| Literature DB >> 31788074 |
Yuexiong Yi1, Yanyan Liu1, Kejia Wu1, Wanrong Wu1, Wei Zhang1.
Abstract
The present study aimed to identify the core genes and pathways involved in depression in patients with ovarian cancer (OC) who suffer from high or low-grade depression. The dataset GSE9116 from Gene Expression Omnibus database was analyzed to identify differentially expressed genes (DEGs) in these patients. To elucidate how certain genes could promote depression in patients with OC, pathway crosstalk, protein-protein interaction (PPI) and comprehensive gene-pathway analyses were determined using WebGestalt, ToppGene and Search Tool for the Retrieval of Interacting Genes and gene ontology analysis. Key genes and pathways were extracted from the gene-pathway network, and gene expression and survival analysis were evaluated. A total of 93 DEGs were identified from GSE9116 dataset, including 84 upregulated genes and nine downregulated genes. The PPI, pathway crosstalk and comprehensive gene-pathway analyses highlighted C-C motif chemokine ligand 2 (CCL2), Fos proto-oncogene, AP-1 transcription factor subunit (FOS), serpin family E member 1 (SERPINE1) and serpin family G member 1 (SERPING1) as core genes involved in the promotion of depression in patients with OC. These core genes were involved in the following four pathways 'Ensemble of genes encoding ECM-associated proteins including ECM-affiliated proteins', 'ECM regulators and secreted factors', 'Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins' and 'MAPK signaling pathway and IL-17 signaling pathway'. The results from gene expression and survival analysis demonstrated that these four key genes were upregulated in patients with OC and high-grade depression and could worsen patients' survival. These results suggested that CCL2, FOS, SERPINE1 and SERPING1 may serve a crucial role in the promotion of depression in patients with OC. This finding may provide novel markers for predicting and treating depression in patients with OC; however, the underlying mechanisms remain unknown and require further investigation. Copyright: © Yi et al.Entities:
Keywords: bioinformatics; depression; molecular mechanism; oncogenes; ovarian cancer
Year: 2019 PMID: 31788074 PMCID: PMC6865084 DOI: 10.3892/ol.2019.10934
Source DB: PubMed Journal: Oncol Lett ISSN: 1792-1074 Impact factor: 2.967
Figure 1.Workflow for the identification of core genes promoting depression in patients with ovarian cancer. FC, fold change; DEGs, differentially expressed genes.
Figure 2.Heatmap of all differentially expressed genes from the GSE9116 dataset. The groups indicated at the top of the figure in blue and red represent groups with low-grade depression and high-grade depression, respectively. The numbers in the expression key represent the log2 value of reads for each gene.
Figure 3.Results of GO enrichment analysis for ‘Biological Process’, ‘Cellular Component’ and ‘Molecular Function’ categories. The number on each bar indicates the number of enriched genes annotated with the corresponding GO term. Go, Gene Ontology.
Figure 4.PPI network, pathway crosstalk and gene-pathway analyses of the DEGs from the GSE9116 dataset. (A) PPI network of candidate genes. Red, core genes. Orange, top three up-regulated genes. Blue, other DEGs. (B) Subnetwork of PPI network for hub genes of which nodal degree > average. Red, core genes. Orange, top three up-regulated genes. Blue, other DEGs. (C) Pathway crosstalk analysis of DEGs. Edge thickness represents the average value of Jaccard and Overlapping Coefficient. (D) Subnetwork of pathway crosstalk extracted by the criterion nodal degree > average. (E) Comprehensive gene-pathway network established by mapping the hub genes to the subnetwork. The arrow direction between gene and pathway was determined from Kyoto Gene and Genome Encyclopedia database and BioCarta. Red circle, core genes. Blue circle, other DEGs. Green square, pathways. (F) Subnetwork of gene-pathway collected according to the criterion nodal degree > average; Red circle, core genes. Green square, pathways. ATF3, activating transcription factor 3; CCL2, C-C motif chemokine ligand 2; CTGF, cellular communication network factor 2; DEGs, differentially expressed genes; FOS, Fos proto-oncogene, AP-1 transcription factor subunit; PLAT, plasminogen activator, tissue type; PPI, protein-protein interaction; SERPINE1, serpin family E member 1; SERPING1, serpin family G member 1.
Characteristics of genes identified from protein-protein interaction network.
| Rank | Gene | Degree of each node |
|---|---|---|
| Overall average value | 3.2352 | |
| 1 | FOS | 9 |
| 2 | JUNB | 7 |
| 3 | DUSP1 | 6 |
| 4 | EGR1 | 6 |
| 5 | FOSB | 6 |
| 6 | SERPINE1 | 6 |
| 7 | SPARC | 5 |
| 8 | TIMP3 | 5 |
| 9 | JUND | 5 |
| 10 | SEPP1 | 4 |
| 11 | SERPING1 | 4 |
| 12 | ZFP36 | 4 |
| 13 | ATF3 | 4 |
| 14 | COL3A1 | 4 |
| 15 | DCN | 4 |
| 16 | CCL2 | 4 |
| 17 | LUM | 3 |
| 18 | CTGF | 2 |
| 19 | CXCL12 | 2 |
| 20 | CTSB | 2 |
| 21 | HLA-DPA1 | 2 |
| 22 | CHPT1 | 2 |
| 23 | PLA2G7 | 2 |
| 24 | PLA2G16 | 2 |
| 25 | SMARCA4 | 1 |
| 26 | CST3 | 1 |
| 27 | KLC1 | 1 |
| 28 | PNOC | 1 |
| 29 | TMEM176A | 1 |
| 30 | TMEM176B | 1 |
| 31 | PRELP | 1 |
| 32 | DUSP6 | 1 |
| 33 | PLOD2 | 1 |
| 34 | PLAT | 1 |
Results from pathway enrichment analysis.
