| Literature DB >> 32346408 |
Jing Li1, Hongling Su1, Yan Zhu1, Yunshan Cao1, Xuming Ma1.
Abstract
Heart failure (HF) is a global pandemic cardiovascular disease with increasing prevalence, but the pathogenesis remains to be elucidated. The present study aimed to investigate the underlying mechanism in heart failure (HF) using bioinformatics and experimental validation. A HF-associated dataset GSE84796 was downloaded from the Gene Expression Omnibus database and differentially expressed genes (DEGs) were screened for using Bayes method in the Limma package. Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to perform pathway enrichment analysis of these DEGs using The Database for Annotation, Visualization and Integrated Discovery. A protein-protein interaction (PPI) network of DEG-encoded proteins was subsequently constructed using the Search tool for the Retrieval of Interacting Genes/Proteins, and a transcription factor (TF)/miRNA-target network was constructed according to the WEB-based Gene SeT AnaLysis Tookit. The expression levels of microRNA (miRNA/miR)-155, G-protein coupled receptor 18 (GRP18) and E26 transformation-specific transcription factor 2 (ETS2) were analyzed in clinical HF samples, and functional validations were performed in H9c2 (2-1) cells. A total of 419 DEGs were identified, including 366 upregulated genes and 53 downregulated genes. The upregulated DEGs were significantly enriched in the pathways of 'cytokine-cytokine receptor interaction', 'natural killer cell mediated cytotoxicity' and 'primary immunodeficiency'. A total of two functional modules were identified in the PPI network: Module A was enriched in 3 KEGG pathways and module B was enriched in 15 KEGG pathways. Furthermore, a total of three miRNAs and eight TFs were identified in the TF/miRNA-target network. Specifically, GPR18 was discovered to be targeted by both ETS2 and miR-155. Clinical validation revealed that the expression levels of miR-155 were significantly decreased in the HF samples, whereas the expression levels of ETS2 and GPR18 were significantly increased in HF samples. In conclusion, the present study suggested that GPR18 may be a target of ETS2 and miR-155, and miR-155 may regulate cell viability and apoptosis in H9c2 (2-1) cells through targeting and regulating GPR18. Copyright: © Li et al.Entities:
Keywords: E26 transformation-specific transcription factor 2; G-protein coupled receptor 18; apoptosis; cell viability; heart failure; regulatory network
Year: 2020 PMID: 32346408 PMCID: PMC7185148 DOI: 10.3892/etm.2020.8642
Source DB: PubMed Journal: Exp Ther Med ISSN: 1792-0981 Impact factor: 2.447
Figure 1Heatmap and volcano plot for differentially expressed genes identified in HF. (A) Heatmap and (B) volcano plot. Red columns in the heatmap indicate higher gene expression, while blue columns in the heatmap indicate lower gene expression. For the volcano plot, red plots represent upregulated DEGs, green plots represent downregulated DEGs and black plots represent non-differentially expressed genes. HF, heart failure; DEG, differentially expressed genes.
Top Kyoto Encyclopedia of Genes and Genomes pathways enriched by differentially expressed genes.
| Pathway ID | Pathway name | Count | P-value |
|---|---|---|---|
| hsa04060 | Cytokine-cytokine receptor interaction | 31 | 3.46x10-16 |
| hsa04650 | Natural killer cell mediated cytotoxicity | 22 | 6.05x10-14 |
| hsa05340 | Primary immunodeficiency | 14 | 6.77x10-14 |
| hsa04660 | T cell receptor signaling pathway | 19 | 3.28x10-12 |
| hsa04640 | Hematopoietic cell lineage | 16 | 2.02x10-10 |
| hsa04514 | Cell adhesion molecules | 18 | 6.15x10-9 |
| hsa04062 | Chemokine signaling pathway | 20 | 1.08x10-8 |
| hsa04064 | NF-κB signaling pathway | 13 | 2.47x10-7 |
| hsa05323 | Rheumatoid arthritis | 13 | 2.81x10-7 |
| hsa04672 | Intestinal immune network for IgA production | 10 | 4.78x10-7 |
Figure 2PPI network for DEG-encoded proteins and Module Analysis. (A) PPI network for Module A and B. (B) A total of 17 nodes and 136 relationship pairs with a score of 12 were identified in Module A. (C) A total of 15 nodes and 84 relationship pairs were identified in Module B. Pink circles represent upregulated DEG-encoded proteins, green squares represent downregulated DEG-encoded proteins, and the yellow area represents isolated modules in the network. PPI, protein-protein interaction; DEGs, differentially expressed genes.
