cells that play direct roles on adipose tissue function and the development of metabolic disorders. In livestock species, especially in bovine, significant gaps of knowledge remain in elucidating the roles of adipose tissue cell types and depots on driving the pathogenesis of metabolic disorders and the distinct fat deposition in VAT, SAT, and IMAT in meat animals. This review summarizes the current knowledge on the transcriptional and functional cellular diversity of white adipose tissue revealed by single-cell approaches and highlights the depot-specific function of adipose tissue in different mammalian species, with a particular focus on recent findings and future implications in cattle.
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Affiliation(s)
- Hunter Ford
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA;
| | - Qianglin Liu
- School of Animal Sciences, Agricultural Center, Louisiana State University, Baton Rouge, LA 70803, USA; (Q.L.); (X.F.)
| | - Xing Fu
- School of Animal Sciences, Agricultural Center, Louisiana State University, Baton Rouge, LA 70803, USA; (Q.L.); (X.F.)
| | - Clarissa Strieder-Barboza
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409, USA;
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
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32
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Messmer T, Dohmen RGJ, Schaeken L, Melzener L, Hueber R, Godec M, Didoss C, Post MJ, Flack JE. Single-cell analysis of bovine muscle-derived cell types for cultured meat production. Front Nutr 2023; 10:1212196. [PMID: 37781115 PMCID: PMC10535090 DOI: 10.3389/fnut.2023.1212196] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
Cultured meat technologies leverage the proliferation and differentiation of animal-derived stem cells ex vivo to produce edible tissues for human consumption in a sustainable fashion. However, skeletal muscle is a dynamic and highly complex tissue, involving the interplay of numerous mono- and multinucleated cells, including muscle fibers, satellite cells (SCs) and fibro-adipogenic progenitors (FAPs), and recreation of the tissue in vitro thus requires the characterization and manipulation of a broad range of cell types. Here, we use a single-cell RNA sequencing approach to characterize cellular heterogeneity within bovine muscle and muscle-derived cell cultures over time. Using this data, we identify numerous distinct cell types, and develop robust protocols for the easy purification and proliferation of several of these populations. We note overgrowth of undesirable cell types within heterogeneous proliferative cultures as a barrier to efficient cultured meat production, and use transcriptomics to identify conditions that favor the growth of SCs in the context of serum-free medium. Combining RNA velocities computed in silico with time-resolved flow cytometric analysis, we characterize dynamic subpopulations and transitions between active, quiescent, and committed states of SCs, and demonstrate methods for modulation of these states during long-term proliferative cultures. This work provides an important reference for advancing our knowledge of bovine skeletal muscle biology, and its application in the development of cultured meat technologies.
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Affiliation(s)
- Tobias Messmer
- Mosa Meat B.V., Maastricht, Netherlands
- Maastricht University, Maastricht, Netherlands
| | - Richard G. J. Dohmen
- Mosa Meat B.V., Maastricht, Netherlands
- Maastricht University, Maastricht, Netherlands
| | | | - Lea Melzener
- Mosa Meat B.V., Maastricht, Netherlands
- Maastricht University, Maastricht, Netherlands
| | | | | | | | - Mark J. Post
- Mosa Meat B.V., Maastricht, Netherlands
- Maastricht University, Maastricht, Netherlands
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Bouche A, Borner B, Richard C, Grand Y, Hannouche D, Laumonier T. In vitro-generated human muscle reserve cells are heterogeneous for Pax7 with distinct molecular states and metabolic profiles. Stem Cell Res Ther 2023; 14:243. [PMID: 37679820 PMCID: PMC10486062 DOI: 10.1186/s13287-023-03483-5] [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: 05/25/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND The capacity of skeletal muscles to regenerate relies on Pax7+ muscle stem cells (MuSC). While in vitro-amplified MuSC are activated and lose part of their regenerative capacity, in vitro-generated human muscle reserve cells (MuRC) are very similar to quiescent MuSC with properties required for their use in cell-based therapies. METHODS In the present study, we investigated the heterogeneity of human MuRC and characterized their molecular signature and metabolic profile. RESULTS We observed that Notch signaling is active and essential for the generation of quiescent human Pax7+ MuRC in vitro. We also revealed, by immunofluorescence and flow cytometry, two distinct subpopulations of MuRC distinguished by their relative Pax7 expression. After 48 h in differentiation medium (DM), the Pax7High subpopulation represented 35% of the total MuRC pool and this percentage increased to 61% after 96 h in DM. Transcriptomic analysis revealed that Pax7High MuRC were less primed for myogenic differentiation as compared to Pax7Low MuRC and displayed a metabolic shift from glycolysis toward fatty acid oxidation. The bioenergetic profile of human MuRC displayed a 1.5-fold decrease in glycolysis, basal respiration and ATP-linked respiration as compared to myoblasts. We also observed that AMPKα1 expression was significantly upregulated in human MuRC that correlated with an increased phosphorylation of acetyl-CoA carboxylase (ACC). Finally, we showed that fatty acid uptake was increased in MuRC as compared to myoblasts, whereas no changes were observed for glucose uptake. CONCLUSIONS Overall, these data reveal that the quiescent MuRC pool is heterogeneous for Pax7 with a Pax7High subpopulation being in a deeper quiescent state, less committed to differentiation and displaying a reduced metabolic activity. Altogether, our data suggest that human Pax7High MuRC may constitute an appropriate stem cell source for potential therapeutic applications in skeletal muscle diseases.
