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整合生物信息学和机器学习算法筛选心房颤动炎性标志物与验证

Integrating Bioinformatics and Machine Learning Algorithms to Screen Inflammatory Biomarkers for Atrial Fibrillation and Experimental Validation

    摘要
  • 摘要:
    目的 通过整合生物信息学和机器学习算法及实验研究，筛选并鉴定心房颤动（AF）的潜在生物标志物。
    方法 从GEO和MSigDB数据库中获取AF转录组学并筛选差异表达基因（DEGs），从炎症相关基因集（IRGs）。取交集形成DE-IRGs基因集。采用机器学习算法过滤AF相关DE-IRGs基因后获得特征基因。取12只SPF级雄性SD大鼠，分为对照组和AF组。其中AF组大鼠连续5周尾静脉注射乙酰胆碱（66 μg/mL）和氯化钙（10 mg/kg）构建AF模型；HE染色观察心房肌细胞形态特征、RT-qPCR和免疫组织化学染色测定特征基因表达mRNA和蛋白质变化。
    结果 训练集发现119个DEGs，IRGs与两个共表达模块相关性最高（r=0.6和0.56，P<0.0001）。DEGs与IRGs取交集获得9个DE-IRGs；SVM-RFE和RF算法筛选出的4个特征基因5羟色胺受体2B基因（ 5-hydroxytryptamine receptor 2B gene, HTR2B）、潜在转化生长因子β结合蛋白 2基因（latent-transforming growth factor beta-binding protein 2 gene, LTBP2）、基质重塑关联蛋白5基因（matrix remodeling associated protein 5 gene, MXRA5）和转化生长因子β诱导蛋白基因（transforming growth factor β-induced protein gene, TGFBI）在训练集和验证集AF组均呈高表达且诊断效能较高（AUC>0.77）。AF大鼠心电图肢体导联出现大量AF特征性f波。HE染色显示AF组心房肌细胞排列紊乱、炎性细胞浸润。TUNEL荧光检测AF组凋亡率为（55.34±4.29）%，而对照组为（8.69±3.12）%（P=0.0001）。LTBP2和TGFBI基因相对表达量在AF组（4.97±4.20，2.62±1.85）和对照组（1.12±0.21，1.18±0.77）间差异存在统计学意义（P=0.0137，P=0.0444）。免疫组织化学染色检测AF组LTBP2和TGFBI蛋白阳性率分别为（36.50±1.31）%和（27.39±4.57）%，而对照组分别是（22.95±2.62）%和（18.26±3.70）%（P=0.0008，P=0.0485）。
    结论 特征基因LTBP2和TGFBI在AF中高表达，且较有诊断价值的生物标志物。

     

    Abstract:
    Objective To identify potential biomarkers of atrial fibrillation (AF) using bioinformatics, machine learning (ML) and experimental methods.
    Methods AF transcriptomic data were obtained from the GEO and MSigDB databases to screen for differentially expressed genes (DEGs) and inflammation-related gene sets (IRGs). The overlap between DEGs and IRGs was used to identify the DE-IRGs set. Two machine learning algorithms were used to filter AF-related DE-IRGs. Twelve male SD rats were randomly divided into a control group and an AF group. Rats received acetylcholine (66 μg/mL) and calcium chloride (10 mg/kg) via tail vein injection for five consecutive weeks to establish the AF model. Morphological characteristics of atrial myocytes were assessed with HE staining, while RT-qPCR and immunohistochemistry (IHC) were used to measure changes in mRNA and protein levels.
    Results In the training set, 119 DEGs were identified, with IRGs showing the highest correlation with two co-expression modules (r = 0.60 and 0.56, P < 0.0001). The intersection of DEGs and IRGs yielded nine DE-IRGs. The SVM-RFE and RF algorithms identified 5-hydroxytryptamine receptor 2B gene (HTR2B), latent-transforming growth factor beta-binding protein 2 gene (LTBP2), matrix remodeling associated protein 5 gene ( MXRA5), and transforming growth factor β-induced protein gene (TGFBI) as highly expressed in both the training and test sets in AF groups with high diagnostic efficacy (AUC > 0.77). The electrocardiogram limb leads of AF rats showed numerous f-waves. HE staining revealed disorganized atrial myocyte arrangement and inflammatory cell infiltration in the AF group. The TUNEL fluorescence assay showed an apoptosis rate of (55.34 ± 4.29)% in the AF group, compared to (8.69 ± 3.12)% in the control group (P = 0.0001). There were statistically significant differences in the relative expression levels of LTBP2 and TGFBI between the AF group (4.97 ± 4.20, 2.62 ± 1.85) and the control group (1.12 ± 0.21, 1.18 ± 0.77) (P = 0.0137, P = 0.0444). IHC revealed positive rates of LTBP2 and TGFBI proteins in the AF group of (36.50 ± 1.31)% and (27.39 ± 4.57)%, respectively, compared to (22.95 ± 2.62)% and (18.26 ± 3.70)% in the control group (P = 0.0008, P = 0.0485).
    Conclusion The characteristic genes LTBP2 and TGFBI are highly expressed in AF and serve as valuable diagnostic biomarkers.

     

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