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

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:

• neutrophils
• idiopathic pulmonary fibrosis
• immune infiltration analysis
• weighted gene co-expression network analysis
• consensus cluster analysis
• diagnostic model
• biomarkers

Ethics Approval and Consent to Participate

This study involving animals was carried out in accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocol was approved by the Ethics Committee of Sun Yat-sen University. All efforts were made to minimize animal suffering and to reduce the number of animals used.

Acknowledgments

The authors would like to thank the Department of Anesthesiology, the First Affiliated Hospital, and Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University for providing support and instructions.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors report no conflicts of interest in this work.

Additional information

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.