椎间盘退变相关焦亡基因的综合分析

Integrative analyses of pyroptosis-related genes associated with intervertebral disc degeneration

背景:椎间盘退变早期诊断和治疗尤为重要,髓核细胞焦亡在早期椎间盘退变过程中发挥着重要作用,但髓核细胞焦亡相关分子在早期椎间盘退变中发挥的作用及相关分子标志物仍不明确。目的:探讨焦亡相关差异表达基因在椎间盘退变过程中的诊断及治疗价值。方法:整合GEO数据库椎间盘退变的公开数据集进行差异分析,与之前报道的33个焦亡基因取交集;使用基因本体论、京都基因和基因组百科全书对椎间盘退变焦亡相关基因进行通路富集分析,并使用基因集富集分析对椎间盘退变数据集进行富集分析;构建椎间盘退变样本中的免疫细胞谱,并将差异表达的细胞焦亡相关基因与免疫细胞进行相关性分析;构建蛋白质互作网络,筛选Hub基因以鉴定蛋白质相互作用网络中与椎间盘退变相关的关键基因;整合数据集绘制差异表达焦亡基因的受试者工作特征曲线,计算曲线下面积,探索目标基因的临床诊断价值;qRT-PCR验证正常人髓核细胞与椎间盘退变人髓核细胞之间焦亡相关基因的表达差异。结果与结论:①获得4426个与椎间盘退变相关的差异表达基因,交集后获得14个差异表达的焦亡相关基因;②基因本体论、京都基因和基因组百科全书分析揭示了重要的富集途径,主要与炎症、细胞周期、感染和NOD样受体通路相关;基因集富集分析显示氨基酸代谢、P53转录调节等通路在椎间盘退变患者中显著富集;免疫浸润分析提示椎间盘退变的发生发展与免疫细胞密切相关;③共筛选出5个Hub基因,分别为IL-1β、Caspase-1、AIM2、Caspase-5、NLRC4;④椎间盘退变关键生物标志物的获取及鉴定:将GEO两个数据集与焦亡基因取交集后发现NLRP3具有显著表达差异,受试者工作特征曲线显示NLRP3具有临床诊断意义;⑤qRT-PCR显示IL-1β、Caspase-5和NLRC4等Hub基因在椎间盘退变的髓核细胞中表达显著增加(P<0.05),Caspase-1、AIM2以及NLRP3表达无差异(P>0.05);⑥提示细胞焦亡在椎间盘退变发生发展过程中发挥重要作用,其中焦亡相关基因NLRP3、IL1-β、Caspase-5、NLRC4具有早期诊断和治疗价值。

BACKGROUND:Early diagnosis and treatment of intervertebral disc degeneration is particularly important.Pyroptosis of nucleus pulposus cells plays an important role in the early process of intervertebral disc degeneration,but the role of pyroptosis-related molecules of nucleus pulposus cells in early intervertebral disc degeneration and related molecular markers are still unclear.OBJECTIVE:To explore the diagnostic and therapeutic value of differentially expressed genes related to pyroptosis during intervertebral disc degeneration.METHODS:Public datasets of the GEO database were integrated for differential analysis,and intersected with 33 pyroptosis-related genes previously reported.Using Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes,pathway enrichment analysis was performed in genes related to pyroptosis during intervertebral disc degeneration.Enrichment analysis of the intervertebral disc degeneration dataset was conducted using gene set enrichment analysis.To construct the immune cell spectrum in intervertebral disc degeneration samples,the correlation between the differentially expressed pyroptosis-related genes and immune cells was analyzed.Protein interaction networks were built.Screening of the Hub gene to identify key genes associated with intervertebral disc degeneration in protein interaction networks.The receiver operating characteristic curve of the differentially expressed pyroptosis-related genes was plotted,and the area under the curve was calculated.The clinical diagnostic value of target genes was explored.qRT-PCR was applied to verify the difference in the expression of pyroptosis-related genes between normal human nucleus pulposus cells and degenerated human nucleus pulposus cells with intervertebral discs.RESULTS AND CONCLUSION:(1)4426 differentially expressed genes associated with intervertebral disc degeneration were obtained,and 14 differentially expressed pyroptosis-related genes were obtained after the intersection.(2)Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed important enrichment pathways,mainly related to inflammation,cell cycle,infection and NOD-like receptor pathway.Gene set enrichment analysis showed that pathways such as amino acid metabolism and P53 transcription regulation were significantly enriched in patients with intervertebral disc degeneration.Immune infiltration analysis suggested that the occurrence and development of intervertebral disc degeneration were closely related to immune cells.(3)A total of five Hub genes were screened,namely IL1-β,Caspase-1,AIM2,Caspase-5,and NLRC4.(4)Acquisition and identification of key biomarkers for intervertebral disc degeneration:After intersecting the two datasets of GEO with the pyroptosis-related gene,it was found that NLRP3 had significant expression differences,and the receiver operating characteristic curve showed that NLRP3 had clinical diagnostic significance.(5)qRT-PCR showed that the expression of Hub genes such as IL1-β,Caspase-5 and NLRC4 was significantly increased in the nucleus pulposus cells of intervertebral disc degeneration(P<0.05),and there was no difference in Caspase-1,AIM2 and NLRP3 expression(P>0.05).(6)It is suggested that cell pyroptosis plays an important mechanism in the occurrence and development of intervertebral disc degeneration,among which pyroptosis-related molecules NLRP3,IL1-β,Caspase-5 and NLRC4 have early diagnosis and treatment value.