Gene expression of CD56positive and CD56negative human muscle stem cells from normal and Duchenne Muscular Dystrophy muscles
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE229968 | GEO | 2024/11/18
REPOSITORIES: GEO
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Project description:In Duchenne Muscular Dystrophy (DMD), the absence of the subsarcolemmal dystrophin protein leads to repeated myofiber damages inducing cycles of muscle regeneration that is driven by muscle stem cells (MuSCs). With time, MuSC regenerative capacities are overwhelmed, leading to fibrosis and muscle atrophy. Whether MuSCs from DMD muscle have intrinsic alterations or are primed by their degenerative/regenerative environment is still debated. We investigated cell behavior and gene expression in human using MuSCs derived from DMD or healthy muscles. We found that proliferation, differentiation and fusion were not altered in DMD-MuSCs, but with time, they lost the expression of the myogenic marker CD56 twice as fast as healthy MuSCs. The rapid drift towards a fibroblast-like cell identity was observed at the clonal level, and resulted from the altered expression of epigenetic enzymes required to maintain the myogenic cell fate. Indeed, the reexpression of CBX3, SMC3, H2AFV and H3F3B prevented the MuSC identity drift. Amongst the epigenetic changes, a closing of chromatin at the gene encoding the transcription factor MEF2B caused a down-regulation of its expression and a loss of the myogenic fate. Thus, MEF2B is a key mediator of the myogenic identity in human MuSCs, that is altered in DMD pathology.
2024-06-30 | GSE232667 | GEO
Project description:Background: Skeletal muscle crucially depends on motor innervation, and, when damaged, on the resident muscle stem cells (MuSCs). However, the role and function of MuSCs in the context of denervation remains poorly understood. Methods: Alterations of MuSCs and their myofiber niche after denervation were investigated in a surgery-based mouse model of unilateral sciatic nerve transection. FACS-isolated MuSCs were subjected to RNA-sequencing and mass spectrometry for the analysis of intrinsic changes after denervation and in vivo assays, such as Cardiotoxin-induced muscle injury or MuSC transplantation, were performed to assess MuSC functions after denervation. Bioinformatic and histological analyses were conducted to further examine MuSCs and their myofiber niche after denervation. Results: Muscle cross section analysis revealed a significant increase in Pax7 (p-value= 0.0441), Pax7/Ki67 (p-value= 0.0023), MyoD (p-value= 0.0016) and Myog (p-value= 0.0057) positive cells after denervation, illustrating a break of quiescence and commitment to the myogenic lineage. An Omics approach showed profound intrinsic alterations on the mRNA (2613 differentially expressed genes, p-value <0.05) and protein (1096 differentially abundant proteins, q-value <0.05) level of MuSCs 21 days after denervation. Skeletal muscle injury together with denervation surgery caused deregulated regeneration, indicated by the reduced number of proliferating MuSCs and sustained high levels of developmental myosin heavy chain (Sham: 1 % vs DEN: 40 % of all myofibers), at 21 days post-surgery. In a transplantation assay, MuSCs from a denervated host were still able to engraft and fuse to form new myofibers, irrespective of the innervation status of the recipient muscle. Analysis of myofibers revealed not only massive changes in the expression profile (10492 differentially expressed genes, p-value <0.05) after denervation, but it was also shown that secretion of Opn and Tgfb1 from denervated myofibers was increased 30-fold and 6000-fold, respectively. Bioinformatic analyses indicated strong upregulation of gene expression of the transcription factor Junb in MuSCs from denervated muscles (log2 fold change = 3.27). Of interest, Tgfb1 recombinant protein was able to induce Junb gene expression in vitro, demonstrating that myofiber-secreted ligands can induce gene expression changes in MuSCs, which might result in the phenotypes observed after denervation. Conclusion: Skeletal muscle denervation is altering myofiber secretion, causing MuSC activation and profound intrinsic changes, leading to reduced regenerative capacity. As MuSCs possess a remarkable regenerative potential, they might represent a promising target for novel treatment options for neuromuscular disorders and peripheral nerve injuries.