| Pathways | Source | P-value | Genes in the pathway |
|---|---|---|---|
| Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins | BIOCARTA | 1.19×10−08 | COL3A1, CRISPLD2, FBLN5, SPARC, MXRA5, DCN, EGFL6, TIMP3, PLXNC1, PRELP, SERPINE1, XCL2, CST3, SERPING1, CCL2, PLAT, CTGF, LUM, CTSB, XCL1, PLOD2, CXCL12 |
| Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans | BIOCARTA | 1.73×10−05 | COL3A1, CRISPLD2, FBLN5, SPARC, MXRA5, DCN, PRELP, CTGF, LUM |
| Complement and coagulation cascades | KEGG | 6.90×10−05 | SERPINE1, SERPING1, PLAT, C4A, C4B |
| Pertussis toxin-insensitive CCR5 signaling in Macrophage | BIOCARTA | 1.20×10−04 | FOS, CCL2, CXCL12 |
| Rheumatoid arthritis | KEGG | 1.29×10−04 | ATP6V1B1, HLA-DPA1, FOS, CCL2, CXCL12 |
| Ensemble of genes encoding ECM-associated proteins including ECM-affiliated proteins, ECM regulators and secreted factors | BIOCARTA | 1.85×10−04 | EGFL6, TIMP3, PLXNC1, SERPINE1, XCL2, CST3, SERPING1, CCL2, PLAT, CTSB, XCL1, PLOD2, CXCL12 |
| Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix | BIOCARTA | 3.07×10−04 | TIMP3, SERPINE1, CST3, SERPING1, PLAT, CTSB, PLOD2 |
| MAPK signaling pathway | KEGG | 4.66×10−04 | FOS, DUSP1, DUSP6, JUND, FGFR3, HSPA1A, HSPA1B |
| Pertussis | KEGG | 7.77×10−04 | FOS, SERPING1, C4A, C4B |
| Antigen processing and presentation | KEGG | 8.16×10−04 | HLA-DPA1, CTSB, HSPA1A, HSPA1B |
| Genes encoding proteoglycans | BIOCARTA | 9.00×10−04 | DCN, PRELP, LUM |
| IL-17 signaling pathway | KEGG | 1.65×10−03 | FOS, FOSB, JUND, CCL2 |
| Lectin Induced Complement Pathway | BIOCARTA | 1.87×10−03 | C4A, C4B |
| Fibrinolysis Pathway | BIOCARTA | 1.87×10−03 | SERPINE1, PLAT |
| Ether lipid metabolism | KEGG | 1.88×10−03 | PLA2G7, PLA2G16, CHPT1 |
| Estrogen signaling pathway | KEGG | 2.00×10−03 | FOS, HSPA1A, HSPA1B, GABBR1 |
| AGE-RAGE signaling pathway in diabetic complications | KEGG | 2.08×10−03 | COL3A1, EGR1, SERPINE1, CCL2 |
| Classical Complement Pathway | BIOCARTA | 2.56×10−03 | C4A, C4B |
| Platelet Amyloid Precursor Protein Pathway | BIOCARTA | 2.56×10−03 | SERPINE1, PLAT |
| B Cell Survival Pathway | BIOCARTA | 3.36×10−03 | FOS, JUND |
| Staphylococcus aureus infection | KEGG | 3.51×10−03 | HLA-DPA1, C4A, C4B |
| Genes encoding structural ECM glycoproteins | BIOCARTA | 4.29×10−03 | CRISPLD2, FBLN5, SPARC, MXRA5, CTGF |
| Complement Pathway | BIOCARTA | 4.73×10−03 | C4A, C4B |
| Osteoclast differentiation | KEGG | 5.52×10−03 | FOS, FOSB, JUNB, JUND |
Figure 5.Expression of the core genes CCL2, FOS, SERPINE1 and SERPING1 and the top three up and downregulated genes PLAT, ATF3, CTGF, HSPA1B, ENDOG and EPS8L1 obtained from GSE9116. All core genes were upregulated in the high-grade depression group. ATF3, activating transcription factor 3; CCL2, C-C motif chemokine ligand 2; CTGF, cellular communication network factor 2; DEGs, differentially expressed genes; ENDOG, endonuclease G; EPS8L1, EPS8 like 1; FOS, Fos proto-oncogene, AP-1 transcription factor subunit; HSPA1B, heat shock protein family A (Hsp70) member 1B; PLAT, plasminogen activator, tissue type; PPI, protein-protein interaction; SERPINE1, serpin family E member 1; SERPING1, serpin family G member 1.
Figure 6.Survival analysis of the core genes; CCL2, FOS, SERPINE1 and SERPING1, and the top three up/downregulated genes; PLAT, ATF3, CTGF, HSPA1B, ENDOG and EPS8L1. Vertical dotted line represents no effect for the pooled relative risk estimation. If the confidence intervals for individual gene overlap with this line, it means that the survival between low and high expression is not significant. ATF3, activating transcription factor 3; CCL2, C-C motif chemokine ligand 2; CTGF, cellular communication network factor 2; DEGs, differentially expressed genes; ENDOG, endonuclease G; EPS8L1, EPS8 like 1; FOS, Fos proto-oncogene, AP-1 transcription factor subunit; HSPA1B, heat shock protein family A (Hsp70) member 1B; OS, overall survival; PFS, progression-free survival; PLAT, plasminogen activator, tissue type; PPI, protein-protein interaction; PPS, post-progression survival; SERPINE1, serpin family E member 1; SERPING1, serpin family G member 1.