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Affiliation(s)
- Axelle Bouche
- Cell Therapy and Musculoskeletal Disorders Laboratory, Department of Orthopedic Surgery, Geneva University Hospitals and Faculty of Medicine, University Medical Center, 1 rue Michel Servet, 1211, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Geneva, Switzerland
| | - Benoit Borner
- Cell Therapy and Musculoskeletal Disorders Laboratory, Department of Orthopedic Surgery, Geneva University Hospitals and Faculty of Medicine, University Medical Center, 1 rue Michel Servet, 1211, Geneva, Switzerland
| | - Chloé Richard
- Cell Therapy and Musculoskeletal Disorders Laboratory, Department of Orthopedic Surgery, Geneva University Hospitals and Faculty of Medicine, University Medical Center, 1 rue Michel Servet, 1211, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Geneva, Switzerland
| | - Ysaline Grand
- Cell Therapy and Musculoskeletal Disorders Laboratory, Department of Orthopedic Surgery, Geneva University Hospitals and Faculty of Medicine, University Medical Center, 1 rue Michel Servet, 1211, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Geneva, Switzerland
| | - Didier Hannouche
- Cell Therapy and Musculoskeletal Disorders Laboratory, Department of Orthopedic Surgery, Geneva University Hospitals and Faculty of Medicine, University Medical Center, 1 rue Michel Servet, 1211, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Geneva, Switzerland
| | - Thomas Laumonier
- Cell Therapy and Musculoskeletal Disorders Laboratory, Department of Orthopedic Surgery, Geneva University Hospitals and Faculty of Medicine, University Medical Center, 1 rue Michel Servet, 1211, Geneva, Switzerland.
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Geneva, Switzerland.
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34
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Lin X, Wang P, Wang W, Zhou H, Zhu S, Feng S, Chen Y, Zhou H, Wang Q, Xin H, Shao X, Wang J. Suppressed Akt/GSK-3β/β-catenin signaling contributes to excessive adipogenesis of fibro-adipogenic progenitors after rotator cuff tears. Cell Death Discov 2023; 9:312. [PMID: 37626040 PMCID: PMC10457376 DOI: 10.1038/s41420-023-01618-4] [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: 04/18/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Muscular fatty infiltration is a common and troublesome pathology after rotator cuff tears (RCT), which mainly derives from fibro-adipogenic progenitors (FAPs). Compared to the RCT, fatty infiltration is not so severe in Achilles tendon tears (ATT). The knowledge of why fatty infiltration is more likely to occur after RCT is limited. In this study, more severe fatty infiltration was verified in supraspinatus than gastrocnemius muscles after tendon injury. Additionally, we revealed higher adipogenic differentiation ability of RCT-FAPs in vitro. Activation of Akt significantly stimulated GSK-3β/β-catenin signaling and thus decreased PPARγ expression and adipogenesis of RCT-FAPs, while the inhibition effect was attenuated by β-catenin inhibitor. Furthermore, Wnt signaling activator BML-284 limited adipogenesis of RCT-FAPs, alleviated muscular fatty infiltration, and improved parameters in gait analysis and treadmill test for RCT model. In conclusion, our study demonstrated that suppressed Akt/GSK-3β/β-catenin signaling increased PPARγ expression and thus contributed to excessive adipogenesis in RCT-FAPs. Modulation of Akt/GSK-3β/β-catenin signaling ameliorated excessive fatty infiltration of rotator cuff muscles and improved shoulder function after RCT.
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Affiliation(s)
- Xingzuan Lin
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Wang
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Hao Zhou
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyuan Zhu
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Yuzhou Chen
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Zhou
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qichao Wang
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hanlong Xin
- Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, China.
| | - Xiexiang Shao
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jianhua Wang
- Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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35
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Zou Q, Yuan R, Zhang Y, Wang Y, Zheng T, Shi R, Zhang M, Li Y, Fei K, Feng R, Pan B, Zhang X, Gong Z, Zhu L, Tang G, Li M, Li X, Jiang Y. A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity. eLife 2023; 12:86504. [PMID: 37276016 DOI: 10.7554/elife.86504] [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: 01/29/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Different anatomical locations of the body skin show differences in their gene expression patterns depending on different origins, and the inherent heterogeneous information can be maintained in adults. However, highly resolvable cellular specialization is less well characterized in different anatomical regions of the skin. Pig is regarded as an excellent model animal for human skin research in view of its similar physiology to human. In this study, single-cell RNA sequencing was performed on pig skin tissues from six different anatomical regions of Chenghua (CH) pigs, with a superior skin thickness trait, and the back site of large white (LW) pigs. We obtained 233,715 cells, representing seven cell types, among which we primarily characterized the heterogeneity of the top three cell types, including smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts (FBs). Then, we further identified several subtypes of SMCs, ECs, and FBs, and discovered the expression patterns of site-specific genes involved in some important pathways such as the immune response and extracellular matrix (ECM) synthesis in different anatomical regions. By comparing differentially expressed genes of skin FBs among different anatomical regions, we considered TNN, COL11A1, and INHBA as candidate genes for facilitating ECM accumulation. These findings of heterogeneity in the main skin cell types from different anatomical sites will contribute to a better understanding of inherent skin information and place the potential focus on skin generation, transmission, and transplantation, paving the foundation for human skin priming.
