糖尿病肾脏病免疫相关转录因子的生物信息学分析

Bioinformatic analysis of immune-related transcription factors in diabetic kidney disease

目的 通过生物信息学方法分别对糖尿病肾病(DKD)患者肾小球与肾小管病变的转录组学进行分析,筛选关键的免疫相关转录因子。方法 下载基因表达数据集(GEO)数据库GSE30528、 GSE30529数据集与Karolinska肾脏研究中心转录组测序(RNA-seq)数据集。通过基因集富集分析(GSEA)明确DKD肾小球与肾小管免疫基因表达有无差异。应用R软件limma包和DEseq2包分别对芯片数据及RNA-seq数据进行差异分析,提取其中差异表达的免疫基因及转录因子,通过共表达分析获取免疫相关转录因子。应用蛋白质相互作用的STRING数据库及Cytoscape软件构建转录因子与免疫相关基因的蛋白质互相作用网络(PPI)。最后通过肾基因表达分析工具Nephroseq数据库分析关键的免疫相关转录因子与临床病理参数的相关性。结果与正常对照组织相比,DKD肾小球和肾小管组织免疫基因有明显的表达差异。通过差异分析及共表达分析方法,肾小球转录组共得到50个免疫基因及9个免疫相关转录因子;肾小管转录组共得到131个免疫基因及41个免疫相关转录因子。PPI网络中,肾小球关键的免疫相关转录因子为干扰素调节因子8(IRF8)、乳运铁蛋白(LTF)、 CCAAT/增强子结合蛋白α(CEBPA)、 Runt相关转录因子3(RUNX3),肾小管关键的免疫相关转录因子为FBJ小鼠骨肉瘤病毒癌基因同源蛋白B(FOSB)、核受体亚家族4A组成员1(NR4A1)、 IRF8与信号转导子及转录激活子1(STAT1),以上转录因子均与肾小球滤过率(GFR)呈显著相关性。结论 生物信息学分析获得了DKD发病与免疫调节异常相关的可能基因,进一步验证这些基因的表达及功能有助于DKD的免疫治疗研究。

Objective To identify immune-related transcription factors(TFs)in renal glomeruli and tubules from diabetic kidney disease(DKD)patients by bioinformatics analysis.Methods Gene expression datasets from GEO(GSE30528,GSE30529)and RNA sequencing(RNA-seq)data from the Karolinska Kidney Research Center were used.Gene set enrichment analysis(GSEA)was conducted to examine differences in immune-related gene expression in the glomeruli and tubules(DKD)patients.To identify immune-related genes(IRGs)and TFs,differential expression analysis was carried out using the Limma and DESeq2 software packages.Key immune-related TFs were pinpointed through co-expression analysis.The interaction network between TFs and IRGs was constructed using the STRING database and Cytoscape software.Furthermore,the Nephroseq database was employed to investigate the correlation between the identified TFs and clinical-pathological features.Results When compared to normal control tissues,significant differences in the expression of immune genes were observed in both the glomeruli and tubules of individuals with Diabetic Kidney Disease(DKD).Through differential and co-expression analysis,50 immune genes and 9 immune-related transcription factors(TFs)were identified in the glomeruli.In contrast,131 immune response genes(IRGs)and 41 immune-related TFs were discovered in the renal tubules.The protein-protein interaction(PPI)network highlighted four key immune-related TFs for the glomeruli:Interferon regulatory factor 8(IRF8),lactotransferrin(LTF),CCAAT/enhancer binding protein alpha(CEBPA),and Runt-related transcription factor 3(RUNX3).For the renal tubules,the key immune-related TFs were FBJ murine osteosarcoma viral oncogene homolog B(FOSB),nuclear receptor subfamily 4 group A member 1(NR4A1),IRF8,and signal transducer and activator of transcription 1(STAT1).These identified TFs demonstrated a significant correlation with the glomerular filtration rate(GFR),highlighting their potential importance in the pathology of DKD.Conclusion Bioinformatics analysis identifies potential genes associated with DKD pathogenesis and immune dysregulation.Further validation of the expression and function of these genes may contribute to immune-based therapeutic research for DKD.