Kyoto Encyclopedia Genes and Genomes pathway enrichment analysis results for Module A and Module B.
| A, Module A | ||||
|---|---|---|---|---|
| Pathway ID | Pathway name | Count | P-value | Proteins |
| hsa04062 | Chemokine signaling pathway | 11 | 9.85x10-15 | CCR7, CCR5, CXCR4, CCR2, CXCR6, CXCL9, CCL19, CXCR3, CCL5, CXCL11, CXCL10 |
| hsa04060 | Cytokine-cytokine receptor interaction | 11 | 8.58x10-14 | CCR7, CCR5, CXCR4, CCR2, CXCR6, CXCL9, CCL19, CXCR3, CCL5, CXCL11, CXCL10 |
| hsa04620 | Toll-like receptor signaling pathway | 4 | 6.98x10-04 | CXCL9, CCL5, CXCL11, CXCL10 |
| B, Module B | ||||
| Pathway ID | Pathway name | Count | P-value | Proteins |
| hsa04660 | T cell receptor signaling pathway | 12 | 1.64x10-18 | ITK, PRKCQ, CD3G, CD3D, CD8A, CD3E, CD8B, CD247, LCK, ZAP70, VAV1, LCP2 |
| hsa05340 | Primary immunodeficiency | 6 | 4.12x10-9 | CD3D, CD8A, CD3E, CD8B, LCK, ZAP70 |
| hsa04640 | Hematopoietic cell lineage | 6 | 4.59x10-7 | CD3G, CD3D, CD8A, CD3E, CD8B, HLA-DRB5 |
| hsa04650 | Natural killer cell mediated cytotoxicity | 6 | 2.79x10-6 | PRF1, CD247, LCK, ZAP70, VAV1, LCP2 |
| hsa05166 | HTLV-I infection | 6 | 1.02x10-4 | CD3G, CD3D, CD3E, LCK, HLA-DRB5, HLA-DQA2 |
| hsa04612 | Antigen processing and presentation | 4 | 4.27x10-4 | CD8A, CD8B, HLA-DRB5, HLA-DQA2 |
| hsa05142 | Chagas disease (American trypanosomiasis) | 4 | 1.07x10-3 | CD3G, CD3D, CD3E, CD247 |
| hsa05332 | Graft-versus-host disease | 3 | 1.94x10-3 | PRF1, HLA-DRB5, HLA-DQA2 |
| hsa05162 | Measles | 4 | 2.17x10-3 | PRKCQ, CD3G, CD3D, CD3E |
| hsa05330 | Allograft rejection | 3 | 2.44x10-3 | PRF1, HLA-DRB5, HLA-DQA2 |
| hsa04514 | Cell adhesion molecules (CAMs) | 4 | 2.62x10-3 | CD8A, CD8B, HLA-DRB5, HLA-DQA2 |
| hsa04940 | Type I diabetes mellitus | 3 | 3.13x10-3 | PRF1, HLA-DRB5, HLA-DQA2 |
| hsa05320 | Autoimmune thyroid disease | 3 | 4.77x10-3 | PRF1, HLA-DRB5, HLA-DQA2 |
| hsa05416 | Viral myocarditis | 3 | 5.71x10-3 | PRF1, HLA-DRB5, HLA-DQA2 |
| hsa04064 | NF-kappa B signaling pathway | 3 | 1.29x10-2 | PRKCQ, LCK, ZAP70 |
Figure 3TF/miRNA-target regulatory network in heart failure. Blue triangle represents TFs, the orange diamond represents miRNA, the pink circles represents the upregulated DEGs and the green square represents the downregulated DEGs. TF, transcription factor; miRNA, microRNA; DEGs, differentially expressed genes.
Figure 4mRNA expression levels of GPR18, miR-155 and ETS2 in clinical patients with HF. Expression levels of (A) GPR18, (B) miR-155 and (C) ETS2 in patients with HF compared with normal tissue was assessed using reverse transcription-quantitative PCR. Normal control, n=20; patients with HF, n=20. miR, microRNA; GPR18, G-protein coupled receptor 18; ETS2, E26 transformation-specific transcription factor 2.
Figure 5GPR18 is a target gene of the transcription factor ETS2. (A) mRNA expression levels of GPR18 were determined following the transfection of H9c2 (2-1) cells with an ETS2 overexpressing plasmid. (B) mRNA expression levels of GPR18 were determined following the transfection of H9c2 (2-1) cells with si-ETS2. (C) Protein expression levels of GPR18 following the transfection of cells with either ETS2 overexpression plasmid or si-ETS2. ***P<0.001 vs. control group. GPR18, G-protein coupled receptor 18; si, small interfering RNA; ETS2, E26 transformation-specific transcription factor 2; NC, negative control.
Figure 6miR-155 regulates cell viability and apoptosis through targeting GPR18 in H9c2 (2-1) cells. (A) mRNA expression levels of GPR18 were determined using reverse transcription-quantitative PCR following the overexpression and silencing of miR-155 using a mimic and inhibitor, respectively in H9c2 (2-1) cells. (B) Protein expression levels of GPR18 were determined using western blotting following the overexpression and silencing of miR-155 using a mimic and inhibitor, respectively in H9c2 (2-1) cells. (C) Cell viability of H9c2 (2-1) cells. (D) Semi-quantification of apoptosis in H9c2 (2-1) cells. (E) Apoptosis in H9c2 (2-1) cells. **P<0.01 and ***P<0.001 vs. control group. NC, negative control; miR, microRNA; GPR18, G-protein coupled receptor 18.