2024-02-27 | PXD036993 | Pride
Project description:Muscle stem cells (MuSC) exhibit distinct behaviors during successive phases of developmental myogenesis. However, how their transition to adulthood is regulated is poorly understood. Here we show that fetal MuSC resist progenitor specification and exhibit altered division dynamics, intrinsic features that are progressively lost postnatally. Following transplantation, fetal MuSC more efficiently expand and contribute to muscle repair. Conversely, the efficiency of niche colonization increases in adulthood, indicating a balance between muscle growth and stem cell pool repopulation. Gene expression profiling identified several extracellular matrix (ECM) molecules preferentially expressed in fetal MuSC, including tenascin-C, fibronectin and collagen VI. Loss-of-function experiments confirmed their essential and stage-specific role in regulating MuSC function. Finally, fetal-derived paracrine factors were able to enhance adult MuSC regenerative potential. Together, these findings demonstrate that MuSC change the way in which they remodel their microenvironment to direct stem cell behavior in support of the unique demands of muscle development or repair. MuSCs were isolated through fluorescent-activate cell sorting usinf alpha7-integirn and CD34 as markers to identify the cell population. Total mRNA was then isolated, and samples at different developmental times were compared.
2016-01-20 | E-GEOD-76989 | biostudies-arrayexpress
Project description:During aging, the regenerative capacity of skeletal muscle decreases due to intrinsic changes in muscle stem cells (MuSCs) and alterations in their niche. Here, we used quantitative mass spectrometry to characterize intrinsic changes in the MuSC proteome and remodeling of the MuSC niche during aging. We generated a network connecting age-affected ligands located in the niche and cell surface receptors on MuSCs. Thereby, we revealed signaling via Integrins, Lrp1, Egfr and Cd44 as the major cell communication axes perturbed through aging. We investigated the effect of Smoc2, a secreted protein that accumulates with aging, originating from fibro-adipogenic progenitors. Increased levels of Smoc2 contribute to the aberrant Itgb1/MAPK signaling observed during aging, thereby causing impaired MuSC functionality and muscle regeneration. By connecting changes in the proteome of MuSCs to alterations of their niche, our work will enable a better understanding of how MuSCs are affected during aging.
2021-11-10 | PXD023628 | Pride
Project description:During aging, the regenerative capacity of skeletal muscle decreases due to intrinsic changes in muscle stem cells (MuSCs) and alterations in their niche. Here, we used quantitative mass spectrometry to characterize intrinsic changes in the MuSC proteome and remodeling of the MuSC niche during aging. We generated a network connecting age-affected ligands located in the niche and cell surface receptors on MuSCs. Thereby, we revealed signaling via Integrins, Lrp1, Egfr and Cd44 as the major cell communication axes perturbed through aging. We investigated the effect of Smoc2, a secreted protein that accumulates with aging, originating from fibro-adipogenic progenitors. Increased levels of Smoc2 contribute to the aberrant Itgb1/MAPK signaling observed during aging, thereby causing impaired MuSC functionality and muscle regeneration. By connecting changes in the proteome of MuSCs to alterations of their niche, our work will enable a better understanding of how MuSCs are affected during aging.
