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酒精性肝炎自噬关键基因的筛选及生物信息学分析

袁超, 练庆海, 尼贝贝, 等. 酒精性肝炎自噬关键基因的筛选及生物信息学分析[J]. 器官移植, 2024, 15(1): 90-101. doi: 10.3969/j.issn.1674-7445.2023163
引用本文: 袁超, 练庆海, 尼贝贝, 等. 酒精性肝炎自噬关键基因的筛选及生物信息学分析[J]. 器官移植, 2024, 15(1): 90-101. doi: 10.3969/j.issn.1674-7445.2023163
Yuan Chao, Lian Qinghai, Ni Beibei, et al. Screening and bioinformatics analysis of key autophagy-related genes in alcoholic hepatitis[J]. ORGAN TRANSPLANTATION, 2024, 15(1): 90-101. doi: 10.3969/j.issn.1674-7445.2023163
Citation: Yuan Chao, Lian Qinghai, Ni Beibei, et al. Screening and bioinformatics analysis of key autophagy-related genes in alcoholic hepatitis[J]. ORGAN TRANSPLANTATION, 2024, 15(1): 90-101. doi: 10.3969/j.issn.1674-7445.2023163

酒精性肝炎自噬关键基因的筛选及生物信息学分析

doi: 10.3969/j.issn.1674-7445.2023163
基金项目: 广东省自然科学基金面上项目(2019A1515011850、2022A1515012224)
详细信息
    作者简介:
    通讯作者:

    张彤(ORCID 0000-0001-7602-3856),博士,主任医师,研究方向为肝移植,Email:zhjeff72@sina.com

  • 中图分类号: R617, R318.04

Screening and bioinformatics analysis of key autophagy-related genes in alcoholic hepatitis

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  • 摘要:   目的   筛选酒精性肝炎(AH)的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。  方法  采用基因表达综合数据库(GEO)中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析(WGCNA)获取关键基因。对筛选的关键基因进行基因本体(GO)、京都基因和基因组百科全书(KEGG)功能富集分析,蛋白质相互作用(PPI)分析,免疫浸润分析,构建信使RNA(mRNA)-微小RNA(miRNA)网络,进行酒精性肝病不同分期的自噬相关关键基因的表达差异分析,并进一步通过实时荧光定量逆转录聚合酶链反应(RT-qPCR)在AH患者和小鼠肝脏组织中验证。  结果  本研究筛选得到了11个与AH自噬相关的基因(EEF1A2、CFTR、SOX4、TREM2、CTHRC1、HSPB8、TUBB3、PRKAA2、RNASE1、MTCL1、HGF),均为上调基因。在AH患者和小鼠肝脏组织中,SOX4、TREM2、HSPB8、PRKAA2在AH组中的相对表达量均高于对照组。  结论  SOX4、TREM2、HSPB8、PRKAA2可能是AH潜在的生物标志物和治疗靶点。

     

  • 图  1  AH相关关键基因的筛选

    注:A图为GSE28619的PCA结果;B图为GSE142530的PCA结果;C图为火山图显示GSE28619中的DEG;D图为火山图显示GSE142530中的DEG;E图为GSE28619数据集中所有基因的树状图基于不同度量聚类(1-TOM);F图为GSE142530数据集中所有基因的树状图基于不同度量聚类(1-TOM);G图为GSE28619数据集中基因聚类模块与AH相关性的热图;H图为GSE142530数据集中基因聚类模块与AH的热图。

    Figure  1.  Screening of key genes associated with AH

    图  2  AH中ARG的筛选及功能分析

    注:A图为AH和自噬相关基因的重叠的韦恩图;B图为GSE28619中DEARG的热图;C图为GSE142530中DEARG的热图;D图示DEARG在染色体上的位置;E图为PPI图;F图为KEGG相关通路分析;G、H、I图分别示生物过程、细胞组分、分子功能的KEGG分析。

    Figure  2.  Screening and functional analysis of ARG associated with AH

    图  3  免疫浸润分析-ssGSEA算法

    注:A图为每个样本中免疫细胞含量叠加图;B图示免疫细胞之间的相关性;C图为免疫细胞含量直方图,与对照组比较,aP<0.05;D图为AH患者中的11个关键基因与免疫细胞含量的相关性分析,*P<0.05,**P<0.01,***P<0.001。

    Figure  3.  Immune infiltration analysis-ssGSEA algorithm

    图  4  免疫浸润分析-CIBERSORT算法

    注:A图为每个样本中免疫细胞含量叠加柱状图;B图示免疫细胞之间的相关性;C图为免疫细胞含量直方图,与对照组比较,aP<0.05;D图为AH患者中的11个关键基因与免疫细胞含量的相关性分析,*P<0.05,**P<0.01,***P<0.001。

    Figure  4.  Immune infiltration analysis-CIBERSORT algorithm

    图  5  GSE155907、GSE143318数据集验证和AH不同分期的基因表达

    注:A图为GSE155907数据集PCA的结果图;B图示GSE155907数据集火山图验证了11个基因均上调;C图为GSE155907数据集中11个基因表达情况箱形图;D图为GSE143318数据集PCA的结果图;E图示GSE143318数据集火山图验证了11个基因均上调;F图为GSE143318数据集中11个基因表达情况箱形图;G~P图示酒精性肝病不同分期的10种hub基因表达;与对照组比较,aP<0.05;与酒精性脂肪变性比较,bP<0.05;与急性AH比较,cP<0.05。

    Figure  5.  Datasets validation of GSE155907 and GSE143318 and gene expression of AH at different stages

    图  6  mRNA-miRNA和mRNA-TF网络图

    注:A图为mRNA-miRNA网络图;B图为描述miRNA和通路相关性的热图。

    Figure  6.  mRNA-miRNA and mRNA-TF network diagram

    图  7  RT-qPCR验证结果

    注:A图为RT-qPCR检测AH组(5例)与对照组(6例)患者肝脏组织中hub基因相对表达水平;B图为RT-qPCR检测AH组(8只)与对照组(8只)小鼠肝脏组织中hub基因相对表达水平;与对照组比较,aP<0.05。

    Figure  7.  Results of RT-qPCR validation

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出版历程
  • 收稿日期:  2023-08-24
  • 录用日期:  2023-11-10
  • 网络出版日期:  2023-11-29
  • 刊出日期:  2024-01-11

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