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中华肾病研究电子杂志 ›› 2024, Vol. 13 ›› Issue (01) : 26 -33. doi: 10.3877/cma.j.issn.2095-3216.2024.01.004

论著

急性肾损伤的内质网应激相关基因和通路的生物信息学分析
桑田1, 赵磊2, 佟琰3, 欧阳清3,(), 陈香美3,()   
  1. 1. 100853 北京,中国人民解放军总医院第一医学中心肾脏病医学部、肾脏疾病全国重点实验室、国家慢性肾病临床医学研究中心、肾脏疾病研究北京市重点实验室;100853 北京,解放军医学院;010051 呼和浩特,中国人民解放军联勤保障部队第九六九医院
    2. 100039 北京,解放军总医院第五医学中心感染病医学部
    3. 100853 北京,中国人民解放军总医院第一医学中心肾脏病医学部、肾脏疾病全国重点实验室、国家慢性肾病临床医学研究中心、肾脏疾病研究北京市重点实验室
  • 收稿日期:2023-08-29 出版日期:2024-02-28
  • 通信作者: 欧阳清, 陈香美
  • 基金资助:
    国家自然科学基金青年科学基金项目(82000657)

Bioinformatic analysis of hub genes and pathways related to endoplasmic reticulum stress in acute kidney injury

Tian Sang1, Lei Zhao2, Yan Tong3, Yangqing Ou3,(), Xiangmei Chen3,()   

  1. 1. Department of Nephrology, First Medical Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases Research, Beijing 100853; Chinese PLA Medical School, Beijing 100853; 969th Hospital of Chinese PLA Joint Logistics Support Force, Hohhot 010051, Inner Mongolia Autonomous Region
    2. Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039; China
    3. Department of Nephrology, First Medical Center of Chinese PLA General Hospital, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases Research, Beijing 100853
  • Received:2023-08-29 Published:2024-02-28
  • Corresponding author: Yangqing Ou, Xiangmei Chen
引用本文:

桑田, 赵磊, 佟琰, 欧阳清, 陈香美. 急性肾损伤的内质网应激相关基因和通路的生物信息学分析[J]. 中华肾病研究电子杂志, 2024, 13(01): 26-33.

Tian Sang, Lei Zhao, Yan Tong, Yangqing Ou, Xiangmei Chen. Bioinformatic analysis of hub genes and pathways related to endoplasmic reticulum stress in acute kidney injury[J]. Chinese Journal of Kidney Disease Investigation(Electronic Edition), 2024, 13(01): 26-33.

目的

通过生物信息学方法及动物实验寻找并验证与内质网应激相关的急性肾损伤(AKI)共表达关键基因,探索分析这些基因在AKI的发生和发展中的作用。

方法

本文选取了基因表达综合数据库中的GSE30718数据集,从中筛选与内质网应激相关的差异基因。采用差异分析、分组比较、蛋白相互作用网络分析、相关性分析、受试者工作特征(ROC)曲线分析、基因本体和京都基因与基因组百科全书富集分析等方法,对内质网应激的特征基因的表达特征进行分析。进一步使用了对侧肾切除+单侧肾缺血再灌注损伤小鼠模型进行实验验证,通过在不同时间点(1 d、3 d、7 d和14 d)采集模型小鼠的肾脏组织进行实时荧光定量核酸扩增检测系统(qPCR)实验,对相关基因的表达特征进行分析。

结果

发现11个与内质网应激相关的AKI共表达基因蛋白,包括FOS、VMP1、CEL、HSP90B1、TIMP1、FAS、RDH12、RALYL、PCK2、LCN2和PTX3。通过蛋白相互作用网络分析,找出了与上述基因密切相关的20个节点基因;相关性分析提示除HSP90B1与FOS之间无明显相关性外,其他内质网应激相关差异基因两两之间均密切相关;ROC曲线分析提示上述11个基因的ROC曲线下面积均>0.70;基因本体和京都基因与基因组百科全书富集分析提示,FOS、HSP90B1和LCN2参与了IL-17信号通路,通过影响细胞的增殖、内质网功能、及组装蛋白的分泌,从而影响AKI进展。在对侧肾切除+单侧肾缺血再灌注损伤小鼠模型的qPCR实验中,Timp1、Lcn2基因表达早期显著增高,而Fos仅在14 d时显著增加;Hsp90b1、Ptx3、Rdh12等基因表达呈总体下降趋势,且均在早期出现了显著的下降。Western印迹结果提示Lcn2、Timp1、c-Fos随AKI的进展呈增多趋势。

结论

本研究发现了11个内质网应激相关的AKI共表达基因,可能通过IL-17信号通路影响细胞的增殖、内质网功能、及组装蛋白的分泌进程,参与调节内质网应激,进而影响AKI的进展。内质网应激相关差异基因与炎症反应、细胞凋亡和细胞周期调控等功能具有一定的相关性,且可能对AKI具有较好的诊断价值,其中4个基因在动物实验中得到了关键性验证,为后续探索内质网应激影响AKI的机制研究提供新的靶点和思路。

Objective

To explore the key genes associated with both acute kidney injury (AKI) and endoplasmic reticulum (ER) stress through bioinformatic methods and animal experiments.