2021-11-10 | PXD023643 | Pride
Project description:Background: Skeletal muscle function crucially depends on motor innervation and after injury on the resident muscle stem cells (MuSCs). However, it is poorly understood how innervation affects MuSC properties. Methods: We investigated the alterations of MuSCs and their immediate niche, the myofiber, after denervation in a surgery-based mouse model of unilateral sciatic nerve transection. FACS-isolated MuSCs were subjected to transcriptomics and proteomics analyses to investigate which changes occur after denervation. We performed Cardiotoxin-induced muscle injury, MuSC transplantation and floating myofiber cultures to assess MuSC functionality after denervation in addition to bioinformatics and histological analyses. Results: We observed a significant increase in the number of MuSCs (Pax7 positive; p-value= 0.0441), proliferating MuSCs (Pax7/Ki67 positive; p-value= 0.0023), activated MuSCs (MyoD positive; p-value= 0.0016) and differentiating MuSCs (Myog positive; p-value= 0.0057) after denervation. This aberrant activation and premature commitment of MuSCs to the myogenic lineage was accompanied by profound alterations on the mRNA (2613 differentially expressed genes, adj. p-value <0.05) and protein (1096 differentially abundant proteins, q-value <0.05) level after denervation. MuSCs from denervated hosts still engrafted and fused to form new myofibers irrespective of the innervation status of the recipient, suggesting the MuSC niche is driving alterations in MuSCs after denervation. The myofiber transcriptome after denervation showed massive changes in the general expression profile (10492 DEGs, p-value <0.05) and in several predicted secreted factors. Incubation of myofiber-associated MuSCs with supernatant from denervated myofibers increased cluster formation, reinforcing myofibers as a source of secreted factors driving MuSC alterations after denervation. Opn and Tgfb1 showed an increased secretion by denervated myofibers (30-fold and 6000-fold, respectively), and incubation with Tgfb1 alone induced Junb expression in myogenic cells, one of the genes highly upregulated in MuSCs after denervation (p-value= 1.85e-18, log2fc= 3.27), demonstrating that myofiber-secreted ligands influence MuSC gene expression. A combination of skeletal muscle injury and denervation led to reduced numbers of proliferating MuSCs (Sham: 47 vs DEN: 19.75 cells per cross section 10 days post-injury) and sustained high levels of developmental myosin heavy chain (Sham: 1 % vs DEN: 40 % of all myofibers 21 days post-injury), indicating hampered MuSC functionality due to changes in the microenvironment. Conclusion: Denervation of skeletal muscle causes alterations in myofiber secretion, leading to activation and profound changes of MuSCs, ultimately resulting in a reduced regenerative capacity. As these alterations are partially reversible, MuSCs are a promising target for novel treatment options for neuromuscular disorders and peripheral nerve injuries.
2024-03-04 | GSE217929 | GEO
Project description:Background: Skeletal muscle function crucially depends on motor innervation and after injury on the resident muscle stem cells (MuSCs). However, it is poorly understood how innervation affects MuSC properties. Methods: We investigated the alterations of MuSCs and their immediate niche, the myofiber, after denervation in a surgery-based mouse model of unilateral sciatic nerve transection. FACS-isolated MuSCs were subjected to transcriptomics and proteomics analyses to investigate which changes occur after denervation. We performed Cardiotoxin-induced muscle injury, MuSC transplantation and floating myofiber cultures to assess MuSC functionality after denervation in addition to bioinformatics and histological analyses. Results: We observed a significant increase in the number of MuSCs (Pax7 positive; p-value= 0.0441), proliferating MuSCs (Pax7/Ki67 positive; p-value= 0.0023), activated MuSCs (MyoD positive; p-value= 0.0016) and differentiating MuSCs (Myog positive; p-value= 0.0057) after denervation. This aberrant activation and premature commitment of MuSCs to the myogenic lineage was accompanied by profound alterations on the mRNA (2613 differentially expressed genes, adj. p-value <0.05) and protein (1096 differentially abundant proteins, q-value <0.05) level after denervation. MuSCs from denervated hosts still engrafted and fused to form new myofibers irrespective of the innervation status of the recipient, suggesting the MuSC niche is driving alterations in MuSCs after denervation. The myofiber transcriptome after denervation showed massive changes in the general expression profile (10492 DEGs, p-value <0.05) and in several predicted secreted factors. Incubation of myofiber-associated MuSCs with supernatant from denervated myofibers increased cluster formation, reinforcing myofibers as a source of secreted factors driving MuSC alterations after denervation. Opn and Tgfb1 showed an increased secretion by denervated myofibers (30-fold and 6000-fold, respectively), and incubation with Tgfb1 alone induced Junb expression in myogenic cells, one of the genes highly upregulated in MuSCs after denervation (p-value= 1.85e-18, log2fc= 3.27), demonstrating that myofiber-secreted ligands influence MuSC gene expression. A combination of skeletal muscle injury and denervation led to reduced numbers of proliferating MuSCs (Sham: 47 vs DEN: 19.75 cells per cross section 10 days post-injury) and sustained high levels of developmental myosin heavy chain (Sham: 1 % vs DEN: 40 % of all myofibers 21 days post-injury), indicating hampered MuSC functionality due to changes in the microenvironment. Conclusion: Denervation of skeletal muscle causes alterations in myofiber secretion, leading to activation and profound changes of MuSCs, ultimately resulting in a reduced regenerative capacity. As these alterations are partially reversible, MuSCs are a promising target for novel treatment options for neuromuscular disorders and peripheral nerve injuries.
