基于生物信息学筛选骨关节炎关键基因与信号通路
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R684.3;Q811.4

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四川省重点研发计划项目(2024YFHZ0050); 四川省泸州市科学技术局项目(2024LZXNYDJ035); 西南医科大学护理学院创面修复基础与临床应用研究泸州市重点实验室开放项目(2025KFKTZD21);


Screening of key genes and signaling pathways in osteoarthritis based on bioinformatics
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    摘要:

    目的:基于生物信息学挖掘骨关节炎(OA)的关键基因和通路,并利用体外软骨细胞模型进行验证。方法:本研究基于GEO数据库中的GSE269735数据集,运用加权基因共表达网络分析(WGCNA)识别关键基因模块,结合差异表达基因(DEGs)分析筛选候选基因。对DEGs与WGCNA关键基因模块的共同基因进行GO和KEGG通路分析,通过STRING数据库和Cytoscape软件识别DEGs中的关键基因。为验证筛选结果的稳健性,选用GSE2204879数据集进行交叉验证,并以CSF-1为候选基因,构建质粒在OA软骨细胞中进行转染干扰实验。最终通过Western blot检测CSF-1在细胞水平的表达变化,并评估其对细胞功能的影响,验证其在OA中的潜在作用。结果:WGCNA分析识别出多个与OA表型密切相关的模块,与DEGs共同筛选出关键基因。GO与KEGG分析显示,主要生物过程涉及细胞因子活性、趋化因子活性、胶原结合等。关键基因包括CCL20、CSF-1、CXCL11、CXCL3、CXCL5、CXCR4。在GSE2204879数据集中,CSF-1和CXCR4仍表现出一致的表达趋势。细胞水平方面,CSF和CXCR4在OA模型细胞中表达增加。进一步构建CSF-1敲低质粒并转染OA软骨细胞,结果显示,CSF-1敲低伴随CXCR4的表达水平下降,并降低了细胞中MMP3和MMP13的表达水平,增加了Col2a1的蛋白表达水平,提示CSF-1可能通过调控CXCR4参与OA炎症反应与基质降解过程。结论:本研究基于生物信息学与细胞实验相结合的方法,筛选出多个与OA密切相关的关键基因。其中CSF-1和CXCR4在OA中呈高表达,表明CSF-1可能通过调控CXCR4表达,参与OA炎症反应和基质降解过程。CSF-1可能是OA的关键致病因子和潜在治疗靶点。

    Abstract:

    Objective: To mine key genes and pathways of osteoarthritis (OA) based on bioinformatics and validate them using an in vitro chondrocyte model.Methods: This study was based on the GSE269735 dataset from the GEO database, using Weighted Gene Co-expression Network Analysis (WGCNA) to identify key gene modules, combined with differential expression gene (DEG) analysis to screen candidate genes. GO and KEGG pathway analyses were performed on the common genes between DEGs and WGCNA key gene modules, with the STRING database and Cytoscape software used to identify key genes among the DEGs. To validate the robustness of the screening results, the GSE2204879 dataset was used for cross-validation, and a plasmid was constructed with CSF-1 as the candidate gene for transfection interference experiments in OA chondrocytes. Finally, the expression changes of CSF-1 at the cellular level were detected by Western blot, and its effects on cellular function were evaluated to verify its potential role in OA.Results: WGCNA analysis identified multiple modules closely related to OA phenotypes, and key genes were co-screened with DEGs. GO and KEGG analysis showed that the main biological processes involved cytokine activity, chemokine activity, collagen binding, etc. Key genes included CCL20, CSF-1, CXCL11, CXCL3, CXCL5, and CXCR4. In the GSE2204879 dataset, CSF-1 and CXCR4 still showed a consistent expression trend. At the cellular level, CSF-1 and CXCR4 were upregulated in OA model cells. Furthermore, a CSF-1 knockdown plasmid was constructed and transfected into OA chondrocytes; the results showed that CSF-1 knockdown suppressed CXCR4 expression, reduced the expression levels of MMP3 and MMP13 in the cells, and increased the protein expression level of Col2a1, suggesting that CSF-1 may participate in the OA inflammatory response and matrix degradation process by regulating CXCR4. Conclusion: This study, combining bioinformatics and cellular experiments, has screened out multiple key genes closely related to OA. Among them, CSF-1 and CXCR4 show high expression in OA. The experiments indicate that CSF-1 may participate in the OA inflammatory response and matrix degradation process by regulating CXCR4 expression. In summary, CSF-1 may be a key pathogenic factor and potential therapeutic target for OA.

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艾芯;谢羽婕;罗希;张驰.基于生物信息学筛选骨关节炎关键基因与信号通路[J].川北医学院学报,2026,41(2):141-148.

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  • 在线发布日期: 2026-03-05
  • 出版日期: 2026-02-28
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