| Literature DB >> 34247183 |
Abstract
BACKGROUND Melanoma is one of the most lethal tumors and its treatment is still challenging. It is urgent to detect novel therapy targets in melanoma. MATERIAL AND METHODS The GEO dataset was used to obtain a list of DEGS (differentially-expressed genes). Integrative bioinformatics analyses, including HPRD database, TCGA data, and TIMER, were performed to determine the role of CXCL13 in SKCM (skin cutaneous melanoma) progression and the immune environment. Furthermore, Pearson correlation coefficient analysis was used to measure correlations between CXCL13 and its co-expressed genes. Survival analysis, GO, and KEGG enrichment analysis were performed to investigate the role of CXCL13 in SKCM. RESULTS A total of 41 DEGs were identified in 3 GEO datasets, and 4 out of 41 DEGs are hub genes. Among the 4 hub genes, CXCL13 is involved in the most KEGG terms. CXCL13 is co-expressed with well-known immune checkpoint blockade targets, and it was associated with better overall survival. In addition, CXCL13 levels in infiltrating immune cells (neutrophil and myeloid dendritic cells) affect prognosis and survival in SKCM. Functional enrichment analysis clarified that CXCL13-co-expressed top 30 genes were associated with immune signaling pathways. Network analysis identified CXCL13 as a hub gene that interacts with CXCR5 to participate in immune-related biological process. CONCLUSIONS This study found that CXCL13 is associated with SKCM tumorigenesis and prognosis and immune infiltrations. Our result suggests that CXCL13 has great potential in development of novel immunotherapy targets in melanoma.Entities:
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Year: 2021 PMID: 34247183 PMCID: PMC8280950 DOI: 10.12659/MSM.932052
Source DB: PubMed Journal: Med Sci Monit ISSN: 1234-1010
Figure 1Venn diagram and the most significant KEGG pathways of 41DEGs. (A) The Venn diagram displays the number of DEGs in 3 datasets from the GEO database. (B) Four significant KEGG pathways of 41 DEGs. Adjusted p value <0.01. Figure 1A was produced using the Venny website (https://bioinfogp.cnb.csic.es/tools/venny/index.html, version 2.1). Figure 1B was produced using clusterProfiler packages in R (version 3.6, https://www.r-project.org/).
Figure 2The network and survival plot. (A) The PPI (Protein-Protein Interaction) network of 4 high-degree DEGs (differentially-expressed genes). (B) Kaplan-Meier survival curves show that the expression of CXCL13 is consistently associated with better overall survival (OS) in SKCM. Figure 2A was produced using Cytoscape (version 3.8.2, https://cytoscape.org/). Figure 2B was produced using survival and survminer packages in R (version 3.6, https://www.r-project.org/).
Figure 3CXCL13 associated top 30 co-expressed genes and functional enrichment analysis in SKCM. (A) PCC was used to calculate correlations between CXCL13 and expressed genes in SKCM. Heat map showing top 30 genes positively correlated with CXCL13 in SKCM. (B) The significantly enriched GO annotations of the top 30 high CXCL13 co-expression genes in SKCM were analyzed. Figure 3A was produced using pheatmap packages in R (version 3.6, https://www.r-project.org/) and Figure 3B was produced using clusterProfiler packages in R (version 3.6, https://www.r-project.org/).
Figure 4Gene expression correlation analysis. The scatter plot shows Pearson correlation of CXCL13 expression with expression of PDCD1 (A), CD274 (B), and CTLA4 (C). These figures were produced using ggplot2, ggpubr, and ggpmisc packages in R (version 3.6, https://www.r-project.org/).
Figure 5Kaplan-Meier survival curves show that CXCL13 expression and PDCD1/CD274/CTLA4 expression are significantly associated with OS in TCGA-SKCM cohorts (A) PDCD1, (B) CD274, (C) CTLA4. These figures were produced using survival and survminer packages in R (version 3.6, https://www.r-project.org/).
Figure 6Correlation of CXCL13 expression with immune infiltration level in the TIMER database. (A) Neutrophil cells, (B) macrophages, (C) myeloid dendritic cells and (D) CD4+ T cells. These figures were produced using the TIMMER website (http://timer.cistrome.org, version 2.0).
The 41 common DEGs in GSE15605, GSE46517, and GSE114445.
| 41 differential expressed genes |
|---|
| LAMB4, CHP2, EXPH5,CDHR1, SCGB1D2, CCL27, GATA3, PRAME, CYP3A5, RORA, POU2F3, SCEL, PDZD2, DSC3, SPP1, KLF5, WIF1, GZMB, PHACTR1, TFAP2B, GDF15, RGS1, IGF2BP3, SCGB2A2, CCL3L3, C1QB, MAGEA6, CYP39A1, IL37, MAGEA6, CITED1, MAGEA12, FCGR2A, SLAMF7, MMP1, CXCL13, MAGEA2B, CXCL9, CCL5, UBD, LCE2B |
The KEGG enrichment of 41 DEGs.
| ID | Description | p value | p. adjust | Gene ID | Count |
|---|---|---|---|---|---|
| hsa04061 | Viral protein interaction with cytokine and cytokine receptor | 7.23E-08 | 4.55E-06 | 10850/414062/27178/10563/4283/6352 | 6 |
| hsa04060 | Cytokine-cytokine receptor interaction | 2.73E-06 | 8.58E-05 | 10850/9518/414062/27178/10563/4283/6352 | 7 |
| hsa04062 | Chemokine signaling pathway | 6.28E-05 | 0.00132 | 10850/414062/10563/4283/6352 | 5 |
| hsa04620 | Toll-like receptor signaling pathway | 8.55E-05 | 0.001347 | 6696/414062/4283/6352 | 4 |