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Affiliation(s)
- Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, China
| | - Yu Zhang
- BGI Beijing Genome Institute, Beijing, China
| | - Yifei Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Ting Zheng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Kaixin Fei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Ran Feng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Binyun Pan
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Xinyue Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Zhengyin Gong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, China
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36
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Cai C, Yue Y, Yue B. Single-cell RNA sequencing in skeletal muscle developmental biology. Biomed Pharmacother 2023; 162:114631. [PMID: 37003036 DOI: 10.1016/j.biopha.2023.114631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/01/2023] Open
Abstract
Skeletal muscle is the most extensive tissue in mammals, and they perform several functions; it is derived from paraxial mesodermal somites and undergoes hyperplasia and hypertrophy to form multinucleated, contractile, and functional muscle fibers. Skeletal muscle is a complex heterogeneous tissue composed of various cell types that establish communication strategies to exchange biological information; therefore, characterizing the cellular heterogeneity and transcriptional signatures of skeletal muscle is central to understanding its ontogeny's details. Studies of skeletal myogenesis have focused primarily on myogenic cells' proliferation, differentiation, migration, and fusion and ignored the intricate network of cells with specific biological functions. The rapid development of single-cell sequencing technology has recently enabled the exploration of skeletal muscle cell types and molecular events during development. This review summarizes the progress in single-cell RNA sequencing and its applications in skeletal myogenesis, which will provide insights into skeletal muscle pathophysiology.
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Affiliation(s)
- Cuicui Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610225, China; Guyuan Branch, Ningxia Academy of Agriculture and Forestry Sciences, Guyuan 7560000, China
| | - Yuan Yue
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610225, China.
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37
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Bao H, Cao J, Chen M, Chen M, Chen W, Chen X, Chen Y, Chen Y, Chen Y, Chen Z, Chhetri JK, Ding Y, Feng J, Guo J, Guo M, He C, Jia Y, Jiang H, Jing Y, Li D, Li J, Li J, Liang Q, Liang R, Liu F, Liu X, Liu Z, Luo OJ, Lv J, Ma J, Mao K, Nie J, Qiao X, Sun X, Tang X, Wang J, Wang Q, Wang S, Wang X, Wang Y, Wang Y, Wu R, Xia K, Xiao FH, Xu L, Xu Y, Yan H, Yang L, Yang R, Yang Y, Ying Y, Zhang L, Zhang W, Zhang W, Zhang X, Zhang Z, Zhou M, Zhou R, Zhu Q, Zhu Z, Cao F, Cao Z, Chan P, Chen C, Chen G, Chen HZ, Chen J, Ci W, Ding BS, Ding Q, Gao F, Han JDJ, Huang K, Ju Z, Kong QP, Li J, Li J, Li X, Liu B, Liu F, Liu L, Liu Q, Liu Q, Liu X, Liu Y, Luo X, Ma S, Ma X, Mao Z, Nie J, Peng Y, Qu J, Ren J, Ren R, Song M, Songyang Z, Sun YE, Sun Y, Tian M, Wang S, Wang S, Wang X, Wang X, Wang YJ, Wang Y, Wong CCL, Xiang AP, Xiao Y, Xie Z, Xu D, Ye J, Yue R, Zhang C, Zhang H, Zhang L, Zhang W, Zhang Y, Zhang YW, Zhang Z, Zhao T, Zhao Y, Zhu D, Zou W, Pei G, Liu GH. Biomarkers of aging. SCIENCE CHINA. LIFE SCIENCES 2023; 66:893-1066. [PMID: 37076725 PMCID: PMC10115486 DOI: 10.1007/s11427-023-2305-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 04/21/2023]
Abstract
Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.
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Affiliation(s)
- Hainan Bao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengting Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Min Chen
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Chen
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiao Chen
- Department of Nuclear Medicine, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Yanhao Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yutian Chen
- The Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhiyang Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China
| | - Jagadish K Chhetri
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junlin Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Chuting He
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Yujuan Jia
- Department of Neurology, First Affiliated Hospital, Shanxi Medical University, Taiyuan, 030001, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Jing
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Dingfeng Li
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyi Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Qinhao Liang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Liang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zuojun Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jianwei Lv
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jingyi Ma
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kehang Mao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Jiawei Nie
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinpei Sun
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China
| | - Xiaoqiang Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianfang Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Wang
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Xuan Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuhan Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Rimo Wu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Kai Xia
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fu-Hui Xiao
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yingying Xu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Haoteng Yan
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Liang Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Ruici Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuanxin Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yilin Ying
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China
| | - Le Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weiwei Zhang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China
| | - Wenwan Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xing Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Min Zhou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Qingchen Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengmao Zhu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Feng Cao
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China.
| | - Zhongwei Cao
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Piu Chan
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, 510000, China.
| | - Hou-Zao Chen
- Department of Biochemistryand Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Bi-Sen Ding
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Feng Gao
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Kai Huang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China.
| | - Qing-Peng Kong
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Baohua Liu
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518060, China.
| | - Feng Liu
- Metabolic Syndrome Research Center, The Second Xiangya Hospital, Central South Unversity, Changsha, 410011, China.
| | - Lin Liu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300000, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China.
| | - Qiang Liu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China.
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
- Tianjin Institute of Immunology, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
| | - Yong Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China.
| | - Shuai Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Jing Nie
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Yaojin Peng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Center for Aging and Cancer, Hainan Medical University, Haikou, 571199, China.
| | - Moshi Song
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China.
