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Bulk RNA-sequencing of unsorted and PAX7::GFP-sorted ESC-derived myogenic progenitors

ABSTRACT: Bulk RNA-sequencing of unsorted and PAX7::GFP-sorted ESC-derived myogenic progenitors

PROVIDER: PRJNA740333 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14892660_1.fastq.gz	Fastqsanger.gz
	SRR14892660_2.fastq.gz	Fastqsanger.gz
	SRR14892661_1.fastq.gz	Fastqsanger.gz
	SRR14892661_2.fastq.gz	Fastqsanger.gz
	SRR14892662_1.fastq.gz	Fastqsanger.gz

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Bulk RNA-sequencing of unsorted and PAX7::GFP-sorted ESC-derived myogenic progenitors

Project description:Tissue engineering strategies that combine human pluripotent stem cell-derived myogenic progenitors (hPDMs) with advanced biomaterials provide promising tools for engineering 3D skeletal muscle grafts to model tissue development in vitro and promote muscle regeneration in vivo. We recently demonstrated (i) the potential for obtaining large numbers of hPDMs using a combination of two small molecules and (ii) the application of electrospun fibrin microfiber bundles for functional skeletal muscle restoration following volumetric muscle loss. In this study, we demonstrate that the biophysical cues provided by the microfiber bundles can induce unsorted hPDMs to form multinucleated myotubes that express desmin and myosin heavy chain. To reduce the batch-to-batch variability of these samples, we tested a genetic PAX7 reporter line (PAX7::GFP) to sort for more homogenous populations of hPDMs. RNA sequencing and gene set enrichment analyses confirmed that PAX7::GFP-sorted hPDMs exhibited higher expression of myogenic genes while unsorted hPDMs demonstrated increased expression of genes associated with embryonic, neural crest, and fibroadipogenic progenitor lineages. We tested engineered skeletal muscle grafts derived from either PAX7::GFP-sorted or unsorted hPDMs within in vivo skeletal muscle defects. The unsorted hPDM-derived grafts also exhibited greater fibrosis and more proinflammatory responses. In contrast, the PAX7::GFP-sorted groups had moderately high vascular infiltration, more implanted cell association with embryonic myosin heavy chain (eMHC) regions, and greater CD206:CD86 ratios compared to unsorted hPDMs and acellular fibers suggesting they induced more pro-regenerative microenvironments. These findings demonstrated some promise for the use of PAX7::GFP-sorted hPDMS on fibrin microfiber bundles and provided some insights for improving the cell-biomaterial system to stimulate more robust in vivo skeletal muscle regeneration.

2022-12-09 | GSE178784 | GEO

Identification of PAX7-induced transcriptional changes and PAX7 genomic binding during skeletal myogenic differentiation of H9 embryonic stem cells

Project description:Skeletal myogenic commitment of human pluripotent cells can be achieved by doxycycline-inducible expression of the transcription factor PAX7. To gain further insights on PAX7 function during this process, we performed a time course whole transcriptome analysis of differentiating H9 human embryonic stem cells from doxycycline-treated and untreated cultures. In addition, we identified the genomic binding of PAX7 in one of the selected time point (referred as PAX7+ proliferating myogenic progenitors).

2017-06-30 | GSE98976 | GEO

Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro

Project description:Satellite cells (SC) are muscle stem cells which can regenerate adult muscles upon injury. Most SC originate from PAX7+ myogenic precursors set aside during development. Although myogenesis has been studied in mouse and chicken embryos, little is known about human muscle development. Here, we report the generation of human induced pluripotent stem cell (iPSC) reporter lines in which fluorescent proteins have been introduced into the PAX7 and MYOG loci. We use single cell RNA sequencing to analyze the developmental trajectory of the iPSC-derived PAX7+ myogenic precursors. We show that the PAX7+ cells generated in culture can produce myofibers and self-renew in vitro and in vivo. Together, we demonstrate that cells exhibiting characteristics of human fetal satellite cells can be produced in vitro from iPSC, opening interesting avenues for muscular dystrophy cell therapy. This work provides significant insights into the development of the human myogenic lineage.

