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中华脑科疾病与康复杂志(电子版) ›› 2025, Vol. 15 ›› Issue (03) : 171 -179. doi: 10.3877/cma.j.issn.2095-123X.2025.03.006

临床研究

基于生物信息学和机器学习探究前庭神经鞘瘤生物标志物在免疫微环境中的相关功能
夏炎, 朱帅帅, 张岩松()   
  1. 210029 南京,南京医科大学附属脑科医院神经外科
  • 收稿日期:2025-03-13 出版日期:2025-06-15
  • 通信作者: 张岩松

Exploring the functional relevance of biomarkers in the immune microenvironment of vestibular schwannomas using bioinformatics and machine learning

Yan Xia, Shuaishuai Zhu, Yansong Zhang()   

  1. Department of Neurosurgery, Brain Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
  • Received:2025-03-13 Published:2025-06-15
  • Corresponding author: Yansong Zhang
  • Supported by:
    Nanjing Health Youth Talent Training Program(QRX11010)
引用本文:

夏炎, 朱帅帅, 张岩松. 基于生物信息学和机器学习探究前庭神经鞘瘤生物标志物在免疫微环境中的相关功能[J/OL]. 中华脑科疾病与康复杂志(电子版), 2025, 15(03): 171-179.

Yan Xia, Shuaishuai Zhu, Yansong Zhang. Exploring the functional relevance of biomarkers in the immune microenvironment of vestibular schwannomas using bioinformatics and machine learning[J/OL]. Chinese Journal of Brain Diseases and Rehabilitation(Electronic Edition), 2025, 15(03): 171-179.

目的

结合生物信息学技术及机器学习技术筛选前庭神经鞘瘤(VS)相关的生物标志物,分析其在免疫微环境中的生物学功能与机制。

方法

从基因表达综合数据库(GEO)获取VS患者的信息(GSE56597和GSE39645),使用差异表达基因(DEGs)分析、加权基因共表达网络分析(WGCNA)获取特征基因。采用最小绝对收缩和选择算子(LASSO)回归、随机森林(RF)和Boruta算法3种机器学习策略进一步精确鉴定VS免疫微环境的生物标志物,并使用受试者工作特征(ROC)曲线评估其诊断价值。采用拟时序分析探究生物标志物在VS免疫微环境中的细胞分布和作用。

结果

(1)DEGs分析筛选出1331个VS的DEGs。(2)WGCNA分析筛选出7个与VS相关的基因模块,共2055个候选基因。(3)从DEGs和模块核心基因中筛选出了722个重叠基因,3种机器学习策略鉴定出4个特征基因,即C10orf11、NCAM2、MLLT4、PI16。(4)NCAM2、PI16、C10orf11和MLLT4在数据集(GSE56597)的ROC曲线下面积(AUC)分别为0.982、0.918、1、1,在验证集(GSE39645)的ROC的AUC分别为1、0.968、1、1。(5)单细胞数转录组测序数据集(GSE216783)分析结果显示,VS肿瘤微环境中具有不同的细胞簇,包括髓系细胞、自然杀伤细胞、非髓鞘化施万细胞等。NCAM2基因在非髓鞘化施万细胞中的表达水平与分布密度均较高。(6)对单细胞数据中NCAM2+和NCAM2-施万细胞进行拟时序分析,结果显示NCAM2+施万细胞具有更强的分化能力,而且细胞通信分析发现NCAM2+细胞通过MIF-(CD74+CD44)和MIF-(CD74+CXCR4)受体配体对与其他细胞类型建立稳定的联系。

结论

C10orf11、NCAM2、MLLT4和PI16是VS的生物学标志物,在免疫微环境中发挥作用并具有诊断价值。

Objective

To identify biomarkers associated with vestibular schwannomas (VS) by integrating bioinformatics and machine learning techniques, and to investigate their biological functions and mechanisms within the immune microenvironment.

Methods

VS patient data (GSE56597 and GSE39645) were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA) were employed to identify feature genes. Least absolute shrinkage and selection operator (LASSO) regression, random forest (RF) and Boruta algorithm were applied to precisely identify VS immune microenvironment biomarkers. Diagnostic value was evaluated using receiver operating characteristic (ROC) curve analysis. Pseudotime trajectory analysis was performed to explore the cellular distribution and functional roles of these biomarkers.

