Neutrophil-Related Gene Expression Signatures in Idiopathic Pulmonary Fibrosis: Implications for Disease Characteristic and Identification of Diagnostic Hub Genes

Yingying Lin; Xiaofan Lai; Tianxiang Lei; Yuan Qiu; Qiwen Deng; Qi Liu; Zhongxing Wang; Wenqi Huang

doi:10.2147/JIR.S414734

Neutrophil-Related Gene Expression Signatures in Idiopathic Pulmonary Fibrosis: Implications for Disease Characteristic and Identification of Diagnostic Hub Genes

J Inflamm Res. 2023 Jun 14:16:2503-2519. doi: 10.2147/JIR.S414734. eCollection 2023.

Authors

Yingying Lin^#¹, Xiaofan Lai^#¹, Tianxiang Lei^#², Yuan Qiu³, Qiwen Deng¹, Qi Liu¹, Zhongxing Wang¹, Wenqi Huang¹

Affiliations

¹ Department of Anesthesiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.
² Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.
³ Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, People's Republic of China.

^# Contributed equally.

Abstract

Background: Idiopathic pulmonary fibrosis (IPF) is a disease with unclear etiology and a poor prognosis. Although the involvement of neutrophils in IPF pathogenesis has been suggested, the exact nature of this relationship remains unclear.

Methods: We analyzed data from the Gene Expression Omnibus (GEO) using immune infiltration analysis, weighted gene co-expression network analysis (WGCNA), and consensus cluster analysis. Neutrophil-related genes and hub genes related to neutrophils were identified and differentially expressed between IPF patients and healthy controls. We also validated the expression differences of hub genes in a bleomycin-induced mice model.

Results: Immune infiltration analysis revealed a significantly decreased percentage of neutrophils in the lung tissue of IPF patients compared with healthy controls (P<0.001) in both the train and validation sets. Neutrophil-related genes in IPF were identified by WGCNA, and functional enrichment analysis showed that these genes were mainly involved in the cytokine-cytokine receptor interaction pathway and correlated with lung disease, consistent with DEGs between IPF and healthy controls. Eight hub genes related to neutrophils were identified, including MMP16, ARG1, IL1R2, PROK2, MS4A2, PIR, and ZNF436. Consensus cluster analysis revealed a low neutrophil-infiltrating cluster that was correlated with IPF (P<0.001), and a principal component analysis-generated score could distinguish IPF patients from healthy controls, with an area under the curve of 0.930 in the train set and 0.768 in the validation set. We also constructed a diagnostic model using hub genes related to neutrophils, which showed a reliable diagnostic value with an area under the curve of 0.955 in the train set and 0.995 in the validation set.

Conclusion: Our findings provide evidence of a low neutrophil-infiltrating characteristic in the IPF microenvironment and identify hub genes related to neutrophils that may serve as diagnostic biomarkers for the disease.

Keywords: biomarkers; consensus cluster analysis; diagnostic model; idiopathic pulmonary fibrosis; immune infiltration analysis; neutrophils; weighted gene co-expression network analysis.

Grants and funding

This research was funded by grants from the National Natural Science Foundation of China (Grant no. 82200073 to Xiaofan Lai and Grant no. 81971877 to Zhongxing Wang), Regional Joint Fund-Youth Fund Projects of Guangdong Province (Grant no. 2020A1515110118 to Xiaofan Lai). The funding sources had no involvement in study design; collection, analysis, and interpretation of data; writing the report; or the decision to submit the article for publication.