2020-06-15 | GSE149451 | GEO

Expression data from differentiating mouse embryonic stem cells wild type and lacking functional Pax7 gene

Project description:Myogenic differentiation relies on Pax7 function. We used embryonic stem cells lacking functional Pax7 to follow its role in derivation of skeletal myoblasts. Microarray analysis allowed us to compare transcriptomes of undifferentiated and differentiating embryonic stem cells of two genotypes, i.e. Pax7+/+ and Pax7-/- at day 7 and 21 of culture. Undifferentiated mouse embryonic stem cells, embryiod bodies at day 7, and embryoid body outgrowths at day 21 of differentiation were collected for RNA extraction and hybridization on Affymetrix microarrays.

2016-02-26 | E-GEOD-66483 | biostudies-arrayexpress

Identification of Pax7 binding sites in mouse skeletal muscle progenitors

Project description:Using dox-inducible mouse ES cells, we generated myogenic progenitors expressing the transcription factor Pax7. These cells were used for determining the genomic occupancy of the transcription factor Pax7.

2020-10-31 | GSE147057 | GEO

Expression data from mouse embryonic fibroblasts wild type and lacking functional Pax7 gene

Project description:Myogenic differentiation relies on Pax7 function. We used mouse embryonic fibroblasts lacking functional Pax7 to follow its role in terminally differentiated cells. Microarray analysis allowed us to compare transcriptomes of mouse embryonic fibroblasts of two genotypes, i.e. Pax7+/+ and Pax7-/-.

2016-10-26 | GSE80658 | GEO

Myogenic Progenitor Cell Lineage Specification by CRISPR/Cas9-based Transcriptional Activators

Project description:Engineered CRISPR/Cas9-based transcriptional activators can potently and specifically activate endogenous fate-determining genes to direct differentiation of pluripotent stem cells. Here, we demonstrate that endogenous activation of the PAX7 transcription factor results in stable epigenetic remodeling and directly reprograms human pluripotent stem cells into skeletal myoblast progenitor cells. Compared to the exogenous overexpression of PAX7 cDNA, we find that endogenous activation results in the generation of more proliferative myogenic progenitors that can maintain PAX7 expression over multiple passages in serum-free conditions while preserving the capacity for terminal myogenic differentiation. Transplantation of human myogenic progenitors derived from endogenous activation of PAX7 into immunodeficient mice resulted in a greater number of human dystrophin+ myofibers compared to exogenous PAX7 overexpression. RNA-seq analysis also revealed transcriptome-wide differences between myogenic progenitors generated via CRISPR-based endogenous activation of PAX7 and exogenous PAX7 cDNA overexpression. These studies demonstrate the utility of CRISPR/Cas9-based transcriptional activators for progenitor cell specification and their potential for regenerative medicine.

2020-04-10 | GSE145575 | GEO

PAX7::GFP hESC-derived myogenic progenitor(MPC) cell gene expression profile change after primary transplantation into murine muscle

Project description:To understand the mechanism of why in vivo PAX7::GFP+ cells having better engraftment capability

2022-02-01 | GSE190233 | GEO

Expression data from differentiating mouse embryonic stem cells wild type and lacking functional Pax7 gene

2016-02-26 | GSE66483 | GEO

SIX1 and SIX4 homeoproteins regulate PAX7+ progenitor cell properties during fetal epaxial myogenesis

Project description:Identification of the gene targets of the SIX transcription factors in myogenic stem cells and in whole back muscles during murine fetal development Pax7 expression marks stem cells in developing skeletal muscles and adult satellite cells during homeostasis and muscle regeneration. The genetic determinants that control the entrance into the myogenic program and the appearance of PAX7+ cells during embryogenesis are poorly understood. SIX homeoproteins are encoded by the Sine oculis homeobox related Six1-Six6 genes in vertebrates. Six1, Six2, Six4 and Six5 are expressed in the muscle lineage. Here we tested the hypothesis that Six1 and Six4 could participate in the genesis of myogenic stem cells. We show that fewer PAX7+ cells occupy a satellite cell position between the myofiber and its associated basal lamina in Six1 and Six4 (s1s4KO) at E18. However, PAX7+ cells are detected in remaining muscle masses present in the epaxial region of the double mutant embryos and are able to divide and contribute to muscle growth. To further characterize the properties of s1s4KO PAX7+ cells, we analyzed their transcriptome and tested their properties after transplantation in adult regenerating tibialis anterior (TA) muscle. Mutant stem cells form hypotrophic myofibers that are not innervated but retain the ability to self-renew.

2020-10-07 | GSE159079 | GEO

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