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《中华肺部疾病杂志》[ISSN:1006-6977/CN:61-1281/TN]

卷:

期数:

2024年03期

页码:

356-362

栏目:

论著

出版日期:

2024-06-25

文章信息/Info

Title:

Significance of extracellular matrix associated markers and fibroblasts in the progression of pulmonary arterial hypertension

作者:

朱佑君¹; 付万垒²; 毛 杨³; 李德峰³

400037 重庆,陆军(第三)军医大学第二附属医院心内科¹、病理科²、临床医学研究中心³

Author(s):

Zhu Youjun¹;  Fu Wanlei²;  Mao Yang³;  Li Defeng³.

¹Department of Cardiology, Second Affiliated Hospital of Army Medical University, Chongqing 400037, China; ²Department of Pathology, Second Affiliated Hospital of Army Medical University, Chongqing 400037, China; ³Clinical Medical Research Center, Second Affiliated Hospital of Army Medical University, Chongqing 400037, China

关键词:

肺动脉高压;  差异表达基因;  细胞拟时序;  细胞通讯

Keywords:

Pulmonary arterial hypertension;  Differentially expressed genes;  Cell pseudotime;  Cell communication

分类号:

R563

DOI:

10.3877/cma.j.issn.1674-6902.2024.03.003

摘要:

目的 本文通过分析高通量基因表达及单细胞RNA测序数据,探讨肺动脉高压(pulmonaryarterial hypertension, PAH)患者组织中差异表达基因(differentially expressed genes, DEGs)及细胞间交流的特征,以揭示PAH的分子机制和细胞行为异质性。方法 从NCBI的GEO数据库下载基因表达数据集GSE244830和单细胞表达数据集GSE228644。使用limma包进行差异基因分析,clusterProfiler包进行功能富集分析。单细胞数据采用Seurat包和monocle包分析细胞分群和拟时序变化。利用CellChat包分析细胞间交流。所有分析在R语言环境下完成。结果 从GSE244830数据集中鉴定出81个显著的DEGs,其中70个在PAH组表现为上调,而11个则显示下调。明确PPI分析81个DEGs得到8个枢纽基因。富集结果显示差异基因主要涉及上皮细胞和内皮细胞的增殖等生物过程,参与调节糖蛋白的AGE-RAGE信号通路。单细胞细胞类型注释表明,16 430个细胞被划分为9个细胞类型,包括单核细胞、CD8⁺ T细胞、脂肪细胞、自然杀伤(natural killer cell, NK)细胞、内皮细胞、上皮细胞、成纤维细胞、造血干细胞和巨噬细胞。单细胞拟时序分析结果表明,在PAH进展过程中,多个基因被激活,涉及包括细胞黏附、细胞骨架稳定及细胞介导的免疫反应。细胞通讯结果显示,成纤维细胞与脂肪细胞是PAH发展过程中的主要通讯细胞,尤其在COLLAGEN信号传导方面。结论 细胞水平揭示PAH患者组织特异性的基因表达模式,为深入理解PAH的病理生理机制提供新的视角,有望为开发针对PAH治疗策略具有临床意义。

Abstract:

Objective This study aims to explore the characteristics of differentially expressed genes(DEGs)and intercellular communication in the tissues of patients with pulmonary arterial hypertension(PAH)by analyzing high-throughput gene expression and single-cell RNA sequencing data. The ultimate goal is to unveil the molecular mechanisms and cellular behavior heterogeneity associated with PAH. Methods Gene expression datasets GSE244830 and single-cell expression dataset GSE228644 were downloaded from the GEO databaseof NCBI. Differential gene analysis was carried out using the limma package, and functional enrichment analysis using the clusterProfiler package. Single-cell data were analyzed for cell clustering and pseudotime trajectories using the Seurat and monocle packages, respectively. Intercellular communication was assessed with the CellChat package. All analyses were performed in the R programming environment. Results From the GSE244830 dataset, 81 significant DEGs were identified, with 70 upregulated and 11 downregulated in the PAH group. Further PPI analysis identified 8 hub genes fromthe 81 DEGs. Enrichment results showed that the DEGs are primarily involved in biological processes such as proliferation of epithelial and endothelial cells and participate in the regulation of the glycoprotein-mediated AGE-RAGE signaling pathway. Single-cell type annotation revealed that 16,430 cells were classified into 9 cell types, including monocytes, CD8⁺ T cells, adipocytes, NK cells, endothelial cells, epithelial cells, fibroblasts, hematopoietic stem cells, and macrophages. The single-cell pseudotime analysis indicated activation of multiple genes during the progression of PAH, involving cellular adhesion, cytoskeletal stability, and cell-mediated immune response. The cell communication results highlighted that fibroblasts and adipocytes are the main communicative cells in the development of PAH, particularly in the COLLAGEN signaling pathway. Conclusion This study reveals tissue-specific gene expression patterns in PAH patients at the cellular level, providing new insights into the pathophysiological mechanisms of PAH, and holds potential clinical significance for developing targeted treatment strategies.

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备注/Memo

备注/Memo:

基金项目: 国家自然科学基金资助项目(82002446)
通信作者: 李德峰, Email: Ldf201407@tmmu.edu.cn

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更新日期/Last Update: 2024-06-25