| Literature DB >> 33354437 |
Jie Zhang1, Changli Zhu1, Hong Gao1, Xun Liang2, Xiaoqian Fan3, Yulong Zheng1, Song Chen4, Yufeng Wan1.
Abstract
We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein-protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD. ©2020 Zhang et al.Entities:
Keywords: Chronic obstructive pulmonary disease; Functional enrichment analysis; Logistic regression model; Protein–protein interaction; Stage
Year: 2020 PMID: 33354437 PMCID: PMC7733647 DOI: 10.7717/peerj.10513
Source DB: PubMed Journal: PeerJ ISSN: 2167-8359 Impact factor: 2.984
Figure 1Results of soft clustering for genes.
Changes in colors (red-blue–green) indicate the coincidence degree of a gene change with the central variation of the cluster. Red indicates a high degree and green indicates a low degree of coincidence.Cluster1-10 (A–J).
Upregulated genes with enriched functions of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG).
| BP | GO:0006952 | defense response | 22 | 3.84E−07 |
| BP | GO:0006954 | inflammatory response | 16 | 5.18E−07 |
| BP | GO:0009611 | response to wounding | 20 | 7.08E−07 |
| BP | GO:0006955 | immune response | 22 | 2.45E−06 |
| CC | GO:0009891 | positive regulation of biosynthetic process | 35 | 0.002989929 |
| CC | GO:0051173 | positive regulation of nitrogen compound metabolic process | 22 | 0.004929606 |
| CC | GO:0031328 | positive regulation of cellular biosynthetic process | 22 | 0.006361208 |
| CC | GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolic process | 51 | 0.006484061 |
| KEGG | hsa05322 | Systemic lupus erythematosus | 8 | 4.11E−04 |
| KEGG | hsa04620 | Toll-like receptor signaling pathway | 6 | 0.012939 |
| KEGG | hsa04060 | Cytokine-cytokine receptor interaction | 9 | 0.028464 |
Notes.
biological process
cellular component
Downregulated genes with enriched functions of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG).
| BP | GO:0046649 | lymphocyte activation | 11 | 1.89E−06 |
| BP | GO:0001775 | cell activation | 12 | 7.79E−06 |
| BP | GO:0045321 | leukocyte activation | 11 | 1.08E−05 |
| BP | GO:0048534 | lymphoid organ development | 10 | 1.19E−04 |
| BP | GO:0002520 | immune system development | 10 | 1.87E−04 |
| BP | GO:0030097 | hemopoiesis | 9 | 3.33E−04 |
| BP | GO:0030098 | lymphocyte differentiation | 6 | 9.42E−04 |
| BP | GO:0042110 | T cell activation | 6 | 0.002303352 |
| BP | GO:0002521 | leukocyte differentiation | 6 | 0.0027276 |
| BP | GO:0042113 | B cell activation | 4 | 0.018182557 |
| BP | GO:0030217 | T cell differentiation | 3 | 0.081968615 |
| CC | GO:0009897 | external side of plasma membrane | 4 | 0.120963049 |
| CC | GO:0009986 | cell surface | 5 | 0.235650749 |
| CC | GO:0044459 | plasma membrane part | 24 | 0.033231996 |
| CC | GO:0031226 | intrinsic to plasma membrane | 14 | 0.088759042 |
| CC | GO:0005886 | plasma membrane | 34 | 0.099440061 |
| CC | GO:0005887 | integral to plasma membrane | 13 | 0.136364905 |
| KEGG | hsa04940 | Type I diabetes mellitus | 4 | 0.001194 |
| KEGG | hsa04630 | Jak-STAT signaling pathway | 5 | 0.007356 |
| KEGG | hsa05330 | Allograft rejection | 3 | 0.014236 |
| KEGG | hsa05332 | Graft-versus-host disease | 3 | 0.016588 |
| KEGG | hsa04660 | T cell receptor signaling pathway | 4 | 0.016985 |
Notes.
biological process
cellular component
Regulatory microRNAs of gene sets.
| Hsa-TGGTGCT | miR-29a, miR-29b, miR-29c | 6 | |
| Hsa-AAGGGAT | miR-188 | 3 | |
| Hsa-GTGCCTT | miR-506 | 7 | |
| Hsa-ACACTAC | miR-142-3p | 3 | |
| Hsa-TGCACTG | miR-148a, miR-152, miR-148b | 4 | |
| Hsa-ACTGAAA | miR-30a-3p, miR-30e−3p | 3 | |
| Hsa-GGGACCA | miR-133a, miR-133b | 3 | |
| Hsa-CTTTGCA | miR-527 | 3 | |
| Hsa-CATTTCA | miR-203 | 3 | |
| Hsa-TTTGTAG | miR-520d | 3 | |
| Hsa-TAGCTTT | miR-9 | 4 | |
| Hsa-AAGCACA | miR-218 | 4 | |
| Hsa-TGGTGCT | miR-29a, miR-29b, miR-29c | 4 | |
| Hsa-GCACTTT | miR-17-5p, miR-20a, miR-106a, miR-106b, miR-20b, miR-519d | 4 | |
| Hsa-AAGCCAT | miR-135a, miR-135b | 3 | |
| Hsa-TGCACTT | miR-519c, miR-519b, miR-519a | 3 | |
| Hsa-CTTTGTA, | miR-524 | 3 | |
| Hsa-TGAATGT | miR-181a, miR-181b, miR-181c, miR-181d | 3 | |
| Hsa-TGCTGCT | miR-15a, miR-16, miR-15b, miR-195, miR-424, miR-497 | 3 |
Figure 2The integrated network of protein–protein interactions and miRNA-target gene regulatory relations for upregulated genes (A) and downregulated genes (B).
Red circles indicate upregulated genes, green circles indicate downregulated genes, and blue diamonds indicate miRNA.
Results of univariate logistic regression analysis.
| Factor | Coefficient | |
|---|---|---|
| Age | 0.2796 | 0.0389 |
| Gender | 0.1545 | 0.2383 |
| TLR2 | 0.9265 | 2.1068E−07 |
| IL-10 | 0.3250 | 0.1524 |
| MMP9 | 0.2702 | 0.0059 |
| HMOX1 | 0.3163 | 0.0713 |
| CCR1 | 0.3503 | 0.0298 |
| CD79A | −0.3443 | 0.0002 |
| PLCG1 | −0.7284 | 0.0037 |
Notes.
factors that may affect clinical grading
regression coefficient ( > 0, positive 3 correlation; < 0, negative correlation)
Results of multivariate logistic regression analysis.
| Factor | Coefficients | |
|---|---|---|
| Age | 0.1069 | 0.4220 |
| TLR2 | 0.6894 | 0.0027 |
| MMP9 | 0.0374 | 0.7310 |
| CCR1 | 0.0282 | 0.8695 |
| CD79A | −0.1930 | 0.0450 |
| PLCG1 | −0.1267 | 0.6488 |
Notes.
factors that may affect clinical grading
regression coefficient (> 0, positive 3 correlation; < 0, negative correlation)
Figure 3The relationships between TLR2 and inflammatory factors in COPD progression.
The levels of IL-6 (A), IL-8 (B), TNF-α (C), and IFN-γ (D) in the serum and TLR2 in the peripheral blood mononuclear cells of the patients (E). The sensitivity and specificity of IL-6 (F), IL-8 (G), TNF-α (H), IFN-γ (I) and TLR2 (J) in the prediction of COPD . The TLR2 expression levels were correlated with the serum levels of IL-6 (K), IL-8 (L), TNF-α (M), and IFN-γ (N).