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中华肺部疾病杂志(电子版)

中华肺部疾病杂志(电子版) ›› 2024, Vol. 17 ›› Issue (02) : 212 -217. doi: 10.3877/cma.j.issn.1674-6902.2024.02.008

论著

基于转录组学筛选特发性肺纤维化的枢纽基因和信号通路
邱凌霄1, 王创业1, 卿斌1, 刘锦程1, 张鑫烨2, 武文娟3, 邢德冰4, 郭亮1, 徐智1, 王斌1,†()   
  1. 1. 400037　重庆，陆军（第三）军医大学第二附属医院呼吸与危重症医学科
    2. 450052　郑州，郑州大学第一附属医院胸外科
    3. 450003　郑州，河南省人民医院老年医学科
    4. 400037　重庆，陆军（第三）军医大学第二附属医院中医科
  • 收稿日期:2023-11-23 出版日期:2024-04-25
  • 通信作者: 王斌
  • 基金资助:
    重庆市科卫联合医学科研项目(2020FYYX179); 陆军军医大学第二附属医院"青博计划"(2023YQB057)

Identifying hub genes and pathways in idiopathic pulmonary fibrosis based on transcriptomics

Lingxiao Qiu1, Chuangye Wang1, Bin Qing1, Jincheng Liu1, Xinye Zhang2, Wenjuan Wu3, Debing Xing4, Liang Guo1, Zhi Xu1, Bin Wang1,†()   

  1. 1. Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Army Medical University, Chongqing 400037, China
    2. Thoracic Surgery Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
    3. Department of Geriatrics, Henan Provincial People′s Hospital, Zhengzhou 450003, China
    4. Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Army Medical University, Chongqing 400037, China
  • Received:2023-11-23 Published:2024-04-25
  • Corresponding author: Bin Wang
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邱凌霄, 王创业, 卿斌, 刘锦程, 张鑫烨, 武文娟, 邢德冰, 郭亮, 徐智, 王斌. 基于转录组学筛选特发性肺纤维化的枢纽基因和信号通路[J]. 中华肺部疾病杂志(电子版), 2024, 17(02): 212-217.

Lingxiao Qiu, Chuangye Wang, Bin Qing, Jincheng Liu, Xinye Zhang, Wenjuan Wu, Debing Xing, Liang Guo, Zhi Xu, Bin Wang. Identifying hub genes and pathways in idiopathic pulmonary fibrosis based on transcriptomics[J]. Chinese Journal of Lung Diseases(Electronic Edition), 2024, 17(02): 212-217.

目的

基于转录组学数据筛选特发性肺纤维化(idiopathic pulmonary fibrosis, IPF)致病的枢纽基因和相关信号通路。

方法

从基因表达综合(gene expression omnibus, GEO)数据库中下载GSE17978数据集，应用GEO2R筛选差异表达基因(differentially expressed genes, DEGs)，采用R软件ggplot2包和Heatmap包分别绘制DEGs的火山图和热图。采用R软件的clusterProfiler包进行DEGs基因本体论(gene ontology, GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)通路分析。采用R软件中的ggplot2包绘制气泡图。运用STRING和Cytoscape软件构建DEGs的蛋白质互作网络，应用Cytoscape的Cytohubba插件筛选参与IPF发病的枢纽基因。采用GSE10667数据集验证DEGs的差异表达。

结果

共获得92个DEGs，其中上调基因49个，下调基因43个；GO分析和KEGG通路富集结果显示，DEGs主要在细胞外基质组织、胶原蛋白结合、PI3K-Akt信号通路及TGF-β信号通路等显著富集。运用STRING和cytoscape构建了DEGs的蛋白质互作网络，与IPF相关10个枢纽基因为FN1、CXCL12、DCN、COL1A1、MMP2、SPARC、SPP1、POSTN、COL1A2和COL3A1，其中9个枢纽基因在验证数据集GSE10667中有显著差异表达。

结论

获得的92个DEGs和9个枢纽基因可能是IPF潜在的生物标志物。

关键词: 特发性肺纤维化, 差异表达基因, 基因表达综合数据库
Objective

Based on transcriptomic data, identify hub genes and related signaling pathways involved in the pathogenesis of idiopathic pulmonary fibrosis (IPF).

Methods

GSE17978 dataset was downloaded from the GEO database. GEO2R tool was utilized to screen differentially expressed genes (DEGs). Ggplot2 package and Heatmap package in the R software were used to draw volcano maps and heat maps for DEGs. The R software clusterProfiler package was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis on DEGs. The R software ggplot2 package was used to draw bubble charts. Using STRING and Cytoscape software to construct a protein-protein interaction network of DEGs. Cytohubba plugin in Cytoscape was performed to screen the hub genes involved in IPF. The GSE10667 dataset was used to verify the hub genes of DEGs.

