Background: The regeneration of muscle cells from stem cells is an intricate process, and various genes are included in the process such as myoD, mf5, mf6, etc. The key genes and pathways in the differentiating stages are various. Therefore, the differential expression of key genes after 4 weeks of differentiation were investigated in our study.
Method: Three published gene expression profiles, GSE131125, GSE148994, and GSE149055, about the comparisons of pluripotent stem cells to differentiated cells after 4 weeks were obtained from the Gene Expression Omnibus (GEO) database. Common differentially expressed genes (DEGs) were obtained for further analysis such as protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and GSEA analysis. After hub genes and key pathways were obtained, we manipulated in vitro cell research for substantiation such as immunohistochemical staining and semi-quantitative analysis and quantitative real-time PCR.
Results: A total of 824 DEGs including 350 upregulated genes and 474 downregulated genes were identified in the three GSEs. Nineteen hub genes were identified from the PPI network. The GO and KEGG pathway analyses confirmed that myogenic differentiation at 4 weeks was strongly associated with pathway in cancer, PI3K pathway, actin cytoskeleton regulation and metabolic pathway, biosynthesis of antibodies, and cell cycle. GSEA analysis indicated the differentiated cells were enriched in muscle cell development and myogenesis. Meanwhile, the core genes in each pathway were identified from the GSEA analysis. The in vitro cell research revealed that actin cytoskeleton and myoD were upregulated after 4-week differentiation.
Conclusions: The research revealed the potential hub genes and key pathways after 4-week differentiation of stem cells which contribute to further study about the molecular mechanism of myogenesis regeneration, paving a way for more accurate treatment for muscle dysfunction.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7784349 | PMC |
| http://dx.doi.org/10.1186/s13018-020-01979-x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Identification of circadian rhythm-related biomarkers and development of diagnostic models for Crohn's disease using machine learning algorithms.
Comput Methods Biomech Biomed Engin
January 2025
Department of Gastroenterolgy, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China.
The global rise in Crohn's Disease (CD) incidence has intensified diagnostic challenges. This study identified circadian rhythm-related biomarkers for CD using datasets from the GEO database. Differentially expressed genes underwent Weighted Gene Co-Expression Network Analysis, with 49 hub genes intersected from GeneCards data.
View Article and Find Full Text PDFComprehensive Analysis of Immune Characteristics of Fluorosis and Cuprotosis-Related Genes in Fluorosis Targeted Drugs.
Biol Trace Elem Res
January 2025
Department of Environmental Health, School of Public Health, Zhengzhou University, Zhengzhou, Henan, 450001, P. R. China.
This study aims to investigate the role of cuprotosis in fluorosis and identify potential targeted drugs for its treatment. The GSE70719 and GSE195920 datasets were merged using the inSilicoMerging package. DEGs between the exposure and control groups were found using R software.
View Article and Find Full Text PDFIdentification and Characterization of Genes Associated with Intestinal Ischemia-Reperfusion Injury and Oxidative Stress: A Bioinformatics and Experimental Approach Integrating High-Throughput Sequencing, Machine Learning, and Validation.
J Inflamm Res
January 2025
Department of Pain Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530007, People's Republic of China.
Purpose: Intestinal ischemia-reperfusion injury (IIRI) occurs as a result of temporary blood flow interruption, leading to tissue damage upon reperfusion. Oxidative stress plays a critical role in this process, instigating inflammation and cell death. Identifying and characterizing genes associated with the oxidative stress response can offer valuable insights into potential therapeutic targets for managing IIRI.
View Article and Find Full Text PDFDeciphering Immunometabolic Landscape in Rheumatoid Arthritis: Integrative Multiomics, Explainable Machine Learning and Experimental Validation.
J Inflamm Res
January 2025
Medical Imaging Centre, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, People's Republic of China.
Purpose: Immunometabolism is pivotal in rheumatoid arthritis (RA) pathogenesis, yet the intricacies of its pathological regulatory mechanisms remain poorly understood. This study explores the complex immunometabolic landscape of RA to identify potential therapeutic targets.
Patients And Methods: We integrated genome-wide association study (GWAS) data involving 1,400 plasma metabolites, 731 immune cell traits, and RA outcomes from over 58,000 participants.
Screening key genes for intracranial aneurysm rupture using LASSO regression and the SVM-RFE algorithm.
Front Med (Lausanne)
January 2025
Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China.
Background: Although an intracranial aneurysm (IA) is widespread and fatal, few drugs can be used to prevent its rupture. This study explored the molecular mechanism and potential targets of IA rupture through bioinformatics methods.
Methods: The gene expression matrices of GSE13353, GSE122897, and GSE15629 were downloaded.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!