背景:骨肉瘤(OS)是一种常见的原发性恶性骨肿瘤,主要发生在儿童和青少年。在专利中已经报道了IL-8抑制剂化合物的用途,可用于治疗和/或预防骨肉瘤,但骨肉瘤的发病机制仍有待研究。目前,成骨细胞和破骨细胞在OS的发生发展中起着重要作用。然而,成骨细胞和破骨细胞在OS患者中的具体参与机制与炎症反应的关系尚未进一步研究。
方法:转录组,临床资料,和其他与OS相关的数据从GEO数据库下载,以分析它们与200个已知的炎症反应基因。我们设定筛选条件为p<0.05和|log2FC|>0.50,筛选与OS相关的差异表达基因(DEGs),测试了OSINF基因与临床风险之间的相关系数,并对生存预后进行分析。我们用GO/KEGG进一步富集和分析了OS的DEGs和炎症反应基因,以探索OS炎症反应基因的潜在生物学功能和信号通路机制。此外,基于FDA药物库进行OS药物敏感性的虚拟筛选,探索潜在的靶向调节OS成骨和破骨细胞炎症的治疗药物,最后,对OS核心蛋白和潜在药物进行分子动力学模拟验证,探讨潜在药物与核心蛋白的结合稳定性及机制。
结果:通过对GSE39058,GSE36001,GSE87624以及与OS成骨细胞和破骨细胞密切相关的其他三个数据集的差异分析,我们发现有一个上调基因(CADM1)和一个下调基因(PHF15)与OS相关。此外,对OS的DEGs的GSEA富集分析表明,它主要通过生物学功能参与OS的发展,如氧化光合作用,急性交界处,和上皮-间质转化。OSDEGs的富集分析表明,它们主要通过参与肌动蛋白骨架的调控来影响OS的发生和发展,PI3KAkt信号通路,补体和凝血级联。根据CSF3R在OS患者中的表达,建立了风险系数模型和诊断模型。结果发现,OS患者的CSF3R基因差异越显著,疾病的危险系数越大(p<0.05)。CSF3R基因曲线下的AUC大于0.65,对OS具有较好的诊断意义。以上结果表明,与OS炎症相关的预后风险基因CSF3R与OS患者的生存状态密切相关。最后,通过ZINC药物库的虚拟筛选和分子动力学模拟,发现核心蛋白CSF3R与化合物形成的对接模型,亚叶酸和甲氨蝶呤,是最稳定的,提示亚叶酸和甲氨蝶呤化合物可能通过与OS的炎症反应相关因子CSF3R联合作用于OS的治疗。
结论:CSF3R通过调节成骨细胞和破骨细胞的炎症反应参与OS骨破坏的发生和发展,影响OS患者的生存预后。
BACKGROUND: Osteosarcoma (OS) is a common primary malignant bone tumor that mainly occurs in children and adolescents. The use of IL-8 inhibitor compounds has been reported in patents, which can be used to treat and/or prevent osteosarcoma, but the pathogenesis of osteosarcoma remains to be investigated. At present, osteoblasts and osteoclasts play an important role in the occurrence and development of OS. However, the relationship between osteoblasts and osteoclasts in the specific participation mechanism and inflammatory response of OS patients has not been further studied.
METHODS: The transcriptome, clinical data, and other data related to OS were downloaded from the GEO database to analyze them with 200 known inflammatory response genes. We set the screening conditions as p < 0.05 and | log2FC| > 0.50, screened the differentially expressed genes (DEGs) related to OS, tested the correlation coefficient between the OS INF gene and clinical risk, and analyzed the survival prognosis. We further enriched and analyzed the DEGs and inflammatory response genes of OS with GO/KEGG to explore the potential biological function and signal pathway mechanism of OS inflammatory response genes. Moreover, the virtual screening of drug sensitivity of OS based on the FDA drug library was also carried out to explore potential therapeutic drugs targeted to regulate OS osteogenesis and osteoclast inflammation, and finally, the molecular dynamics simulation verification of OS core protein and potential drugs was carried out to explore the binding stability and mechanism between potential drugs and core protein.
RESULTS: Through differential analysis of GSE39058, GSE36001, GSE87624, and three other data sets closely related to OS osteoblasts and osteoclasts, we found that there was one upregulated gene (CADM1) and one down-regulated gene (PHF15) related to OS. In addition, GSEA enrichment analysis of the DEGs of OS showed that it was mainly involved in the progress of OS through biological functions, such as oxidative photosynthesis, acute junction, and epithelial-mesenchymal transition. The enrichment analysis of OS DEGs revealed that they mainly affect the occurrence and progress of OS by participating in the regulation of the actin skeleton, PI3K Akt signal pathway, complement and coagulation cascade. According to the expression of
CSF3R in OS patients, a risk coefficient model and a diagnostic model were established. It was found that the more significant the difference in the
CSF3R gene in OS patients, the greater the risk coefficient of disease (p < 0.05). The AUC under the curve of the
CSF3R gene was greater than 0.65, which had a good diagnostic significance for OS. The above results showed that the prognosis risk gene CSF3R related to OS inflammation was closely related to the survival status of OS patients. Finally, through the virtual screening of the ZINC drug library and molecular dynamics simulation, it was found that the docking model formed by the core protein CSF3R and the compounds, Leucovorin and Methotrexate, were the most stable, which revealed that the compounds Leucovorin and Methotrexate might play a role in the treatment of OS by combining with the inflammatory response related factor
CSF3R of OS.
CONCLUSIONS: CSF3R participates in the occurrence and development of OS bone destruction by regulating the inflammatory response of osteoblasts and osteoclasts and can affect the survival prognosis of OS patients.