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The altered protein profiles in pigmented nodular synovitis revealed the important role of epithelial-to-mesenchymal transition in disease promotion

ABSTRACT: The altered protein profiles in pigmented nodular synovitis revealed the important role of epithelial-to-mesenchymal transition in disease promotion

PROVIDER: PRJNA848677 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR19635703_1.fastq.gz	Fastqsanger.gz
	SRR19635703_2.fastq.gz	Fastqsanger.gz
	SRR19635707_1.fastq.gz	Fastqsanger.gz
	SRR19635707_2.fastq.gz	Fastqsanger.gz

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The altered protein profiles in pigmented nodular synovitis revealed the important role of epithelial-to-mesenchymal transition in disease promotion

Project description:To investigate the synovium in the PVNS and determine the key role of epithelial–mesenchymal transition (EMT) we mapped the RNA-seq and identified the core molecular regulatory networks in synovial tissue of PVNS patients by RNA extraction, RNA-Seq library preparation 6 control, 7 OA and 19 PVNS samples.

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Immune Cell Infiltration Characteristics of Pigmented Villous Nodular Synovitis and Prediction of Potential Diagnostic Markers Based on Bioinformatics.

Project description:BackgroundPigmented villous nodular synovitis (PVNS) is a tumor-like proliferative disease characterized by impairment of daily activities, decreased quality of life, and a high recurrence rate. However, the specific pathological mechanisms are still ill-defined and controversial. The purpose of this study was to define potential diagnostic markers and evaluate immune cell infiltration in the pathogenesis of PVNS.MethodThe expression profile of GSE3698 was reanalyzed in the Gene Expression Omnibus (GEO) database. First, differentially expressed genes (DEGs) were identified using the R package "limma" and analyzed by Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Next, the DEGs were imported into the STRING database and Cytoscape to construct a protein-protein interaction (PPI) network. Then, cytoHubba and ROC curve analyses were used to determine potential diagnostic biomarkers of PVNS. Finally, we used CIBERSORT to estimate the proportions of 22 immune cell subtypes in PVNS and analyzed the correlation between diagnostic markers and infiltrating immune cells.ResultWe found 139 DEGs (including 93 upregulated genes and 46 downregulated genes). TYROBP, FCER1G, LAPTM5, and HLA-DPB1 were identified as potential diagnostic biomarkers of PVNS. Immune cell infiltration analysis indicated that neutrophils and M2 macrophages might be associated with the genesis and progression of PVNS. Furthermore, our correlation analysis of diagnostic markers and infiltrating immune cells found that TYROBP, FCER1G, LAPTM5, and HLA-DPB1 were positively correlated with M2 macrophage infiltration and that neutrophils, TYROBP, FCER1G, and LAPTM5 were negatively correlated with plasma cell infiltration.ConclusionsWe identified TYROBP, FCER1G, LAPTM5, and HLA-DPB1 as potential diagnostic markers for PVNS and concluded that immune cell infiltration plays an important role in the genesis and progression of PVNS.

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