Chen Haoran, Chen Xiaobing, Ding Jinqiu, Xue Haoyue, Tang Xinyi, Li Xiaomin, Xie Yongpeng
Kangda College of Nanjing Medical University, Lianyungang City, Jiangsu Province Zip Code 222000, China.
The Institute of Emergency Medicine of Lianyungang, Lianyungang City, Jiangsu Province Zip Code 222000, China.
Gene. 2025 Feb 5;936:149131. doi: 10.1016/j.gene.2024.149131. Epub 2024 Nov 30.
This study aims to find the gene expression profile specifically in basal cells from pulmonary acute respiratory distress syndrome (ARDSp) patients using single-cell level analysis.
Single nuclear RNA sequencing (snRNA-seq) data of lung samples, including 18 ARDSp participants and 7 healthy participants, were sourced from the GEO database (GSE171524). The differentially expressed genes (DEGs) were screened by | log2FC | >1 and P < 0.05. Functional enrichment was constructed via Gene Ontology (GO) analysis. Pathway enrichment was conducted via Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The protein-protein interaction (PPI) network of the DEGs was performed via the STRING database. Cytoscape software was employed to find hub genes. The hub genes were sequenced and validated via data set after constructing the rat model of ARDSp.
Using DESeq2 package, 299 genes were disclosed to be downregulated, while 228 were upregulated in ARDSp participants. GO analysis disclosed DEGs were enriched in processes like actin filament organization, regulation of small GTPase-mediated signal transduction, response to unfolded protein, wound healing, and response to oxygen levels. Meanwhile, KEGG analysis disclosed DEGs were involved in protein digestion and absorption, Th17 cell differentiation, iron death, and other biological effects. Ten hub genes, including FN1, HIF1A, HSP90AA1, SMAD3, FOS, CDKN2A, COL1A1, HSPA8, FLNA, and NFKBIA were highlighted based on their network centrality and biological significance. HIF1A, HSPA8, NFKBIA, and CDKN2A were differentially expressed in the validation dataset.
Basal cells in ARDSp exhibit significant changes in gene expression, with ten hub genes identified. Among them, four (HIF1A, HSPA8, NFKBIA, CDKN2A) were validated experimentally using RNA-Seq data from an ARDSp rat model. This study emphasizes the role of basal cells in ARDSp, highlighting the altered gene networks involved in repair and inflammatory responses, providing potential targets for further therapeutic exploration. These findings suggest that alterations in these hub genes may be crucial to basal cell-driven inflammatory and reparative responses in ARDSp.
本研究旨在通过单细胞水平分析，找出肺急性呼吸窘迫综合征（ARDSp）患者基底细胞中的基因表达谱。
从基因表达综合数据库（GEO数据库，GSE171524）获取肺样本的单核RNA测序（snRNA-seq）数据，其中包括18名ARDSp参与者和7名健康参与者。通过| log2FC | >1且P < 0.05筛选差异表达基因（DEGs）。通过基因本体论（GO）分析进行功能富集。通过京都基因与基因组百科全书（KEGG）分析进行通路富集。通过STRING数据库构建DEGs的蛋白质-蛋白质相互作用（PPI）网络。使用Cytoscape软件找出枢纽基因。构建ARDSp大鼠模型后，通过数据集对枢纽基因进行测序和验证。
使用DESeq2软件包，发现ARDSp参与者中有299个基因下调，228个基因上调。GO分析显示，DEGs富集于肌动蛋白丝组织、小GTP酶介导的信号转导调节、未折叠蛋白反应、伤口愈合和对氧水平的反应等过程。同时，KEGG分析显示，DEGs参与蛋白质消化和吸收、Th17细胞分化、铁死亡等生物学效应。基于网络中心性和生物学意义，突出了10个枢纽基因，包括纤连蛋白1（FN1）、缺氧诱导因子1α（HIF1A）、热休克蛋白90α家族成员1（HSP90AA1）、SMAD家族成员3（SMAD3）、原癌基因Fos（FOS）、细胞周期蛋白依赖性激酶抑制剂2A（CDKN2A）、Ⅰ型胶原α1链（COL1A1）、热休克蛋白70家族成员8（HSPA8）、细丝蛋白A（FLNA）和核因子κB抑制蛋白α（NFKBIA）。HIF1A、HSPA8、NFKBIA和CDKN2A在验证数据集中差异表达。
ARDSp中的基底细胞在基因表达上表现出显著变化，鉴定出10个枢纽基因。其中，4个基因（HIF1A、HSPA8、NFKBIA、CDKN2A）通过ARDSp大鼠模型的RNA-Seq数据进行了实验验证。本研究强调了基底细胞在ARDSp中的作用，突出了参与修复和炎症反应的基因网络变化，为进一步的治疗探索提供了潜在靶点。这些发现表明，这些枢纽基因的改变可能对ARDSp中基底细胞驱动的炎症和修复反应至关重要。
