Related Experiment Video
Updated: Sep 22, 2025
Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry
Published on: June 26, 2018
Identification of hub biomarkers and immune cell infiltration in polymyositis and dermatomyositis
Si Chen1,2, Haolong Li1, Haoting Zhan1
1Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
Objective:
Polymyositis (PM) and dermatomyositis (DM) are heterogeneous disorders. However, the etiology of PM/DM development has not been thoroughly clarified.
Methods:
Gene expression data of PM/DM were obtained from Gene Expression Omnibus. We used robust rank aggregation (RRA) to identify differentially expressed genes (DEGs). Gene Ontology functional enrichment and pathway analyses were used to investigate potential functions of the DEGs. Weighted gene co-expression network analysis (WGCNA) was used to establish a gene co-expression network. CIBERSORT was utilized to analyze the pattern of immune cell infiltration in PM/DM. Protein-protein interaction (PPI) network, Venn, and association analyses between core genes and muscle injury were performed to identify hub genes. Receiver operating characteristic analyses were executed to investigate the value of hub genes in the diagnosis of PM/DM, and the results were verified using the microarray dataset GSE48280.
Results:
Five datasets were included. The RRA integrated analysis identified 82 significant DEGs. Functional enrichment analysis revealed that immune function and the interferon signaling pathway were enriched in PM/DM. WGCNA outcomes identified MEblue and MEturquoise as key target modules in PM/DM. Immune cell infiltration analysis revealed greater macrophage infiltration and lower regulatory T-cell infiltration in PM/DM patients than in healthy controls. PPI network, Venn, and association analyses of muscle injury identified five putative hub genes: TRIM22, IFI6, IFITM1, IFI35, and IRF9.
Conclusions:
Our bioinformatics analysis identified new genetic biomarkers of the pathogenesis of PM/DM. We demonstrated that immune cell infiltration plays a pivotal part in the occurrence of PM/DM.
Insights
This study identifies key genes and immune cell patterns involved in polymyositis and dermatomyositis, offering new biomarkers for these inflammatory muscle diseases.
Area of Science:
- Immunology and Genetics
- Bioinformatics and Computational Biology
Background:
- Polymyositis (PM) and dermatomyositis (DM) are complex inflammatory myopathies with unclear etiologies.
- Understanding the genetic and molecular underpinnings is crucial for developing effective diagnostic and therapeutic strategies.
Purpose of the Study:
- To identify differentially expressed genes (DEGs) and key genetic biomarkers in PM/DM.
- To elucidate the role of immune cell infiltration in the pathogenesis of PM/DM.
- To evaluate the diagnostic potential of identified hub genes in PM/DM.
Main Methods:
- Utilized robust rank aggregation (RRA) to analyze gene expression data from multiple PM/DM datasets.
- Performed Gene Ontology (GO) and pathway analyses for functional enrichment of DEGs.
- Employed weighted gene co-expression network analysis (WGCNA), CIBERSORT, and protein-protein interaction (PPI) network analysis to identify hub genes and immune cell infiltration patterns.
Main Results:
- Identified 82 significant DEGs, with enrichment in immune function and interferon signaling pathways.
- Discovered distinct immune cell infiltration patterns: increased macrophage and decreased regulatory T-cell infiltration in PM/DM patients.
- Identified five hub genes (TRIM22, IFI6, IFITM1, IFI35, IRF9) associated with muscle injury and PM/DM pathogenesis.
Conclusions:
- Bioinformatics analysis revealed novel genetic biomarkers contributing to PM/DM pathogenesis.
- Immune cell infiltration, particularly macrophages and regulatory T-cells, plays a significant role in the development of PM/DM.
- The identified hub genes hold potential as diagnostic biomarkers for PM/DM.