Methods

The gene expression omnibus (GEO) dataset GSE30718 was selected for this study, and differentially expressed genes (DEGs) related to ER stress were screened. Differential analysis, group comparison, protein-protein interaction (PPI) network analysis, correlation analysis, receiver operating characteristic (ROC) curve analysis, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to analyze the expression characteristics of ER stress-related genes. Furthermore, an experimental validation was conducted using a unilateral ischemia-reperfusion injury with contralateral nephrectomy (uIRIx) mouse model, and real-time fluorescence quantitative polymerase chain reaction (qPCR) experiments were performed on kidney tissues collected at different time points (1 d, 3 d, 7 d, and 14 d) to analyze the expression characteristics of the relevant genes.

Results

Eleven ER stress-related genes co-expressed in AKI were discovered, including FOS, VMP1, CEL, HSP90B1, TIMP1, FAS, RDH12, RALYL, PCK2, LCN2, and PTX3. Through PPI network analysis, 20 node genes closely related to the above-mentioned genes were found. Correlation analysis suggested that all ER stress-related DEGs except for HSP90B1 and FOS were closely correlated with each other. ROC analysis suggested that the area under the curve for the above 11 genes was greater than 0.70. GO and KEGG enrichment analysis suggested that FOS, HSP90B1, and LCN2 were involved in the IL-17 signaling pathway, affecting cell proliferation, endoplasmic reticulum function, and assembly of secreted proteins, thereby influencing the progression of AKI. In the uIRIx model of animals, qPCR experiments showed that Timp1 and Lcn2 were significantly elevated early on, while Fos only significantly increased after 14 days. The expression of Hsp90b1, Ptx3, Rdh12, and other genes showed an overall downward trend with significant decreases early on. Western blot experiments suggested that Lcn2, Timp1, and c-Fos increased with the progression of AKI.

Conclusion

Eleven ER stress-related genes co-expressed in AKI were discovered that might affect the progression of AKI through the IL-17 signaling pathway, affecting cell proliferation, endoplasmic reticulum function, and assembly of secreted proteins. ER stress-related DEGs were also related to inflammation, cell apoptosis, and cell cycle regulation, and might have good diagnostic value for AKI. Four of these genes were critically validated in animals experiments, providing new targets and ideas for further exploration of the mechanisms by which ER stress may affect AKI.

图1 生信分析方法及流程图注:PPI:蛋白质相互作用网络;AKI:急性肾损伤;GO:基因本体;KEGG:京都基因与基因组百科全书
图2 差异分析注:A:表达差异基因的火山图,横坐标为差异表达倍数以2为底的对数,纵坐标-log10(P值)为矫正后的显著性水平以10为底的负对数;B:内质网应激相关的差异基因的热图;C:差异基因与内质网应激关键基因的韦恩图;D:11个内质网应激相关的差异基因在GSE30718数据集中的AKI组与正常对照组的表达水平比较,与正常对照组比较,aP<0.01、bP<0.05
图3 蛋白质互作网络分析图注:该蛋白质互作网络图展示了内质网应激相关的差异基因之间的互作关系,连线的粗细与互作的密切程度成正比,颜色说明不同的互作关系(互作阈值>0.4,中等置信)
图4 相关性分析图注:该相关性分析图展示了内质网应激差异表达基因在GSE30718数据集选取的样本中表达相关性,其中蓝色代表负相关,红色代表正相关,aP<0.05
图5 受试者工作特征曲线分析AUC:曲线下面积
图6 GO及KEGG富集分析注:A:GO及KEGG富集分析的柱状图(BP:biological process,生物学过程;CC:cellular component,细胞组分;KEGG:KEGG通路);B:GO及KEGG富集分析网络图(节点圆圈大小与富富集基因的数量成正比)
表1 关键基因的GO及KEGG富集分析结果
图7 uIRIx小鼠模型不同时间点的肾脏病理组织学及血清肌酐、血清尿素氮变化注:A:100倍(左列)和400倍(右列)光镜下uIRIx模型不同时间点(1 d,3 d,7 d,14 d)以及假手术组取材的肾脏组织的PAS染色照片;B:uIRIx小鼠模型不同时间点取材以及假手术组的肾脏PAS病理染色的肾小管损伤评分、血清肌酐和尿素氮的变化趋势(n=6);与假手术比较,aP<0.001
图8 各组小鼠不同时间取材肾组织实时荧光定量核酸扩增检测系统检测差异基因表达比较注:与假手术组比较,a P<0.001、bP<0.01
表2 实时荧光定量PCR扩增引物序列
图9 各组小鼠不同时间取材Western印迹检测Lcn2、Timp1、c-FOS的蛋白表达与比较注:与假手术组比较,a P<0.001、bP<0.01
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