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yu Sun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA, 98195, USA.
| | - Mei Tian
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
| | - Shusen Wang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China.
| | - Si Wang
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaoning Wang
- Institute of Geriatrics, The second Medical Center, Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Yunfang Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China.
| | - Andy Peng Xiang
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China.
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, 100101, China.
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Jing Ye
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China.
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Cuntai Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China.
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical Genetics, Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, 421001, China.
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dahai Zhu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Pei
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Biomedicine, The Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China.
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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Fahrner A, Luca E, Krützfeldt J. microRNA-501 controls myogenin +/CD74 + myogenic progenitor cells during muscle regeneration. Mol Metab 2023; 71:101704. [PMID: 36907509 PMCID: PMC10033748 DOI: 10.1016/j.molmet.2023.101704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/14/2023] Open
Abstract
OBJECTIVE Skeletal muscle regeneration is markedly impaired during aging. How adult muscle stem cells contribute to this decrease in regenerative capacity is incompletely understood. We investigated mechanisms of age-related changes in myogenic progenitor cells using the tissue-specific microRNA 501. METHODS Young and old C57Bl/6 mice were used (3 months or 24 months of age, respectively) with or without global or tissue-specific genetic deletion of miR-501. Muscle regeneration was induced using intramuscular cardiotoxin injection or treadmill exercise and analysed using single cell and bulk RNA sequencing, qRT-PCR and immunofluorescence. Muscle fiber damage was assessed with Evan`s blue dye (EBD). In vitro analysis was performed in primary muscle cells obtained from mice and humans. RESULTS Single cell sequencing revealed myogenic progenitor cells in miR-501 knockout mice at day 6 after muscle injury that are characterized by high levels of myogenin and CD74. In control mice these cells were less in number and already downregulated after day 3 of muscle injury. Muscle from knockout mice had reduced myofiber size and reduced myofiber resilience to injury and exercise. miR-501 elicits this effect by regulating sarcomeric gene expression through its target gene estrogen-related receptor gamma (Esrrg). Importantly, in aged skeletal muscle where miR-501 was significantly downregulated and its target Esrrg significantly upregulated, the number of myog+/CD74+ cells during regeneration was upregulated to similar levels as observed in 501 knockout mice. Moreover, myog+/CD74+-aged skeletal muscle exhibited a similar decrease in the size of newly formed myofibers and increased number of necrotic myofibers after injury as observed in mice lacking miR-501. CONCLUSIONS miR-501 and Esrrg are regulated in muscle with decreased regenerative capacity and loss of miR-501 is permissive to the appearance of CD74+ myogenic progenitors. Our data uncover a novel link between the metabolic transcription factor Esrrg and sarcomere formation and demonstrate that stem cell heterogeneity in skeletal muscle during aging is under miRNA control. Targeting Esrrg or myog+/CD74+ progenitor cells might improve fiber size and myofiber resilience to exercise in aged skeletal muscle.
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Affiliation(s)
- Alexandra Fahrner
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Zurich, Switzerland; Life Science Zurich Graduate School, Biomedicine, University of Zurich, 8057, Zurich, Switzerland
| | - Edlira Luca
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Jan Krützfeldt
- Division of Endocrinology, Diabetes, and Clinical Nutrition, University Hospital Zurich, 8091, Zurich, Switzerland; Life Science Zurich Graduate School, Biomedicine, University of Zurich, 8057, Zurich, Switzerland.
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Wang R, Kumar B, Bhat-Nakshatri P, Khatpe AS, Murphy MP, Wanczyk KE, Simpson E, Chen D, Gao H, Liu Y, Doud EH, Mosley AL, Nakshatri H. A human skeletal muscle stem/myotube model reveals multiple signaling targets of cancer secretome in skeletal muscle. iScience 2023; 26:106541. [PMID: 37102148 PMCID: PMC10123345 DOI: 10.1016/j.isci.2023.106541] [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: 09/07/2022] [Revised: 12/16/2022] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle dysfunction or reprogramming due to the effects of the cancer secretome is observed in multiple malignancies. Although mouse models are routinely used to study skeletal muscle defects in cancer, because of species specificity of certain cytokines/chemokines in the secretome, a human model system is required. Here, we establish simplified multiple skeletal muscle stem cell lines (hMuSCs), which can be differentiated into myotubes. Using single nuclei ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq), we document chromatin accessibility and transcriptomic changes associated with the transition of hMuSCs to myotubes. Cancer secretome accelerated stem to myotube differentiation, altered the alternative splicing machinery and increased inflammatory, glucocorticoid receptor, and wound healing pathways in hMuSCs. Additionally, cancer secretome reduced metabolic and survival pathway associated miR-486, AKT, and p53 signaling in hMuSCs. hMuSCs underwent myotube differentiation when engrafted into NSG mice and thus providing a humanized in vivo skeletal muscle model system to study cancer cachexia.