2024-03-04 | GSE217928 | GEO
Project description:In aging, skeletal muscle strength and regenerative capacity declines due, in part, to functional impairment of muscle stem cells MuSCs, yet the underlying mechanisms remain elusive. Here we capitalize on mass-cytometry to identify high CD47 expression as a hallmark of dysfunctional MuSCs CD47hi with impaired regenerative capacity that predominate with aging. The prevalent CD47 hi MuSC subset suppresses the residual functional CD47 lo MuSC subset through a paracrine signaling loop, leading to impaired proliferation. We uncover that elevated CD47 levels on aged MuSCs result from increased U1 snRNA expression, which disrupts alternative polyadenylation. The deficit in aged MuSC function in regeneration can be overcome either by morpholino-mediated blocking of CD47 alternative polyadenylation or antibody blockade of CD47 signaling, leading to improved regeneration in aged mice, with therapeutic implications. Our findings highlight a previously unrecognized age-dependent alteration in CD47 levels and function in MuSCs, which underlies reduced muscle repair in aging.
2022-11-16 | GSE198249 | GEO
Project description:The maintenance of cell lineage and cell fate are essential for the function of adult stem cells. Despite this, the epigenetic mechanisms that regulate muscle stem cell (MuSC) identity are not well understood. In this study, we performed Cut&Tag of the activating histone marks H3K4me3 and H3K27ac on freshly isolated quiescent MuSCs and found that a large number of genes without transcription still maintained the permissive mark H3K4me3 but lacked the marker of active enhancers, H3K27ac. These genes included those that are essential for non-myogenic lineage determination. We found that many of the genes that were not transcribed but enriched for H3K4me3, were also enriched for the RE-1 binding motif, the motif recognized by the repressive transcription factor REST. Using a genetic mouse model where REST is conditionally knocked out of MuSCs, we further investigated the role of REST in the maintenance of quiescent MuSC cell identity. Investigation of the transcriptome and chromatin accessibility of WT and REST deficient MuSCs determined that the loss of REST results in the gain of expression of key genes of several non-myogenic tissues, particularly neuronal genes. Additionally, the loss of REST led to the dramatic reduction of the MuSC pool and the induction of muscle atrophy. The unstable cell identity caused by the genetic deletion of REST results in the MuSCs undergoing apoptosis and is the main driver of the observed loss of the MuSC pool. Together, the data presented in this study establishes a novel function of the transcription factor REST, where it safeguards the identity and myogenic lineage of MuSCs, through the repression of alternative lineages.
2024-06-11 | GSE266726 | GEO
Project description:The maintenance of cell lineage and cell fate are essential for the function of adult stem cells. Despite this, the epigenetic mechanisms that regulate muscle stem cell (MuSC) identity are not well understood. In this study, we performed Cut&Tag of the activating histone marks H3K4me3 and H3K27ac on freshly isolated quiescent MuSCs and found that a large number of genes without transcription still maintained the permissive mark H3K4me3 but lacked the marker of active enhancers, H3K27ac. These genes included those that are essential for non-myogenic lineage determination. We found that many of the genes that were not transcribed but enriched for H3K4me3, were also enriched for the RE-1 binding motif, the motif recognized by the repressive transcription factor REST. Using a genetic mouse model where REST is conditionally knocked out of MuSCs, we further investigated the role of REST in the maintenance of quiescent MuSC cell identity. Investigation of the transcriptome and chromatin accessibility of WT and REST deficient MuSCs determined that the loss of REST results in the gain of expression of key genes of several non-myogenic tissues, particularly neuronal genes. Additionally, the loss of REST led to the dramatic reduction of the MuSC pool and the induction of muscle atrophy. The unstable cell identity caused by the genetic deletion of REST results in the MuSCs undergoing apoptosis and is the main driver of the observed loss of the MuSC pool. Together, the data presented in this study establishes a novel function of the transcription factor REST, where it safeguards the identity and myogenic lineage of MuSCs, through the repression of alternative lineages.
2024-06-11 | GSE266725 | GEO