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基于生物信息学方法探讨非酒精性脂肪性肝炎免疫浸润特征及风险模型构建

Study on Immune Infiltration Characteristics and Risk Model of Non-alcoholic Steatohepatitis Based on Bioinformatics

  • 摘要: 非酒精性脂肪性肝炎(non-alcoholic steatohepatitis,NASH)已成为严重影响患者生活质量和预期寿命的肝脏疾病,且发病机制复杂。为探讨免疫浸润在NASH发病机制中的作用,从高通量基因表达(gene expression omnibus, GEO)数据库中下载肝脏单纯性脂肪变性(simple steatosis, SS)、 NASH和健康受试者的数据集。使用R limma软件包对差异表达基因(differentially expressed genes, DEGs)进行筛选。通过功能注释和富集分析探讨DEGs的生物学功能。用无监督的一致性聚类及单样本基因集富集分析(single sample gene set enrichment analysis, ssGSEA)观察聚类模式所对应的免疫浸润类型。结果共获得1 569个DEGs,以及与NASH进展相关或不相关的两种修饰模式A、 B。模式B相较模式A对应较高的肝纤维化程度、小叶炎症程度、气球样变程度以及非酒精性脂肪性肝病(non-alcoholic fatty liver disease, NAFLD)活动度评分。ssGSEA结果显示,具有免疫应答或促炎功能的细胞以及免疫抑制作用的细胞均在模式B中富集。基因集变异分析(gene set variation analysis, GSVA)结果显示模式B富集了细胞黏附分子等免疫相关通路及神经鞘脂质代谢等代谢相关通路。最后通过多元逐步Cox回归分析确定了5个核心基因用于风险模型的构建,预测模型训练集和验证集的AUC(area under curve)值分别为0.982和0.987。本研究结果有助于更深入地了解NASH的发病机制,且为临床预测NASH的发病风险提供参考。

     

    Abstract: Non-alcoholic steatohepatitis(NASH) has come to be a liver disease that seriously affects the quality of life and life expec-tancy of patients, and its pathogenesis is complex. To investigate the role of immune infiltration in the pathogenesis of NASH, data sets for hepatic simple steatosis(SS), NASH, and healthy subjects were downloaded from the high-through put gene expression omnibus(GEO) database. Differentially expressed genes(DEGs) were identified by using R software limma package. The biological function was discussed by functional annotation and enrichment analysis. The immune infiltration types corresponding to clustering patterns were observed by using unsupervised consistency clustering and single sample gene set enrichment analysis(ssGSEA). A total of 1 569 DEGs were obtained, and two modification patterns A and B were obtained via univariate regression evaluation and cluster analysis. The degree of hepatic fibrosis, lobular inflammation, ballooning degeneration and non-alcoholic fatty liver disease(NAFLD) activity score in pattern B were greater than these in pattern A. ssGSEA results showed that cells with immune response or pro-inflammatory function, as well as immunosuppressive cells were enriched in pattern B. Gene set variation analysis(GSVA) results showed that immune-related pathways such as cell adhesion molecules and metabolic pathways such as sphingolipid metabolism were enriched in pattern B. Finally, 5 core genes were determined by multiple stepwise Cox regression analysis to construct the hazard model. The AUC(area under curve) value of the training set and verification set of the prediction model were 0.982 and 0.987 respectively. These findings are helpful to have a deeper understanding of the pathophysiological mechanism of NASH and provide reference form edical prediction of the risk of NASH.

     

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