基于生物信息学分析ApoE-ε4-/+阿尔茨海默病Braak分级的差异基因及其潜在治疗靶点

Differential genes and potential therapeutic targets of ApoE-ε4-/+Alzheimer's disease Braak grading based on bioinformatics analysis

目的比较载脂蛋白E(ApoE)-ε4阳性与ApoE-ε4阴性的阿尔茨海默病(AD)患者在braak不同阶段的差异表达特征,筛选ApoE-ε4+AD的治疗靶点。方法从基因表达综合数据库(GEO)下载数据集GSE29652,利用R语言比较分析基因表达情况,筛选差异表达基因(DEGs);利用STRING数据库和Cytoscape软件进行蛋白互作网络分析及关键靶基因的筛查;利用基因本体功能注释(GO)和京都基因与基因组百科全书通路富集分析(KEGG)差异表达基因进行功能富集及通路分析。结果AD患者BraakⅠ~Ⅱ阶段筛选出ApoE-ε4阴性与ApoE-ε4阳性相关的差异表达基因共1417个,基于多种算法得到6个关键靶基因,分别为TNF、IL17A、CD8A、IL7R、TLR2、IL18;其中IL7R显著下调(P<0.05),TLR2和CD8A显著上调(P<0.05);GO和KEGG分析显示3个靶基因主要富集在淋巴细胞介导的免疫、细胞膜传递、NAD+核苷酶活性等,涉及原发性免疫缺陷、抗原处理和呈递、PI3K-Akt等信号通路。BraakⅢ~Ⅳ阶段筛选出ApoE-ε4阴性与ApoE-ε4阳性的差异表达基因共1050个,基于多种算法得到5个关键靶基因,分别为IGF1、LEP、PTGS2、INS、PTPN11;其中,PTPN11呈上调趋势(P<0.05);GO和KEGG分析显示其功能富集主要为ERK1和ERK2级联、肽基酪氨酸磷酸化、激素分泌的调节、蛋白酪氨酸激酶和激素受体结合等方面,涉及JAK-STAT和Ras信号通路。BraakⅤ~Ⅵ阶段,筛选出ApoE-ε4阴性与ApoE-ε4阳性相关的差异表达基因共364个,基于Degree算法得到12个关键靶基因,其中RAC1显著下调(P<0.05),MYH6显著上调(P<0.05);GO和KEGG分析显示2个靶基因主要富集在肌动蛋白丝聚合、钙调素结合等,涉及细胞凋亡等信号通路。结论AD早期阶段,ApoE-ε4可能与调控TLR2、IL7R和CD8A基因促进早期炎症有关;中期阶段,ApoE-ε4可导致PTPN11基因依赖的激素功能失调加速AD病理;AD晚期阶段,ApoE-ε4可能与RAC1和MYH6对钙离子调控密切相关。

Objective To compare the differential genes in different stages of Braak between apolipoprotein E(ApoE)-ε4 positive and ApoE-ε4 negative Alzheimer's disease(AD)patients.To provide important targets for blocking the pathological progression of AD patients carrying ApoE-ε4.Methods Download the dataset GSE29652 from the Gene Expression Integrated Database(GEO)and use R language to identify differentially expressed genes(DEGs).Using STRING database and Cytoscape software for protein interaction network analysis and screening of key target genes.Perform functional enrichment and pathway analysis of key target genes using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes.Results A total of one thousand four hundred and seventeen differentially expressed genes related to ApoE-ε4 negative and ApoE-ε4 positive were screened for BraakⅠ-Ⅱstage in AD patients.Six key target genes were obtained based on multiple algorithms:TNF、IL17A、CD8A、IL7R、TLR2、IL18.Among them,IL7R was significantly down regulated(P<0.05),TLR2 and CD8A were significantly upregulated(P<0.05).GO and KEGG analysis showed that the three target genes were mainly enriched in lymphocyte-mediated immunity,cell membrane transmission,NAD+nucleosidase activity,and involved signaling pathways such as primary immunodeficiency,antigen processing and presentation,and PI3K-Akt signal pathway,and so on.During the BraakⅢ-Ⅳstage,one thousand and fifty differentially expressed genes were screened for ApoE-ε4 negative and ApoE-ε4 positive,and five key target genes were obtained based on multiple algorithms:IGF1、LEP、PTGS2、INS and PTPN11.Among them,PTPN11 was significantly upregulated(P<0.05).GO and KEGG analysis showed that its functional enrichment is mainly related to the ERK1 and ERK2 cascade,peptidyl-tyrosine phosphorylation,regulation of hormone secretion,protein tyrosine kinase and hormone receptor binding,involving the JAK-STAT and Ras signaling pathways.In the BraakⅤ-Ⅵstage,a total of three hundred and sixty-four differentially expressed genes related to ApoE-ε4 negative and ApoE-ε4 positive were screened.Based on the Degree algorithm,twelve key target genes were obtained,among which RAC1 was significantly downregulated(P<0.05)and MYH6 was significantly upregulated(P<0.05).GO and KEGG analysis showed that the two target genes were mainly enriched in actin filament polymerization and calmodulin binding,involving signaling pathways such as cell apoptosis.Conclusion In the early stages,ApoE-ε4 mainly promotes early inflammation by regulating TLR2、IL7R and CD8A genes.In the mid-term stage,ApoE-ε4 can lead to hormone dysfunction dependent on PTPN11 gene and accelerate AD pathology.In the late stage of AD,ApoE-ε4 may be closely related to the regulation of calcium ions by RAC1 and MYH6.