Results

A total of 92 DEGs were obtained, including 49 up-regulated genes and 43 down-regulated genes. GO analysis and KEGG pathway enrichment analysis showed that DEGs are mainly enriched in extracellular matrix organization, collagen-containing extracellular matrix, PI3K-Akt signaling pathway, and TGF-beta signaling pathway. Protein-protein interaction networks of DEGs was constructed using STRING and Cytoscape, and 10 hub genes(FN1, CXCL12, DCN, COL1A1, MMP2, SPARC, SPP1, POSTN, COL1A2 and COL3A1) related to IPF were identified. Among above 10 hub genes, 9 genes showed significant differential expression in the validation dataset GSE10667.

Conclusion

The obtained 92 DEGs and 9 hub genes may be potential biomarkers of IPF.

Key words: Idiopathic pulmonary fibrosis, Differentially expressed genes, Gene Expression Omnibus database
图1 GSE17978数据集中DEGs火山图。注：火山图中每个点代表一个基因，红色：差异上调基因，蓝色：差异下调基因，灰色：无差异表达基因，X轴：差异倍数取log2后数值，Y轴：校正后P值取－log10后数值
图2 GSE17978数据集中前20个DEGs热图。注：横坐标：差异表达蛋白；纵坐标：样本；红色：样本中高表达基因；蓝色：样本中低表达的基因；FN1：纤连蛋白1; ASPN：无孢蛋白；POSTN：骨膜素；CTHRC1：含有1的胶原三螺旋重复序列；BDKRB1:缓激肽B1受体；CNN1:钙蛋白酶1; LUM:光蛋白聚糖；COL1A2: Ⅰ型胶原α2链；COL1A1: Ⅰ型胶原α1链；THBS1：血小板反应蛋白1; FLT1: fms相关受体酪氨酸激酶1; IL1R2:白介素1受体2; THEDC1:油酰基ACP水解酶；IL18R1：白介素18受体1; DEFA3:防御素α3; ARG1：精氨酸酶1; S10:核糖体蛋白S10; MMP25：基质金属蛋白酶25; FHL2：四个半LIM域2; NUMA1：核有丝分裂器蛋白1
图3 GSE17978数据集中DEGs的GO及KEGG富集分析。注：A：BP富集分析结果；B：CC富集分析结果；C：MF富集分析结果；D：KEGG富集分析。圆圈大小代表富集基因的数量，圆圈颜色代表校正后P值；细胞外结构组织(extracellular structure organization)；细胞外基质组织(extracellular matrix organization)；白细胞迁移(leukocyte migration)；免疫系统过程的负调控(negative regulation of immune system process)；胶原原纤维组织(collagen fibril organization)；含有胶原的细胞外基质(collagen-containing extracellular matrix)；胶原三聚体(collagen trimer)；胶原三聚体复合物(complex of collagen trimers)；带状胶原原纤维(banded collagen fibril)；原纤维胶原三聚体(fibrillar collagen trimer)；细胞外基质结构成分(extracellular matrix structural constituent)；生长因子结合(growth factor binding)；细胞因子结合(cytokine binding)；胶原结合(collagen binding)；整合素结合(integrin binding)；PI3K-Akt信号通路(PI3K-Akt signaling pathway)；癌症中的蛋白聚糖(Proteoglycans in cancer)；阿米巴病(Amoebiasis)；TGF-β信号通路(TGF-beta signaling pathway)；ECM受体相互作用(ECM-receptor interaction)
图4 DEGs蛋白质互作网络及枢纽基因。注：每个圆圈代表一个基因，红色圆圈代表差异表达上调的基因，蓝色圆圈代表差异表达下调的基因，圆圈之间的直线代表基因编码的蛋白之间存在相互作用
图5 COL1A1、POSTN、COL1A2、COL3A1、MMP2、SPARC、CXCL12、SPP1、DCN、FN1在GSE10667数据集中表达情况。注：normal：正常肺组织组，IPF：特发性肺纤维化组织组。两组间比较采用t检验。ns，P>0.05；**，P<0.01；***，P<0.001。小提琴图中位于中间的横线标记均值，最上面横线和最下面横线分别标记正负标准差。COL1A1：Ⅰ型胶原α1链；POSTN:骨膜蛋白；COL1A2：Ⅰ型胶原α2链；COL3A1：Ⅲ型胶原α1链；MMP2：基质金属肽酶2；SPARC：富含半胱氨酸的酸性蛋白；CXCL12：趋化因子配体12；SPP1：分泌型磷蛋白1；DCN：核心蛋白聚糖；FN1：纤连蛋白1
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