Identification of Genes Related to Endoplasmic Reticulum Stress (ERS) in Chronic Obstructive Pulmonary Disease (COPD) and Clinical Validation

Figures & data

Figure 1 The detailed analysis process of this study.

Table 1 The Specific Expression Levels of ERS-Related Genes

Gene_symbol	logFC	P.Value	adj.P.Val	Changes
APAF1	1.216286	3.01E-09	4.57E-07	Up
BAX	1.438751	1.13E-10	4.05E-08	Up
PMAIP1	1.11692	6.64E-05	0.001034	Up
PPP1R3C	−1.97802	5.52E-05	0.000897	Down
PTPN1	−0.43386	0.000136	0.00181	Up
STC2	1.094189	0.001726	0.012153	Up

Abbreviations: logFC, logfoldchange; adj.P.Val, adjust P value; ERS, Endoplasmic Reticulum Stress.

Figure 2 Screening of ERS-related genes in COPD and healthy samples.

Notes: (A) GSE38974 exhibited robust data repeatability. (B) Intersection analysis was conducted between genes associated with COPD and factors related to endoplasmic reticulum stress. (C and D) Significantly differentially expressed genes were respectively illustrated using volcano plots and heat maps. (E) Chromosomal localization of pivotal genes.

Figure 3 Expressions of ERS-related genes in the GSE38974 dataset. **Indicates p<0.01, ***Indicates p < 0.001.

Figure 4 The interaction relationship of ERS-related genes. *Indicates p< 0.05, **Indicates p<0.01.

Notes: (A) Interactions among six genes associated with ERS. (B) The quantity of interactions for each gene. (C) Relationships among six ERS-related DEGs in the GSE38974 dataset.

Figure 5 Enrichment analysis of ERS genes.

Notes: (A and B) Conducting differential gene enrichment analysis using R software for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

Figure 6 GSEA pathway enrichment analysis of ERS genes.

Notes: (A) Jak Stat Signaling Pathway. (B) TP53 Network. (C) TP53 Regulates Transcription of Caspase Activators and Caspases. (D) II1 and Megakaryocytes In Obesity. (E) Neutrophil Degranulation. (F) Cytokine Cytokine Receptor Interaction. (G) Interleukin 10 Signaling. (H) Apoptosis. (I) Photodynamic Therapy-induced Nfkb Survival Signaling.

Table 2 Correlation Analysis Between the ERS-Related Gene Expression Levels and Clinical Indicators

		CFEV1	FEV1%	CFVC	CFVC%	CFEV1/FVC	EOS	LYM
APAF	CC	−0.082	0.419	0.092	0.245	0.423	−0.038	−0.290
	P	0.790	0.154	0.766	0.419	0.150	0.892	0.294
BAX	CC	−0.314	−0.338	0.160	−0.148	−0.410	−0.092	−0.191
	P	0.296	0.258	0.600	0.630	0.164	0.755	0.514
PTPN1	CC	−0.324	−0.684*	0.024	−0.483	−0.769**	−0.077	0.442
	P	0.331	0.020	0.944	0.132	0.006	0.822	0.173
STC2	CC	−0.215	0.368	0.535	0.431	0.260	0.672*	−0.612*
	P	0.502	0.240	0.073	0.162	0.415	0.017	0.034

Note: *Indicates p< 0.05, **Indicates p<0.01.

Abbreviations: ERS, Endoplasmic Reticulum Stress; CC, Correlation coefficient; P, P value.

Figure 7 The qRT-PCR validation of key genes clinical samples. *Indicates p< 0.05, ***Indicates p < 0.001, ****Indicates p < 0.0001.

Notes: (A) The differential expression of APAF1 between two groups. (B) The differential expression of BAX between two groups. (C) The differential expression of PMAIP1 between two groups. (D) The differential expression of PPP1R3C between two groups. (E) The differential expression of PTPN1 between two groups. (F) The differential expression of STC2 between two groups.

Figure 8 Key genes-related MicroRNA analysis.

Figure 9 Correlation analysis between PTPN1 and STC2 and pulmonary function indicators (EOS and LYM).

Notes: (A) PTPN1 exhibits a negative correlation with pulmonary function FEV1%. (B) PTPN1 demonstrates a negative correlation with pulmonary function FEV1/FVC. (C) STC2 shows a positive correlation with EOS. (D) STC2 displays a negative correlation with LYM.