Screening of Lipid Metabolism-Related Genes as Diagnostic Indicators in Chronic Obstructive Pulmonary Disease

Figures & data

Table 1 Demographic and Baseline Characteristics of the Samples in GSE76925

Characteristic	Control (n=38)	COPD (n=111)	P value
Age (years)	66.76 (59.25–73.17)	63.00 (60.00–67.00)	0.061
Male, n (%)	13 (34.21)	52 (46.84)	0.175
BMI (kg/m^2)	28.23 (24.32–30.63)	25.20 (21.96–29.32)	0.007
Smoking (Packyears)	30.00 (16.88–45.00)	55.00 (41.00–78.00)	0.000
FEV1%pred (%)	98.50 (85.75–107.25)	25.00 (19.00–32.00)	0.000
FEV1/FVC (%)	78.25 (73.75–82.20)	30.00 (25.00–37.00)	0.000

Figure 1 A flowchart of the study.

Abbreviations: GEO, Gene Expression Omnibus; KEGG, Kyoto Encyclopedia of Genes and Genomes; MsigDB, Molecular Signatures Database; LMRGs, lipid metabolism-related genes; DEGs, differentially expressed genes; DeLMRGs, differentially expressed lipid metabolism-related genes; GO, Gene Ontology; ROC, receiver operating characteristic; BCHE, butyrylcholinesterase; PLA2G7, phospholipase A2 Group VII; ELISA, Enzyme linked immunosorbent assay.

Figure 2 Identification of DeLMRGs in COPD patients. (A) Volcano plot of COPD-related DEGs, graphed with log2FoldChange on the abscissa and -log10 on the ordinate (adjusted P value): Nodes in red represent DEGs up-regulated, nodes in blue represent DEGs down-regulated, and nodes in gray represent genes not significantly differentially expressed. (B) Heat map of top 20 COPD-related DEGs: disease samples are indicated by group1, normal control samples by group2, and high gene expression is indicated by red with low gene expression by blue; (C) Venn diagram of DeLMRGs derived from DEGs and LMRGs intersection: green represents LMRGs, blue represents upregulated DEGs and pink represents downregulated DEGs.

Abbreviations: DEGs, differentially expressed genes; LMRGs, lipid metabolism-related genes; DeLMRGs, differentially expressed lipid metabolism-related genes.

Figure 3 Enrichment analysis of DEGs and DeLMRGs in COPD patients. (A) GO and KEGG enrichment analysis of 587 DEGs. (B) KEGG analysis of 587 DEGs. (C) GO enrichment analysis of 20 DeLMRGs. (D) KEGG enrichment analysis of 20 DeLMRGs.

Abbreviations: DEGs, differentially expressed genes; DeLMRGs, differentially expressed lipid metabolism-related genes; GO, gene ontology; KEGG, kyoto encyclopedia of genes and genomes.

Table 2 Table of Detailed Information About 10 Hub DeLMRGs

Gene	Description	Log2FC	Adjust P value	Regulation
PLA2G7	Phospholipase A2 Group VII	1.306	0.000	Up
HPGDS	Hematopoietic Prostaglandin D Synthase	−1.083	0.000	Down
LEP	Leptin	−1.344	0.000	Down
PTGES3	Prostaglandin E Synthase 3	−1.301	0.001	Down
LEPR	Leptin Receptor	−1.076	0.001	Down
PLA2G2D	Phospholipase A2 Group IID	−1.064	0.000	Down
MED21	Mediator Complex Subunit 21	−1.870	0.000	Down
SPTLC1	Serine Palmitoyltransferase Long Chain Base Subunit 1	−1.108	0.000	Down
BCHE	Butyrylcholinesterase	−1.283	0.000	Down
PLA2G4A	Phospholipase A2 group IVA	−1.425	0.000	Down

Figure 4 PPI network of DeLMRGs. (A) PPI network of 20 DeLMRGs: upregulated genes are shown in red, while downregulated genes are shown in blue. (B) PPI network of 10 hub DeLMRGs: The darker the color, the greater the contribution of genes to the PPI network. The black line indicates the presence of genes that interact.