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Affiliation(s)
- Ruizhong Wang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brijesh Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Aditi S. Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael P. Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Kristen E. Wanczyk
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Edward Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Duojiao Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
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40
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Kotsaris G, Qazi TH, Bucher CH, Zahid H, Pöhle-Kronawitter S, Ugorets V, Jarassier W, Börno S, Timmermann B, Giesecke-Thiel C, Economides AN, Le Grand F, Vallecillo-García P, Knaus P, Geissler S, Stricker S. Odd skipped-related 1 controls the pro-regenerative response of fibro-adipogenic progenitors. NPJ Regen Med 2023; 8:19. [PMID: 37019910 PMCID: PMC10076435 DOI: 10.1038/s41536-023-00291-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Skeletal muscle regeneration requires the coordinated interplay of diverse tissue-resident- and infiltrating cells. Fibro-adipogenic progenitors (FAPs) are an interstitial cell population that provides a beneficial microenvironment for muscle stem cells (MuSCs) during muscle regeneration. Here we show that the transcription factor Osr1 is essential for FAPs to communicate with MuSCs and infiltrating macrophages, thus coordinating muscle regeneration. Conditional inactivation of Osr1 impaired muscle regeneration with reduced myofiber growth and formation of excessive fibrotic tissue with reduced stiffness. Osr1-deficient FAPs acquired a fibrogenic identity with altered matrix secretion and cytokine expression resulting in impaired MuSC viability, expansion and differentiation. Immune cell profiling suggested a novel role for Osr1-FAPs in macrophage polarization. In vitro analysis suggested that increased TGFβ signaling and altered matrix deposition by Osr1-deficient FAPs actively suppressed regenerative myogenesis. In conclusion, we show that Osr1 is central to FAP function orchestrating key regenerative events such as inflammation, matrix secretion and myogenesis.
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Affiliation(s)
- Georgios Kotsaris
- Institute of Chemistry and Biochemistry, Musculoskeletal Development and Regeneration Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Taimoor H Qazi
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Julius Wolff Institute, Augustenburger Platz 1, 13353, Berlin, Germany
- Department of Bioengineering, University of Pennsylvania, 19104, Philadelphia, USA
- Weldon School of Biomedical Engineering, Purdue University, 47907, West Lafayette, IN, USA
| | - Christian H Bucher
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Julius Wolff Institute, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117, Berlin, Germany
| | - Hafsa Zahid
- Institute of Chemistry and Biochemistry, Musculoskeletal Development and Regeneration Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
- International Max Planck Research School for Biology and Computing IMPRS-BAC, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Sophie Pöhle-Kronawitter
- Institute of Chemistry and Biochemistry, Musculoskeletal Development and Regeneration Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Vladimir Ugorets
- Institute of Chemistry and Biochemistry, Cell Signaling Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - William Jarassier
- Institut NeuroMyoGène, CNRS UMR 5261, Inserm U1315, Université Claude Bernard Lyon 1, 69008, Lyon, France
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | | | | | - Fabien Le Grand
- Institut NeuroMyoGène, CNRS UMR 5261, Inserm U1315, Université Claude Bernard Lyon 1, 69008, Lyon, France
| | - Pedro Vallecillo-García
- Institute of Chemistry and Biochemistry, Musculoskeletal Development and Regeneration Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Petra Knaus
- Berlin-Brandenburg School for Regenerative Therapies, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany
- Institute of Chemistry and Biochemistry, Cell Signaling Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Sven Geissler
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Julius Wolff Institute, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117, Berlin, Germany
- Berlin Center for Advanced Therapies (BECAT), Charité Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, Germany
| | - Sigmar Stricker
- Institute of Chemistry and Biochemistry, Musculoskeletal Development and Regeneration Group, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.
- Berlin-Brandenburg School for Regenerative Therapies, Charité - Universitätsmedizin Berlin, 13353, Berlin, Germany.
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Southerland KW, Xu Y, Peters DT, Wei X, Lin X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y. Pro-inflammatory macrophages impair skeletal muscle regeneration in ischemic-damaged limbs by inducing precocious differentiation of satellite cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.01.535211. [PMID: 37066299 PMCID: PMC10103943 DOI: 10.1101/2023.04.01.535211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Chronic limb-threatening ischemia (CLTI), representing the end-stage of peripheral arterial disease (PAD), is associated with a one-year limb amputation rate of ∼15-20% and significant mortality. A key characteristic of CLTI is the failure of the innate regenerative capacity of skeletal muscle, though the underlying mechanisms remain unclear. Here, single-cell transcriptome analysis of ischemic and non-ischemic muscle from the same CLTI patients demonstrated that ischemic-damaged tissue is enriched with pro-inflammatory macrophages. Comparable results were also observed in a murine CLTI model. Importantly, integrated analyses of both human and murine data revealed premature differentiation of muscle satellite cells (MuSCs) in damaged tissue and indications of defects in intercellular signaling communication between MuSCs and their inflammatory niche. Collectively, our research provides the first single-cell transcriptome atlases of skeletal muscle from CLTI patients and murine models, emphasizing the crucial role of macrophages and inflammation in regulating muscle regeneration in CLTI through interactions with MuSCs.
