The identification of Necroptosis-Related Genes and Immune Cell Infiltration in Chronic Obstructive Pulmonary Disease based on bioinformatics and experimental validation

Abstract

Globally, chronic obstructive pulmonary disease(COPD) is the third leading cause of death. Necroptosis is a programmed regulated necrosis and contributes to the progression of lung disease. However, the function of necroptosis in COPD needs to be further elucidated. This study aimed to unravel the role of necroptosis in COPD via bioinformatics analysis and experimental validation. The GSE38974 and GSE8581 datasets were downloaded from the GEO database. Identified of differentially expressed genes(DEGs) from GSE38974. The GO, KEGG and GSEA enrichment analyses for DEGs.Differentially expressed genes of necroptosis(NR-DEGs) were obtained by combining DEGs and 159 necroptosis-related genes and the GO and KEGG were performed. The AUC values of NR-DEGs were assessed in the GSE38974 dataset and further were verified in the GSE8581 dataset. To further verify NR-DEGs in CSE-induced BEAS-2B cells by using RT-qPCR. The level of immune cell infiltration was quantified by ssGSEA analysis and the correlation analysis was performed between NR-DEGs and immune cell infiltration. We identified 646 DEGs and acquired 5 NR-DEGs(IL1B, IL-33, TNFAIP3, TNFRSF1A and CHMP4B) by combining 646 DEGs and 159 necroptosis-related genes. The GO, KEGG and GSEA enrichment analyses for the DEGs and NR-DEGs mainly involved in regulating of inflammatory response, cytokine-mediated signaling pathway, cytokine activity, receptor ligand activity and necroptosis. The AUC values of the NR-DEGs were 0.797, 0.971, 0.908, 1 and 1 from GSE38974 dataset and further were verified in the GSE8581 dataset were 0.741 and 0.737. The results of RT-qPCR showed that mRNA expression levels of IL1B and TNFAIP3 were up-regulated compared with control group(P<0.05). The analysis result of ssGSEA displayed that IL1B was significantly associated with Plasmacytoid.dendritic.cell, Activated.dendritic.cell, Macrophage, Central.memory.CD8.T.cell, Natural.killer.cell, Type.17.T.helper.cell, MDSC, and TNFAIP3 was significantly associated with Type.17.T.helper.cell, Natural.killer.cell, Macrophage, Central.memory.CD8.T.cell, Activated.dendritic.cell, Plasmacytoid.dendritic.cell, MDSC, Immature.B.cell, Gamma.delta.T.cell. According to the study, we found that necroptosis with COPD pathogenesis and immune cell infiltration is closely related, in particular, IL1B may through necroptosis-dependent pathway activate immune cell infiltration to promote the development of COPD, these may allow us to better understand the role of necroptosis in patients with COPD and provide better immunotherapeutic targets.