Results

(1) DEGs analysis identified 1331 VS-associated DEGs. (2) WGCNA screened seven gene modules related to VS, yielding 2055 candidate genes. (3) From the overlapping DEGs and module hub genes, 722 genes were selected. LASSO regression, Boruta, and RF algorithms identified four signature genes (C10orf11, NCAM2, MLLT4, PI16). (4) In dataset GSE56597, the area under the ROC curve (AUC) values for NCAM2, PI16, C10orf11, and MLLT4 were 0.982, 0.918, 1, and 1, respectively. In validation set GSE39645, the AUCs were 1, 0.968, 1, and 1. (5) Single-cell RNA sequencing (GSE216783) revealed heterogeneous cell clusters in the VS tumor microenvironment, including myeloid cells, natural killer cells, non-myelinating Schwann cells, fibroblasts, myelinating Schwann cells, circulating cells, and B cells/plasma cells, all contributing to tumor progression. NCAM2 exhibited high expression and density in non-myelinating Schwann cells. (6) Pseudotime analysis of single-cell RNA sequencing data revealed that NCAM2+ Schwann cells exhibit enhanced differentiation capacity compared to NCAM2-counterparts. Further cell-cell communication analysis and pathway enrichment analysis demonstrated that NCAM2+ Schwann cells establish robust interactions with other cell types through MIF-(CD74+CD44) and MIF-(CD74+CXCR4) ligand-receptor pairs, indicating more active intercellular communication.

Conclusions

C10orf11, NCAM2, MLLT4, and PI16 were identified as biomarkers of VS, demonstrating significant roles in the immune microenvironment and high diagnostic value.

图1 差异基因表达分析筛选对照组与VS组的差异基因A:主成分分析图;B:基因表达火山图;C:基因表达热图;VS:前庭神经鞘瘤
Fig.1 Differential gene expression analysis between the control group and the VS group
图2 加权相关网络分析筛选的数据集GSE56597中VS相关基因模块间相关性热图红色表示正相关,蓝色表示负相关;VS:前庭神经鞘瘤
Fig.2 Heatmap of correlation between VS-associated gene modules in the GSE56597 dataset screened by weighted gene co-expression network analysis
图3 对722个重叠基因进行LASSO回归分析、RF算法及Boruta算法分析筛选最优特征基因A:差异表达基因与WGCNA模块基因的交集Venn图;B:LASSO回归系数图,左侧图中的每条系数曲线代表一个单独的基因,右侧图中的实线垂直线表示部分似然偏差,曲线最低点对应的基因数量(n=15)为LASSO最适合的特征基因;C:随机森林中重叠候选基因的相对重要性计算(前42个基因的权重>0);D:Boruta算法分析图,绿色框表示确认的231个重要特征;E:LASSO、随机森林和Boruta算法共同筛选最优特征基因Venn图;VS:前庭神经鞘瘤
Fig.3 Screening of optimal feature genes from 722 overlapping genes using LASSO regression, random forest, and Boruta algorithms
图4 训练集中2组样本特征基因C10orf11、MLLT4、NCAM2和PI16的表达A:C10orf11;B:MLLT4;C:NCAM2;D:PI16;2组比较,P<0.05;VS:前庭神经鞘瘤
Fig.4 Expression of feature genes C10orf11, MLLT4, NCAM2 and PI16 in two groups of samples in the training set
图5 外部验证数据集中2组样本特征基因C10orf11、MLLT4、NCAM2和PI16的表达A:C10orf11;B:MLLT4;C:NCAM2;D:PI16;2组比较,P<0.05;VS:前庭神经鞘瘤
Fig.5 Expression of feature genes C10orf11, MLLT4, NCAM2 and PI16 in two groups of samples in the external validation dataset
图6 单细胞RNA测序数据降维及可视化分析A:21个细胞簇的UMAP非线性降维图;B:细胞注释揭示了10种不同的细胞表型;C:4种标记基因表达水平的UMAP降维可视化图;D:4种标记基因密度的UMAP降维可视化图
Fig.6 Single-cell RNA sequencing data dimensionality reduction and visualization analysis
图7 VS免疫微环境单细胞测序数据的轨迹分析和细胞通信分析A~D:NCAM2+和NCAM2-非髓鞘化施万细胞的拟时间轨迹分析图(A)、Y型拟时间分布图(B)、三状态分布图(C)、分化潜能图谱(D);E:细胞轨迹与表型双散点图,NCAM2+非髓鞘化施万细胞定位分化成熟区,NCAM2-定位低分化区;F:NCAM2+、NCAM2-细胞在肿瘤作用下与不同细胞的配体-受体相互作用;G:不同类型细胞作用于NCAM2+、NCAM2-细胞中的肿瘤性配体-受体相互作用
Fig.7 Single-cell sequencing data analysis of VS immune microenvironment: trajectory inference and cell-cell communication
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