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Andre AB, Rees KP, O’Connor S, Severson GW, Newbern JM, Wilson-Rawls J, Plaisier CL, Rawls A. Single cell analysis reveals satellite cell heterogeneity for proinflammatory chemokine expression. Front Cell Dev Biol 2023; 11:1084068. [PMID: 37051469 PMCID: PMC10083252 DOI: 10.3389/fcell.2023.1084068] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/16/2023] [Indexed: 03/28/2023] Open
Abstract
Background: The expression of proinflammatory signals at the site of muscle injury are essential for efficient tissue repair and their dysregulation can lead to inflammatory myopathies. Macrophages, neutrophils, and fibroadipogenic progenitor cells residing in the muscle are significant sources of proinflammatory cytokines and chemokines. However, the inducibility of the myogenic satellite cell population and their contribution to proinflammatory signaling is less understood.Methods: Mouse satellite cells were isolated and exposed to lipopolysaccharide (LPS) to mimic sterile skeletal muscle injury and changes in the expression of proinflammatory genes was examined by RT-qPCR and single cell RNA sequencing. Expression patterns were validated in skeletal muscle injured with cardiotoxin by RT-qPCR and immunofluorescence.Results: Satellite cells in culture were able to express Tnfa, Ccl2, and Il6, within 2 h of treatment with LPS. Single cell RNA-Seq revealed seven cell clusters representing the continuum from activation to differentiation. LPS treatment led to a heterogeneous pattern of induction of C-C and C-X-C chemokines (e.g., Ccl2, Ccl5, and Cxcl0) and cytokines (e.g., Tgfb1, Bmp2, Il18, and Il33) associated with innate immune cell recruitment and satellite cell proliferation. One cell cluster was enriched for expression of the antiviral interferon pathway genes under control conditions and LPS treatment. Activation of this pathway in satellite cells was also detectable at the site of cardiotoxin induced muscle injury.Conclusion: These data demonstrate that satellite cells respond to inflammatory signals and secrete chemokines and cytokines. Further, we identified a previously unrecognized subset of satellite cells that may act as sensors for muscle infection or injury using the antiviral interferon pathway.
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Affiliation(s)
- Alexander B. Andre
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, United States
| | - Katherina P. Rees
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, United States
| | - Samantha O’Connor
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, United States
- Biomedical Engineering Graduate Program, Arizona State University, Tempe, AZ, United States
| | - Grant W. Severson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, United States
| | - Jason M. Newbern
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | | | - Christopher L. Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, United States
| | - Alan Rawls
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- *Correspondence: Alan Rawls,
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Mechanisms of skeletal muscle-tendon development and regeneration/healing as potential therapeutic targets. Pharmacol Ther 2023; 243:108357. [PMID: 36764462 DOI: 10.1016/j.pharmthera.2023.108357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Skeletal muscle contraction is essential for the movement of our musculoskeletal system. Tendons and ligaments that connect the skeletal muscles to bones in the correct position at the appropriate time during development are also required for movement to occur. Since the musculoskeletal system is essential for maintaining basic bodily functions as well as enabling interactions with the environment, dysfunctions of these tissues due to disease can significantly reduce quality of life. Unfortunately, as people live longer, skeletal muscle and tendon/ligament diseases are becoming more common. Sarcopenia, a disease in which skeletal muscle function declines, and tendinopathy, which involves chronic tendon dysfunction, are particularly troublesome because there have been no significant advances in their treatment. In this review, we will summarize previous reports on the development and regeneration/healing of skeletal muscle and tendon tissues, including a discussion of the molecular and cellular mechanisms involved that may be used as potential therapeutic targets.
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Abbassi-Daloii T, el Abdellaoui S, Voortman LM, Veeger TTJ, Cats D, Mei H, Meuffels DE, van Arkel E, 't Hoen PAC, Kan HE, Raz V. A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location. eLife 2023; 12:80500. [PMID: 36744868 PMCID: PMC9988256 DOI: 10.7554/elife.80500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/03/2023] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscles support the stability and mobility of the skeleton but differ in biomechanical properties and physiological functions. The intrinsic factors that regulate muscle-specific characteristics are poorly understood. To study these, we constructed a large atlas of RNA-seq profiles from six leg muscles and two locations from one muscle, using biopsies from 20 healthy young males. We identified differential expression patterns and cellular composition across the seven tissues using three bioinformatics approaches confirmed by large-scale newly developed quantitative immune-histology procedures. With all three procedures, the muscle samples clustered into three groups congruent with their anatomical location. Concomitant with genes marking oxidative metabolism, genes marking fast- or slow-twitch myofibers differed between the three groups. The groups of muscles with higher expression of slow-twitch genes were enriched in endothelial cells and showed higher capillary content. In addition, expression profiles of Homeobox (HOX) transcription factors differed between the three groups and were confirmed by spatial RNA hybridization. We created an open-source graphical interface to explore and visualize the leg muscle atlas (https://tabbassidaloii.shinyapps.io/muscleAtlasShinyApp/). Our study reveals the molecular specialization of human leg muscles, and provides a novel resource to study muscle-specific molecular features, which could be linked with (patho)physiological processes.
