Chinese Journal of Tissue Engineering Research ›› 2025, Vol. 29 ›› Issue (31): 6697-6707.doi: 10.12307/2025.614
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Tian Yushi1, Fu Qiang1, Li Ji2
Received:
2024-05-22
Accepted:
2024-06-27
Online:
2025-11-08
Published:
2025-02-25
Contact:
Li Ji, PhD, Chief physician, Professor, Doctoral supervisor, Postdoctoral instructor, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
About author:
Tian Yushi, PhD candidate, School of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin 150040, Heilongjiang Province, China
Supported by:
CLC Number:
Tian Yushi, Fu Qiang, Li Ji . Bioinformatics identification and validation of mitochondrial genes related to acute myocardial infarction[J]. Chinese Journal of Tissue Engineering Research, 2025, 29(31): 6697-6707.
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2.2 急性心肌梗死特征基因模块鉴定结果 WGCNA分析可进一步识别急性心肌梗死数据集GSE66360的特征基因模块,探索基因网络与表型之间的关联性。结果显示,第一个到达无标度拓扑拟合指数(0.8)的数值为14,因此选择power值为14,数值开始持平,表明网络的连通性好。在GSE66360数据集中共识别出10个模块,其中Blue模块包含4 992个基因,是最大的基因模块。将急性心肌梗死的差异基因和Blue模块基因上传至Venny 2.1.0平台,共获得116个交集基因,见图2。 2.3 特征基因的PPI分析结果 为进一步识别116个基因中的核心,将116个基因上传至STRING平台后,共得到116个节点,604条边线,下载tsv文件并导入至Cytoscape 3.9.1软件中进行可视化分析。利用CytoHubba插件筛选出排名前10位的核心靶点基因,分别为肿瘤坏死因子、白细胞介素1B、白细胞介素6、Toll样受体4 (Toll-like receptor 4,TLR4)、白细胞介素10、Toll样受体2(Toll-like receptor 2,TLR2)、整合素αM(integrin subunit alpha M,ITGAM)、Fcγ受体IIIa(Fc fragment of IgG receptor IIIa,FCGR3A)、Fcγ受体IIIb(FCGR3B,Fc fragment of IgG receptor IIIb)和跨膜免疫信号配体TYROBP(transmembrane immune signaling adaptor TYROBP,TYROBP),见图3。"
2.4 特征基因的富集分析结果 将交集靶点基因导入DAVID数据进行GO和KEGG富集分析。GO分析共得到81个条目(P < 0.05),其中BP共有49个条目,主要涉及炎症反应、肿瘤坏死因子产生的正调控、细胞表面受体信号通路等;CC共有18个条目(P < 0.05),主要涉及三级颗粒膜、质膜外层、质膜等;MF共有14个条目(P < 0.05),主要涉及免疫球蛋白G结合、跨膜信号受体活性、趋化因子活性等;KEGG分析共得到31条通路(P < 0.05),主要为肿瘤坏死因子信号通路、白细胞介素17信号通路和核转录因子κB信号通路等,见图4。 2.5 急性心肌梗死中差异线粒体基因的鉴定结果 将116个核心急性心肌梗死差异表达基因与1 136个人类线粒体基因上传至Venny 2.1.0平台,明确急性心肌梗死中差异线粒体基因的特征和变化趋势,最终获得8个交集基因,分别为佛波醇-12-肉豆酸酯-13-乙酰基诱导蛋白1(phorbol-12-myristate-13-acetate-induced protein1,PMAIP1)、BCL2-相关蛋白A1 (BCL2 related protein A1,BCL2A1)、溶质载体家族25成员37(solute carrier family 25 member 37,SLC25A37)、脱氧核糖核酸聚合酶β(deoxyribonucleic acid polymerase beta,POLB)、F-box和富亮氨酸的重复蛋白4(F-box and leucine rich repeat protein 4,FBXL4)、锌结合醇脱氢酶结构域2(zinc binding alcohol dehydrogenase domain containing 2,ZADH2)、线粒体核糖体蛋白S30(mitochondrial ribosomal protein S30,MRPS30)及心磷脂合酶1(cardiolipin synthase 1,CRLS1)。与空白组相比,差异线粒体基因PMAIP1,BCL2A1,SLC25A37,POLB,FBXL4和ZADH2表达下降,而MRPS30及CRLS1表达上升,见图5。 "
2.6 LASSO-cox分析结果 运用LASSO-cox回归分析进一步筛选8个差异线粒体基因中对急性心肌梗死有重要影响的特征基因,最终获得4个特征基因分别为PMAIP1,BCL2A1,SLC25A37和POLB,见图6。 2.7 GSEA分析结果 对4个特征基因进行单基因的GSEA分析,以确定PMAIP1,BCL2A1,SLC25A37和POLB的基因功能和途径。结果显示,PMAIP1主要涉及12个通路,其中最显著的是肿瘤蛋白53(tumor protein 53,p53)信号通路;BCL2A1主要涉及1个通路即氧化磷酸化途径;SLC25A37主要涉及1个通路即硫代谢途径;POLB主要涉及1个通路即甘油磷脂代谢,见图7。 2.8 ROC分析结果 为明确4个差异线粒体基因是否具有预测诊断急性心肌梗死的意义,采用外部数据集GSE12288对PMAIP1,BCL2A1,SLC25A37和POLB进行ROC分析,以明确判断最佳特征基因作为疾病特征基因的准确度,计算AUC,AUC值越接近1,表示预测性能越好。结果显示,在GSE12288数据集中PMAIP1,BCL2A1,SLC25A37和POLB与空白组相比表达显著升高,其中PMAIP1,BCL2A1,SLC25A37和POLB的AUC值分别为0.801 4,0.910 3,0.737 7,0.816 3,表明PMAIP1,BCL2A1,SLC25A37和POLB可作为急性心肌梗死的线粒体功能障碍的诊断标志,见图8。"
2.9 免疫浸润分析结果 采用CIBERSORT算法对GSE66360数据集的对照组和空白组样本进行免疫浸润分析,探究两组之间不同免疫细胞浸润水平的差异。结果显示,空白组样本中幼稚B细胞、T细胞滤泡辅助细胞表达增高(P < 0.05),急性心肌梗死组记忆性静息CD4+T细胞、静息树突状细胞表达显著升高(P < 0.05),见图9;免疫浸润细胞相关性分析显示浆细胞与嗜酸性粒细胞具有最高的正相关性(r=0.48),幼稚CD4+T细胞与活化树突状细胞具有最高的负相关性(r=-0.46)。对差异线粒体基因与免疫细胞之间的相关性进行计算,结果显示PMAIP1与静息树突状细胞呈负相关性(r=-0.40,P < 0.01),BCL2A1与静息树突状细胞(r=-0.55,P < 0.01)、幼稚B细胞(r=-0.33,P < 0.05)呈负相关,SLC25A37与静息树突状细胞呈负相关性(r=-0.48,P < 0.01),POLB与静息树突状细胞呈负相关性(r=-0.57,P < 0.01),见图10。 "
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