Abbreviations: DeLMRGs, differentially expressed lipid metabolism-related genes; PPI, Protein-Protein Interaction.

Figure 5 Validation of 9 hub DeLMRGs between COPD and controls in GSE8581. (A) The expressions of BCHE in validation sets. (B) The expressions of HPDGS in validation sets. (C) The expressions of LEP in validation sets. (D) The expressions of LEPR in validation sets. (E) The expressions of PLA2G2D in validation sets. (F) The expressions of PLA2G4A in validation sets. (G) The expressions of PLA2G7 in validation sets. (H) The expressions of PTGES3 in validation sets. (I) The expressions of SPTLC1 in validation sets. *P< 0.05, **P < 0.01.

Abbreviations: DeLMRGs, differentially expressed lipid metabolism-related genes; BCHE, Butyrylcholinesterase; HPDGS, hematopoietic prostaglandin D synthase; LEP, leptin; LEPR, leptin receptor; PLA2G2D, phospholipase A2 group IID; PLA2G4A, phospholipase A2 group IVA; PLA2G7, phospholipase A2 group VII; PTGES3, prostaglandin E synthase 3; SPTLC1, serine palmitoyltransferase long chain base subunit 1.

Figure 6 CeRNA regulatory network of lncRNA-miRNA-DeLMRG. (A) Venn diagram showing that 40 miRNAs from TargetScan and miRDB interact with BCHE. (B) Venn diagram showing that 17 miRNAs from TargetScan and miRDB interact with PLA2G7. (C) CeRNA network of BCHE and PLA2G7: red diamonds represent protein-coding genes, blue circles represent miRNAs, green rectangles represent lncRNAs, and black lines represent the interactions between lncRNAs, miRNAs, and mRNAs.

Abbreviations: BCHE, butyrylcholinesterase; PLA2G7, phospholipase A2 Group VII; ceRNA, competing endogenous RNA; lncRNA, long non-coding RNA; miRNA, microRNA; DeLMRG, differentially expressed lipid metabolism-related genes.

Figure 7 The expression levels of BCHE in macrophages treated with different concentrations of CSE by ELISA. (A) Expression levels of BCHE after different concentrations of CSE treated RAW264.7 cells for 24h. (B) Expression levels of BCHE after different concentrations of CSE treated RAW264.7 cells for 48h. (C) Expression levels of BCHE after different concentrations of CSE treated THP-1 cells for 24h. (D) Expression levels of BCHE after different concentrations of CSE treated THP-1 cells for 48h. Data are presented as mean±sem and differences between groups were assessed by one-way ANOVA. *Indicates the comparison between different CSE administration (0.5–3%) with the blank control group, and *p<0.05; **p<0.01; NS: no significant (P > 0.05).

Abbreviations: BCHE, butyrylcholinesterase; CSE, cigarette smoke extract.

Figure 8 The expression levels of PLA2G7 in macrophages treated with different concentrations of CSE by ELISA. (A) Expression levels of PLA2G7 after different concentrations of CSE treated RAW264.7 cells for 24h. (B) Expression levels of PLA2G7 after different concentrations of CSE treated RAW264.7 cells for 48h. (C) Expression levels of PLA2G7 after different concentrations of CSE treated THP-1 cells for 24h. (D) Expression levels of PLA2G7 after different concentrations of CSE treated THP-1 cells for 48h. Data are presented as mean±sem and differences between groups were assessed by one-way ANOVA. *Indicates the comparison between different CSE administration (0.5–3%) with the blank control group, and *p<0.05; **p<0.01; ***p<0.001; ****p < 0.0001.

Abbreviations: PLA2G7, phospholipase A2 Group VII; CSE, cigarette smoke extract.