Identification and Analysis of Neutrophil Extracellular Trap-Related Genes in Osteoarthritis by Bioinformatics and Experimental Verification

Abstract

Background Osteoarthritis (OA) is a common joint disease with long-term pain and dysfunction that negatively affects the quality of life of patients. Neutrophil extracellular traps (NETs), consisting of DNA, proteins and cytoplasm, are released by neutrophils and play an important role in a variety of diseases. However, the relationship between OA and NETs is unclear. Methods In our study, we used bioinformatics to explore the relationship between OA and NETs and the potential biological markers. GSE55235, GSE55457, GSE117999 and GSE98918 were downloaded from the Gene Expression Omnibus (GEO) database for subsequent analysis.After differential analysis of OA expression matrices, intersection with NET-related genes (NRGs) was taken to identify Differentially expressed NRGs (DE-NRGs) in OA processes. Evaluation of immune cell infiltration by ssGSEA and CIBERSORT algorithm. The GSVA method was used to analyze the activity changes of Neutrophils pathway, Neutrophil degranulation and Neutrophil granule constituents pathway. Results Based on RandomForest (RF), Least Absolute Shrinkage and Selection Operator (LASSO), and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) learning algorithms, five core genes (CRISPLD2, IL1B, SLC25A37, MMP9, and TLR7) were identified to construct an OA-related nomogram model for predicting OA progression. ROC curve results for these genes validated the nomogram’s reliability. Correlation analysis, functional enrichment, and drug predictions were performed for the core genes. TLR7 emerged as a key focus due to its high importance ranking in RF and SVM-RFE analyses. Gene Set Enrichment Analysis (GSEA) revealed a strong association between TLR7 and the Neutrophil extracellular trap pathway. Expression of core genes was demonstrated in mice OA models and human OA samples. TLR7 expression in ATDC5 cell line was significantly higher than control after TNFα induction, along with increased IL6 and MMP13. Conclusion TLR7 may be related to NETs and affects OA.

Comprehensive transcriptomic analysis unveils macrophage-associated genes for establishing an abdominal aortic aneurysm diagnostic model and molecular therapeutic framework

“…For anti-inflammatory genes, we can use corresponding lncRNA preparations to promote their expression. For pro-inflammatory genes, such as IL-1B, we can use corresponding miRNA preparations or IL-1B inhibitors, such as lionassep with diacerein, to inhibit the inflammatory response [ 58 ].…”

Table_1.xlsx

“…Neutrophils are generated in great number in the bone marrow, as a crucial part of the bone marrow microenvironment, release NETs which may influence the bone marrow tumor immune microenvironment and, in turn, affect the prognosis of patients with myeloma. NETs have been implicated in a variety of cancerous disease (26)(27)(28)(29)(30)(31). However, the relationship between NETs and MM has not been reported.…”

Image_1.tiff

“…Neutrophils are generated in great number in the bone marrow, as a crucial part of the bone marrow microenvironment, release NETs which may influence the bone marrow tumor immune microenvironment and, in turn, affect the prognosis of patients with myeloma. NETs have been implicated in a variety of cancerous disease (26)(27)(28)(29)(30)(31). However, the relationship between NETs and MM has not been reported.…”