鉴定 COPD 中性粒细胞炎症相关的新型生物标志物。

Identification of novel biomarkers related to neutrophilic inflammation in COPD.

机构信息

Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Key Laboratory of Pulmonary Diseases of National Health Commission, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.

出版信息

Front Immunol. 2024 May 30;15:1410158. doi: 10.3389/fimmu.2024.1410158. eCollection 2024.

DOI:10.3389/fimmu.2024.1410158

PMID:38873611

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11169582/

Abstract

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is one of the most prevalent chronic respiratory diseases and the fourth cause of mortality globally. Neutrophilic inflammation has a vital role in the occurrence and progression of COPD. This study aimed to identify the novel hub genes involved in neutrophilic inflammation in COPD through bioinformatic prediction and experimental validation.

METHODS

Both the single-cell RNA sequencing (scRNA-seq) dataset (GSE173896) and the RNA sequencing (RNA-seq) dataset (GSE57148) were downloaded from the Gene Expression Omnibus (GEO) database. The Seurat package was used for quality control, dimensions reduction, and cell identification of scRNA-seq. The irGSEA package was used for scoring individual cells. The Monocle2 package was used for the trajectory analysis of neutrophils. The CIBERSORT algorithm was used for analysis of immune cell infiltration in the lungs of COPD patients and controls in RNA-seq dataset, and weighted gene co-expression network analysis (WGCNA) correlated gene modules with neutrophil infiltration. The Mendelian randomization (MR) analysis explored the causal relationship between feature DEGs and COPD. The protein-protein interaction (PPI) network of novel hub genes was constructed, and real-time quantitative polymerase chain reaction (qRT-PCR) was used to validate novel hub genes in clinical specimens.

RESULTS

In scRNA-seq, the gene sets upregulated in COPD samples were related to the neutrophilic inflammatory response and TNF-α activation of the NF-κB signaling pathway. In RNA-seq, immune infiltration analysis showed neutrophils were upregulated in COPD lung tissue. We combined data from differential and modular genes and identified 51 differential genes associated with neutrophilic inflammation. Using MR analysis, 6 genes were explored to be causally associated with COPD. Meanwhile, 11 hub genes were identified by PPI network analysis, and all of them were upregulated. qRT-PCR experiments validated 9 out of 11 genes in peripheral blood leukocytes of COPD patients. Furthermore, 5 genes negatively correlated with lung function in COPD patients. Finally, a network of transcription factors for NAMPT and PTGS2 was constructed.

CONCLUSION

This study identified nine novel hub genes related to the neutrophilic inflammation in COPD, and two genes were risk factors of COPD, which may serve as potential biomarkers for the clinical severity of COPD.

摘要

背景

慢性阻塞性肺疾病（COPD）是最常见的慢性呼吸道疾病之一，也是全球第四大致死原因。中性粒细胞炎症在 COPD 的发生和发展中起着至关重要的作用。本研究旨在通过生物信息学预测和实验验证，鉴定 COPD 中性粒细胞炎症相关的新的枢纽基因。

方法

从基因表达综合数据库（GEO）下载单细胞 RNA 测序（scRNA-seq）数据集（GSE173896）和 RNA 测序（RNA-seq）数据集（GSE57148）。使用 Seurat 包进行 scRNA-seq 的质量控制、降维和细胞鉴定。使用 irGSEA 包对个体细胞进行评分。使用 Monocle2 包进行中性粒细胞轨迹分析。使用 CIBERSORT 算法分析 COPD 患者和对照者的肺组织中的免疫细胞浸润，并将加权基因共表达网络分析（WGCNA）相关基因模块与中性粒细胞浸润进行关联。使用孟德尔随机化（MR）分析探索特征 DEGs 与 COPD 之间的因果关系。构建新的枢纽基因的蛋白质-蛋白质相互作用（PPI）网络，并使用实时定量聚合酶链反应（qRT-PCR）验证临床标本中的新枢纽基因。

结果

在 scRNA-seq 中，COPD 样本中上调的基因集与中性粒细胞炎症反应和 TNF-α 激活的 NF-κB 信号通路有关。在 RNA-seq 中，免疫浸润分析显示 COPD 肺组织中中性粒细胞上调。我们结合差异和模块基因的数据，鉴定了 51 个与中性粒细胞炎症相关的差异基因。使用 MR 分析，探索了 6 个与 COPD 因果相关的基因。同时，通过 PPI 网络分析鉴定了 11 个枢纽基因，这些基因均上调。qRT-PCR 实验验证了 COPD 患者外周血白细胞中的 9 个基因。此外，有 5 个基因与 COPD 患者的肺功能呈负相关。最后，构建了 NAMPT 和 PTGS2 的转录因子网络。