Zheng Qingcong, Lin Rongjie, Li Zhechen, Zheng Qingzhu, Xu Weihong
Department of Spinal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
Department of Orthopedic Surgery, Fujian Medical University Union Hospital, Fuzhou, China.
PLoS One. 2025 Apr 16;20(4):e0318311. doi: 10.1371/journal.pone.0318311. eCollection 2025.
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease closely related to aging with unclear pathogenic mechanisms. This study aims to identify the biomarkers in RA, aging and autophagy using bioinformatics and machine learning and explore the binding stability of taurine to target utilizing computer-aided drug design (CADD).
We identified differentially expressed genes (DEGs) for RA, then crossed with gene libraries for aging and autophagy to identify common genes (Co-genes). We performed Gene Ontology (GO), Kyoto Encyclopedia of the Genome (KEGG), and ClueGO analysis for Co-genes. The Co-genes were subjected to support vector machine-recursive feature elimination (SVM-RFE), Degree, and Betweenness algorithms to get hub genes, then verified by an artificial neural network (ANN). After continuing to perform least absolute shrinkage and selection operator (LASSO) and weighted gene co-expression network analysis (WGCNA) on Co-genes, the results were crossed with hub genes to obtain genes, which were imported into various validation sets for receiver operating characteristics (ROC) to identify key genes. We analyzed the microRNA/TF network, enriched pathways, and immune cell infiltration for key genes. The binding stability of taurine with the target protein was verified by CADD. Finally, we used Western blot for in vitro experimental verification.
We obtained 74 Co-genes enriched in RA, cellular senescence, and regulation of programmed cell death. The model prediction of hub genes works well in ANN. The key genes (MMP9, CXCL10, IL15, FOXO3) were tested in ROC with excellent efficacy. In RA, FOXO3 expression was down-regulated while MMP9, CXCL10, and IL15 expression were upregulated, and FOXO3 was negatively correlated with MMP9, CXCL10, and IL15. Two miRNAs (hsa-mir-21-5p, hsa-mir-129-2-3p) and four TFs (CTCF, KLF, FOXC1, TP53) were associated with key genes. The immune cells positively correlated with MMP9, CXCL10, and IL15 expression and negatively correlated with FOXO3 expression were Plasma cells, CD8 T cells, memory-activated CD4 T cells, and follicular helper T cells, aggregating in RA. The binding stability of taurine with FOXO3 was verified by molecular docking and molecular dynamics simulation. In vitro experiments have indicated that taurine can upregulate the expression of FOXO3 and treat RA through the FOXO3-Parkin signaling pathway.
MMP9, CXCL10, IL15, and FOXO3 are biomarkers of RA, cellular senescence, and autophagy. Taurine might be a promising drug against RA via targeting cellular senescence and autophagy through FOXO3.
类风湿性关节炎（RA）是一种与衰老密切相关的慢性炎症性自身免疫性疾病，其致病机制尚不清楚。本研究旨在利用生物信息学和机器学习确定RA、衰老和自噬中的生物标志物，并利用计算机辅助药物设计（CADD）探索牛磺酸与靶点的结合稳定性。
我们确定了RA的差异表达基因（DEG），然后与衰老和自噬的基因文库进行交叉，以确定共同基因（共基因）。我们对共基因进行了基因本体论（GO）、京都基因与基因组百科全书（KEGG）和ClueGO分析。共基因经过支持向量机递归特征消除（SVM-RFE）、度和介数算法以获得枢纽基因，然后通过人工神经网络（ANN）进行验证。在对共基因继续进行最小绝对收缩和选择算子（LASSO）和加权基因共表达网络分析（WGCNA）后，将结果与枢纽基因交叉以获得基因，将这些基因导入各种验证集进行受试者工作特征（ROC）分析以确定关键基因。我们分析了关键基因的微小RNA/转录因子网络、富集途径和免疫细胞浸润。通过CADD验证了牛磺酸与靶蛋白的结合稳定性。最后，我们使用蛋白质免疫印迹法进行体外实验验证。
我们获得了74个在RA、细胞衰老和程序性细胞死亡调节中富集的共基因。枢纽基因的模型预测在ANN中效果良好。关键基因（MMP9、CXCL10、IL15、FOXO3）在ROC分析中具有优异的效能。在RA中，FOXO3表达下调，而MMP9、CXCL10和IL15表达上调，且FOXO3与MMP9、CXCL10和IL15呈负相关。两个微小RNA（hsa-mir-21-5p、hsa-mir-129-2-3p）和四个转录因子（CTCF、KLF、FOXC1、TP53）与关键基因相关。与MMP9、CXCL10和IL15表达呈正相关且与FOXO3表达呈负相关的免疫细胞是浆细胞、CD8 T细胞、记忆激活的CD4 T细胞和滤泡辅助性T细胞，它们在RA中聚集。通过分子对接和分子动力学模拟验证了牛磺酸与FOXO3的结合稳定性。体外实验表明，牛磺酸可以上调FOXO3的表达，并通过FOXO3-Parkin信号通路治疗RA。
MMP9、CXCL10、IL15和FOXO3是RA、细胞衰老和自噬的生物标志物。牛磺酸可能是一种有前途的抗RA药物，它通过FOXO3靶向细胞衰老和自噬。