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Affiliation(s)
| | - Salma el Abdellaoui
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
| | - Lenard M Voortman
- Division of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Thom TJ Veeger
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
| | - Davy Cats
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Duncan E Meuffels
- Orthopedic and Sport Medicine Department, Erasmus MC, University Medical Center RotterdamRotterdamNetherlands
| | | | - Peter AC 't Hoen
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical CenterRadboudNetherlands
| | - Hermien E Kan
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
- Duchenne Center NetherlandsLeidenNetherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
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MME + fibro-adipogenic progenitors are the dominant adipogenic population during fatty infiltration in human skeletal muscle. Commun Biol 2023; 6:111. [PMID: 36707617 PMCID: PMC9883500 DOI: 10.1038/s42003-023-04504-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Fatty infiltration, the ectopic deposition of adipose tissue within skeletal muscle, is mediated via the adipogenic differentiation of fibro-adipogenic progenitors (FAPs). We used single-nuclei and single-cell RNA sequencing to characterize FAP heterogeneity in patients with fatty infiltration. We identified an MME+ FAP subpopulation which, based on ex vivo characterization as well as transplantation experiments, exhibits high adipogenic potential. MME+ FAPs are characterized by low activity of WNT, known to control adipogenic commitment, and are refractory to the inhibitory role of WNT activators. Using preclinical models for muscle damage versus fatty infiltration, we show that many MME+ FAPs undergo apoptosis during muscle regeneration and differentiate into adipocytes under pathological conditions, leading to a reduction in their abundance. Finally, we utilized the varying fat infiltration levels in human hip muscles and found less MME+ FAPs in fatty infiltrated human muscle. Altogether, we have identified the dominant adipogenic FAP subpopulation in skeletal muscle.
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46
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Tu H, Li YL. Inflammation balance in skeletal muscle damage and repair. Front Immunol 2023; 14:1133355. [PMID: 36776867 PMCID: PMC9909416 DOI: 10.3389/fimmu.2023.1133355] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
Responding to tissue injury, skeletal muscles undergo the tissue destruction and reconstruction accompanied with inflammation. The immune system recognizes the molecules released from or exposed on the damaged tissue. In the local minor tissue damage, tissue-resident macrophages sequester pro-inflammatory debris to prevent initiation of inflammation. In most cases of the skeletal muscle injury, however, a cascade of inflammation will be initiated through activation of local macrophages and mast cells and recruitment of immune cells from blood circulation to the injured site by recongnization of damage-associated molecular patterns (DAMPs) and activated complement system. During the inflammation, macrophages and neutrophils scavenge the tissue debris to release inflammatory cytokines and the latter stimulates myoblast fusion and vascularization to promote injured muscle repair. On the other hand, an abundance of released inflammatory cytokines and chemokines causes the profound hyper-inflammation and mobilization of immune cells to trigger a vicious cycle and lead to the cytokine storm. The cytokine storm results in the elevation of cytolytic and cytotoxic molecules and reactive oxygen species (ROS) in the damaged muscle to aggravates the tissue injury, including the healthy bystander tissue. Severe inflammation in the skeletal muscle can lead to rhabdomyolysis and cause sepsis-like systemic inflammation response syndrome (SIRS) and remote organ damage. Therefore, understanding more details on the involvement of inflammatory factors and immune cells in the skeletal muscle damage and repair can provide the new precise therapeutic strategies, including attenuation of the muscle damage and promotion of the muscle repair.
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Application of Single-Cell and Spatial Omics in Musculoskeletal Disorder Research. Int J Mol Sci 2023; 24:ijms24032271. [PMID: 36768592 PMCID: PMC9917071 DOI: 10.3390/ijms24032271] [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: 11/30/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Musculoskeletal disorders, including fractures, scoliosis, heterotopic ossification, osteoporosis, osteoarthritis, disc degeneration, and muscular injury, etc., can occur at any stage of human life. Understanding the occurrence and development mechanism of musculoskeletal disorders, as well as the changes in tissues and cells during therapy, might help us find targeted treatment methods. Single-cell techniques provide excellent tools for studying alterations at the cellular level of disorders. However, the application of these techniques in research on musculoskeletal disorders is still limited. This review summarizes the current single-cell and spatial omics used in musculoskeletal disorders. Cell isolation, experimental methods, and feasible experimental designs for single-cell studies of musculoskeletal system diseases have been reviewed based on tissue characteristics. Then, the paper summarizes the latest findings of single-cell studies in musculoskeletal disorders from three aspects: bone and ossification, joint, and muscle and tendon disorders. Recent discoveries about the cell populations involved in these diseases are highlighted. Furthermore, the therapeutic responses of musculoskeletal disorders, especially single-cell changes after the treatments of implants, stem cell therapies, and drugs are described. Finally, the application potential and future development directions of single-cell and spatial omics in research on musculoskeletal diseases are discussed.
