Dataset Information

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

ABSTRACT:

Background

Pigmented 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.

Method

The 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.

Result

We 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.

Conclusions

We 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.

SUBMITTER: Zhang J

PROVIDER: S-EPMC9197622 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Publications

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

Zhang Jun J Li Bin B Zhao Boming B Qi Yongjian Y Chen Liaobin L Chen Jun J Chen Biao B

BioMed research international 20220607

<h4>Background</h4>Pigmented 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.<h4>Method</h4>The expression profile of GSE3698 was reanalyzed in the Gen ...[more]

PMID: 35711523

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Project description:This study aimed to investigate efficient diagnostic markers and molecular mechanisms of atherosclerosis and to analyze the role of immune infiltration through bioinformatics analysis. Expression profile datasets (GSE28829 and GSE43292) of patients with atherosclerosis and healthy controls were downloaded from the GEO database. Glutamine (GLN) metabolism-associated genes were obtained from the Molecular Signatures Database (MSigDB). The limma package in R was used to identify differentially expressed genes (DEGs). Significant modules were filtered using Weighted Gene Co-expression Network Analysis (WGCNA). MSigDB sets were subjected to Gene Set Enrichment Analysis and Gene Set Variation Analysis. The biological functions of DEGs were examined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. STRING and Cytoscape software were used to identify hub genes and functional modules through protein-protein interaction (PPI) network analysis. The xCell software was adopted to assess the composition patterns of immune and stromal cells. Correlation analyses were performed for key genes and immune cell subtypes. We identified 308 DEGs and GLN-associated genes. Functional enrichment analysis showed that these genes were strongly enriched in muscle contract, muscle tissue development, cutile fiber, mycobacterial, and actin binding. Enriched KEGG pathways comprised dilated cardiomyopathy, hypertrophic cardiomyopathy, and the cAMP signaling pathway. In the PPI network analysis, 27 genes were identified as hub genes. The area under the curve (AUC) values of 27 biomarkers were relatively high, indicating high diagnostic values. The atherosclerosis group exhibited a markedly higher degree of infiltration than the control group. This study identified 27 GLN-associated genes as potential biomarkers for the diagnosis of atherosclerosis. It provides a new perspective on immune responses that facilitates exploration of the molecular mechanisms of atherosclerosis.

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Project description:PurposeTo review clinical characteristics of pigmented villonodular synovitis (PVNS) in China.MethodsElectronic medical records (EMR) of four Chinese institutes were queried for patients with histologically proven PVNS between January 2005 and February 2014. Their data were collected including gender, age at diagnosis, clinical presentation, affected site, symptom duration, comorbidities, treatment strategy, recurrence and routine laboratories.ResultsA total of 237 patients with biopsy-proven PVNS were investigated. The gender ratio was 1.35 for a female predominance (101 males and 136 females). The average age was 36 years (range, 2 to 83 years). The median delay from initial clinical symptom to diagnosis was 18 months. Main affected areas were the knee (73.84%) and the hip (18.14%). Forty patients had a clear history of joint trauma. Six patients were concurrently diagnosed with PVNS and avascular necrosis (AVN). Five patients suffered from PVNS following implantation of orthopaedic devices including artificial prosthesis, plate and wire. One hundred and twenty-nine patients underwent arthroscopic synovectomy and 108 open synovectomy. Altogether 48 patients (26 males and 22 females) had recurrence of disease. The relapse rate was 24% (knee) and 6.98% (hip), 20.93% (open surgery) and 19.44% (arthroscopy), respectively. Erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) rate were elevated in 45.83% and 38.41% of the patients respectively.ConclusionsTo our knowledge, this study is the largest sample size of PVNS patients reported as well as the largest sample of PVNS with concurrent AVN reported to date. Our outcomes suggest that PVNS shows a female predominance, occurs mostly between 20-40 years and favors the knee and hip. Recurrence is frequent, particularly in the knee. Serum ESR and CRP may be elevated in some patients. Additionally, the present study supports the theory of an association between PVNS and orthopedic surgery, which is not limited to joint replacement.

Dataset Information

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

Background

Method

Result

Conclusions

Publications

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

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