Identification and validation of genetic signature associated with aging in chronic obstructive pulmonary disease

Abstract

Aging plays an essential role in the development for chronic obstructive pulmonary disease (COPD). The aim of this study was to identify and validate the potential aging-related genes of COPD through bioinformatics analysis and experimental validation. Firstly, we compared the gene expression profiles of aged and young COPD patients using two datasets (GSE76925 and GSE47460) from Gene Expression Omnibus (GEO), and identified 244 aging-related different expressed genes (DEGs), with 132 up-regulated and 112 down-regulated. Then, by analyzing the data for cigarette smoke-induced COPD mouse model (GSE125521), a total of 783 DEGs were identified between aged and young COPD mice, with 402 genes increased and 381 genes decreased. Additionally, functional enrichment analysis revealed that these DEGs were actively involved in COPD-related biological processes and function pathways. Meanwhile, six genes were identified as the core aging-related genes in COPD after combining the human DEGs and mouse DEGs. Eventually, five out of six core genes were validated to be up-regulated in the lung tissues collected from aged COPD patients than young COPD patients, namely NKG7, CKLF, LRP4, GDPD3 and CXCL9. Thereinto, the expressions of NKG7 and CKLF were negatively associated with lung function. These results may expand the understanding for aging in COPD.

Keywords: aging; bioinformatics analysis; chronic obstructive pulmonary disease; genetic signature.

Figure 1

DEGs associated with aging in COPD patients. (A) Volcano-plot of the 244 age-associated DEGs in COPD patients. Red circle: upregulated genes; blue circles: downregulated genes. (B) Top 10 GO biological processes analysis of the 244 age-associated DEGs. Outer gray circle: a scatter plot for each term of the logFC of the assigned genes; red circles: upregulated genes; blue circles: downregulated genes. (C) All GO cellular components analysis of the 244 age-associated DEGs. (D) Top 11 GO molecular functions analysis of the 244 age-associated DEGs. (E) Top 7 significantly (P<0.05) enriched KEGG pathways. DEGs, differently expressed genes; COPD, chronic obstructive pulmonary disease; GO, gene ontology; FC, fold change; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 2

Age-associated DEGs in COPD model mice. (A) Volcano plot of the 783 age-associated DEGs. Red circle: upregulated genes; blue circles: downregulated genes. (B) Top 10 GO biological processes of the 783 age-associated DEGs. Outer gray circle: a scatter plot for each term of the logFC of the assigned genes; red circles: upregulated genes; blue circles: downregulated genes. (C) All GO cellular components of the 783 age-associated DEGs. (D) Top 13 GO molecular functions of the 783 age-associated DEGs. (E) Top 13 significantly (P<0.05) enriched KEGG pathways. DEGs, differently expressed genes; COPD, chronic obstructive pulmonary disease; GO, gene ontology; FC, fold change; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 3

Common age-associated DEGs in COPD. (A) A Venn diagram of DEGs of patients with COPD patients and COPD model mice. (B) Heatmap of the six core genes in young and aged COPD patients. (C) Heatmap of the six core genes in young and aged COPD model mice. DEGs, differently expressed genes; COPD, chronic obstructive pulmonary disease.

Figure 4

The expression of the 6 core genes in the lungs of COPD patients. The relative mRNA expressions of six genes in the young COPD patients and aged COPD patients were shown, including (A) NKG7, (B) CKLF, (C) LRP4, (D) MLF1, (E) GOPD3, (F) CXCL9. Results were expressed as median (P25 quartile, P75 quartile); n=16 for young COPD and n=16 for aged COPD; *P<0.05, **P<0.01, ***P<0.001. COPD, chronic obstructive pulmonary disease; NKG7, natural killer cell granule protein 7; CKLF, chemokine like factor; LRP4, LDL receptor related protein 4; MLF1, myeloid leukemia factor 1; GDPD3, glycerophosphodiester phosphodiesterase domain containing 3; CXCL9, C-X-C motif chemokine ligand 9.

Figure 5

The association analysis between the critical aging-related DEGs and lung function in COPD patients. The lung function was negatively associated with (A) NKG7 expression and (B) CKLF expression, whereas no significant associations with the expressions of (C) LRP4, (D) GOPD3 and (E) CXCL9. DEGs, differently expressed genes; COPD, chronic obstructive pulmonary disease; FEV₁ (% predicted), forced expiratory volume in 1 s (FEV1) % predicted; NKG7, natural killer cell granule protein 7; CKLF, chemokine like factor; LRP4, LDL receptor related protein 4; GDPD3, glycerophosphodiester phosphodiesterase domain containing 3; CXCL9, C-X-C motif chemokine ligand 9.