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Xu P, Wang M, Sharma NK, Comeau ME, Wabitsch M, Langefeld CD, Civelek M, Zhang B, Das SK. Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations. Cell Syst 2023; 14:41-57.e8. [PMID: 36630956 PMCID: PMC9852073 DOI: 10.1016/j.cels.2022.12.005] [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: 03/03/2022] [Revised: 09/26/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023]
Abstract
Our knowledge of the cell-type-specific mechanisms of insulin resistance remains limited. To dissect the cell-type-specific molecular signatures of insulin resistance, we performed a multiscale gene network analysis of adipose and muscle tissues in African and European ancestry populations. In adipose tissues, a comparative analysis revealed ethnically conserved cell-type signatures and two adipocyte subtype-enriched modules with opposite insulin sensitivity responses. The modules enriched for adipose stem and progenitor cells as well as immune cells showed negative correlations with insulin sensitivity. In muscle tissues, the modules enriched for stem cells and fibro-adipogenic progenitors responded to insulin sensitivity oppositely. The adipocyte and muscle fiber-enriched modules shared cellular-respiration-related genes but had tissue-specific rearrangements of gene regulations in response to insulin sensitivity. Integration of the gene co-expression and causal networks further pinpointed key drivers of insulin resistance. Together, this study revealed the cell-type-specific transcriptomic networks and signaling maps underlying insulin resistance in major glucose-responsive tissues. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Peng Xu
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Neeraj K Sharma
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Mary E Comeau
- Department of Biostatistics and Data Science, Division of Public Health Sciences, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Eythstr. 24, D-89075 Ulm, Germany
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Mete Civelek
- Center for Public Health Genomics, Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Bin Zhang
- Department of Genetics & Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Swapan K Das
- Department of Internal Medicine, Section of Endocrinology and Metabolism, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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Liu H, Guan L, Deng M, Bolund L, Kristiansen K, Zhang J, Luo Y, Zhang Z. Integrative genetic and single cell RNA sequencing analysis provides new clues to the amyotrophic lateral sclerosis neurodegeneration. Front Neurosci 2023; 17:1116087. [PMID: 36875658 PMCID: PMC9983639 DOI: 10.3389/fnins.2023.1116087] [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: 12/05/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction The gradual loss of motor neurons (MNs) in the brain and spinal cord is a hallmark of amyotrophic lateral sclerosis (ALS), but the mechanisms underlying neurodegeneration in ALS are still not fully understood. Methods Based on 75 ALS-pathogenicity/susceptibility genes and large-scale single-cell transcriptomes of human/mouse brain/spinal cord/muscle tissues, we performed an expression enrichment analysis to identify cells involved in ALS pathogenesis. Subsequently, we created a strictness measure to estimate the dosage requirement of ALS-related genes in linked cell types. Results Remarkably, expression enrichment analysis showed that α- and γ-MNs, respectively, are associated with ALS-susceptibility genes and ALS-pathogenicity genes, revealing differences in biological processes between sporadic and familial ALS. In MNs, ALS-susceptibility genes exhibited high strictness, as well as the ALS-pathogenicity genes with known loss of function mechanism, indicating the main characteristic of ALS-susceptibility genes is dosage-sensitive and the loss of function mechanism of these genes may involve in sporadic ALS. In contrast, ALS-pathogenicity genes with gain of function mechanism exhibited low strictness. The significant difference of strictness between loss of function genes and gain of function genes provided a priori understanding for the pathogenesis of novel genes without an animal model. Besides MNs, we observed no statistical evidence for an association between muscle cells and ALS-related genes. This result may provide insight into the etiology that ALS is not within the domain of neuromuscular diseases. Moreover, we showed several cell types linked to other neurological diseases [i.e., spinocerebellar ataxia (SA), hereditary motor neuropathies (HMN)] and neuromuscular diseases [i.e. hereditary spastic paraplegia (SPG), spinal muscular atrophy (SMA)], including an association between Purkinje cells in brain and SA, an association between α-MNs in spinal cord and SA, an association between smooth muscle cells and SA, an association between oligodendrocyte and HMN, a suggestive association between γ-MNs and HMN, a suggestive association between mature skeletal muscle and HMN, an association between oligodendrocyte in brain and SPG, and no statistical evidence for an association between cell type and SMA. Discussion These cellular similarities and differences deepened our understanding of the heterogeneous cellular basis of ALS, SA, HMN, SPG, and SMA.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China.,BGI-Shenzhen, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Min Deng
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, BGI-Shijiazhuang Medical Laboratory, Shijiazhuang, China.,BGI-Shenzhen, Shenzhen, China
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Zhanchi Zhang
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Hebei Medical University, Shijiazhuang, China
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50
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Perez K, Ciotlos S, McGirr J, Limbad C, Doi R, Nederveen JP, Nilsson MI, Winer DA, Evans W, Tarnopolsky M, Campisi J, Melov S. Single nuclei profiling identifies cell specific markers of skeletal muscle aging, frailty, and senescence. Aging (Albany NY) 2022; 14:9393-9422. [PMID: 36516485 PMCID: PMC9792217 DOI: 10.18632/aging.204435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Aging is accompanied by a loss of muscle mass and function, termed sarcopenia, which causes numerous morbidities and economic burdens in human populations. Mechanisms implicated in age-related sarcopenia or frailty include inflammation, muscle stem cell depletion, mitochondrial dysfunction, and loss of motor neurons, but whether there are key drivers of sarcopenia are not yet known. To gain deeper insights into age-related muscle loss, we performed transcriptome profiling on lower limb muscle biopsies from 72 young, elderly, and frail human subjects using bulk RNA-seq (N = 72) and single-nuclei RNA-seq (N = 17). This combined approach revealed changes in gene expression that occur with age and frailty in multiple cell types comprising mature skeletal muscle. Notably, we found increased expression of the genes MYH8 and PDK4, and decreased expression of the gene IGFN1, in aged muscle. We validated several key genes changes in fixed human muscle tissue using digital spatial profiling. We also identified a small population of nuclei that express CDKN1A, present only in aged samples, consistent with p21cip1-driven senescence in this subpopulation. Overall, our findings identify unique cellular subpopulations in aged and sarcopenic skeletal muscle, which will facilitate the development of new therapeutic strategies to combat age-related frailty.
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Affiliation(s)
- Kevin Perez
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | - Serban Ciotlos
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | - Julia McGirr
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | | | - Ryosuke Doi
- Buck Institute for Research on Aging, Novato, CA 94952, USA
- Drug Discovery Research, Astellas Pharma, Tsukuba, Ibaraki, Japan
| | | | | | | | - William Evans
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | | | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94952, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94952, USA
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