叶海婷, 杨定平, 李鹏艳. 基于生物信息学分析急性肾损伤关键基因及靶向中药筛选[J]. 临床肾脏病杂志, 2024, 24(8): 667-676. DOI: 10.3969/j.issn.1671-2390.2024.08.008
    引用本文: 叶海婷, 杨定平, 李鹏艳. 基于生物信息学分析急性肾损伤关键基因及靶向中药筛选[J]. 临床肾脏病杂志, 2024, 24(8): 667-676. DOI: 10.3969/j.issn.1671-2390.2024.08.008
    Ye Hai-ting, Yang Ding-ping, Li Peng-yan. Key genes and targeted traditional Chinese medicine screening for acute kidney injury based upon bioinformatics[J]. Journal of Clinical Nephrology, 2024, 24(8): 667-676. DOI: 10.3969/j.issn.1671-2390.2024.08.008
    Citation: Ye Hai-ting, Yang Ding-ping, Li Peng-yan. Key genes and targeted traditional Chinese medicine screening for acute kidney injury based upon bioinformatics[J]. Journal of Clinical Nephrology, 2024, 24(8): 667-676. DOI: 10.3969/j.issn.1671-2390.2024.08.008

    基于生物信息学分析急性肾损伤关键基因及靶向中药筛选

    Key genes and targeted traditional Chinese medicine screening for acute kidney injury based upon bioinformatics

    • 摘要:
      目的  为深入了解急性肾损伤(acute kidney injury,AKI)发生的分子机制和探索AKI的中药防治策略,本研究利用生物信息学方法分析了AKI的关键基因,并预测了具有防治作用的中药。
      方法  从基因表达综合数据库(gene expression omnibus database,GEO)下载AKI基因芯片数据集GSE30718并利用GEO2R 在线工具分析, 同时从比较毒理基因组学数据库(comparative toxicogenomics database,CTD)下载AKI的作用靶点,取二者交集即为AKI的差异表达基因(differential expression genes,DEGs);对DEGs进行富集分析和蛋白质相互作用分析,并运用Cytoscape软件计算关键基因;然后利用医学信息检索平台(Coremine Medical)检索关键基因对应的中药,统计出现频次最高的中药,再利用BATMAN-TCM数据库进一步分析其治疗AKI的分子机制。
      结果  该研究共获得了206个DEGs,生物学功能富集分析提示这些DEGs主要与细胞外基质、免疫炎症反应和转录调控有关; FN1ALBCOL1A1 JUNTGFB1FOSPXDNCOL1A2EGFTIMP1 是AKI的关键基因,由此获得可能用于治疗AKI的中药有丹参、人参、当归、三七等;其中以丹参出现频次最高,其治疗AKI的主要信号通路为磷脂酰肌醇3激酶/蛋白激酶B信号通路。
      结论  本研究利用生物信息学工具和方法初步筛选了参与AKI的10个关键基因以及相关防治中药,并具体分析了丹参治疗AKI的分子机制,为AKI的临床治疗提供了新思路,也为后续科研提供了理论依据。

       

      Abstract:
      Objective  To gain a deeper understanding of molecular mechanisms underlying acute kidney injury (AKI), explore traditional Chinese medicine strategies for managing AKI, employ bioinformatics to analyze key genes associated with AKI and predict potential Chinese herbal medicines with therapeutic effects.
      Methods  The AKI gene expression microarray dataset GSE30718 were downloaded from the database of Gene Expression Omnibus (GEO) and GEO2R online tool was utilized for analysis. Simultaneously, AKI target genes were obtained from the Comparative Toxicogenomics Database (CTD) and the intersection of these datasets yielded the differential expression genes (DEGs) associated with AKI. Enrichment analysis and protein-protein interaction analysis were performed on DEGs. Cytoscape software was employed for identifying key genes. Subsequently, a medical information retrieval platform (Coremine Medical) was utilized for searching for traditional Chinese medicines corresponding to these key genes with the most frequently occurring ones identified. Then the database of BATMAN-TCM was employed for detailed analysis of molecular mechanisms involved in their therapeutic effects on AKI.
      Results  For 206 DEGs, functional enrichment analysis confirmed their involvements in extracellular matrix regulation, immune-inflammatory responses and transcriptional regulation. FN1, Alb, COL1A1, JUN, TGFB1, FOS, PXDN, COL1A2, EGF and TIMP1 were identified as key genes for AKI. The potential traditional Chinese medicines for treating AKI included Danshen (Salvia Miltiorrhiza), Renshen (Radix Ginseng), Danggui (Angelica Sinensis) and Sanqi (Radix Notoginseng). And Danshen had the highest frequency. The primary signaling pathway associated with Danshen's therapeutic effects on AKI was signaling pathway of phosphatidylinositide 3-kinase/protein kinase B (PI3K/AKT).
      Conclusion  This study has identified 10 key genes involved in AKI and their associated traditional Chinese medicines. Specific analysis of Danshen's molecular mechanisms in treating AKI provides new insights for clinical interventions and establishes theoretical rationales for subsequent researches.

       

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