Differentially Expression of NCOA4 and NCOA4-related Differential Genes in GBM
The pan-cancer analyses were performed to compare the expression of NCOA4 in the tumor samples of GTEx combined with TCGA and the corresponding normal samples of TCGA by Wilcoxon rank sum test. NCOA4 was significant differential expressed in adrenocortical carcinoma (ACC), bladder urothelial carcinoma (BLCA), breast infiltrating carcinoma (BRCA), cervical squamous cell carcinoma and adenocarcinoma (CESC), cholangiocarcinoma (CHOL), Colon adenocarcinoma (COAD), diffuse large B cell lymphoma (DLBC), Esophageal carcinoma (ESCA), pleomorphic glioma (GBM), head and neck squamous cell carcinoma (HNSC), renal chromophobe cell carcinoma (KICH), renal clear cell carcinoma (KIRC), renal papillary cell carcinoma (KIRP), acute myeloid leukemia (LAML), brain low grade glioma (LGG), Liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), mesothelioma (MESO), ovarian serous cystadenocarcinoma (OV),pancreatic cancer (PAAD), pheochromocytoma and paraganglioma (PCPG), prostate cancer (PRAD), rectum adenocarcinoma (READ), sarcoma(SARC), skin melanoma (SKCM), gastric cancer (STAD), Testicular Germ Cell Tumors (TGCT), thyroid cancer (THCA), thymic cancer (THYM), endometrial cancer (UCEC), uterine sarcoma (UCS), uveal melanoma (UVM) (P < 0.05) (Figure 1A). Secondly, we compared the expression of NCOA4 in 1157 paracancerous samples and 168 GBM samples in TCGA GBM dataset. The expression of NCOA4 was significantly high in GBM samples (P < 0.001) (Figure 1B). ROC was used to analyze the distinguishing efficacy of NCOA4 between GBM tissues and normal paracancerous tissue. The area under the curve (AUC) of NCOA4 is 0.925, suggesting that NCOA4 may be a potentially identification molecule for GBM tissues (Figure 1C). Moreover, in the Human Protein Atlas, NCOA4 protein expression was increased in GBM tissues compared with normal tissues. We divided them into 84 NCOA4 high expression and 84 and low expression using median as the boundary. A total of 37 DEGs, covering 36 upregulated GENEs and 1 downregulated GENEs, were identified to be statistically significant between the two cohorts (adjusted p-value < 0.05, |Log2-fold change| > 2.0) (Figure 1D).
Functional Enrichment and Signaling Pathways of NCOA4 Related Genes in GBM
To search for functional enrichment of NCOA4-related genes, our GO enrichment analysis suggested that nCOA4-related genes were mainly enriched in focal adhesion, collagen-containing extracellular matrix, cell-substrate adherens junction, cell-substrate junction, cell-cell junction. (Figure 2A-B). The high and low expression of NCOA4 in GBM were analyzed by GSEA to search for NCOA4 enrichment signaling pathway. Finally, these signaling pathways include neutrophil Degranulation Pathway, signaling by Interleukins Pathway, r-RNA processing Pathway and translation Pathway (Figures 2C–D). We found from The Human Protein Atlas database that the expression of NCOA4 in GBM tissues was higher than that in normal tissues (Figure 1E-F).
Protein-Protein Interaction (PPI) Network Analysis in the differentially expressed genes
In order to acquire the interactions between the DEGs in the GBM group, a PPI network was constructed using the STRING database. In our study, the top 10 genes included AR, FTL, FTH1, CCDC6, RET, GFRA1, CTNNB1, HSP90AA1, FOXA1, PELP1(Figure.3).
The interrelation Between NCOA4 and Immune Infiltration
The interrelation between the expression level of NCOA4 and immune cell infiltration level quantified by ssGSEA was analyzed. The expression of NCOA4 was negatively interrelated with the infiltration degree of NK CD56bright cells, and positively interrelated with the infiltration degree of mast cells, B cells, T cells, T helper cells. (Figures 4A–K, P < 0.001).
Correlation between NCOA4 and clinical features
The clinical characteristics and expression of NCOA4 in 168 GBM patients in TCGA were analyzed. We analyzed 109 men and 59 women, as shown in Figures 5A-F and Table 1, overexpressed NCOA4 was significantly correlated with IDH status (wild type vs. mutational type, P = 0.027). Interestingly, Our Logistic regression analysis showed that NCOA4 overexpression was also related to IDH mutation (wild type vs. mutational type, P = 0.024). (Table 2).
The OS rate of patients with high NCOA4 expression was significantly higher than that of patients with low NCOA4 expression (P = 0.042; Figure 6A). However, there were no significant differences in DSS rate and PFI between NCOA4 group and NCOA4 group (P = 0.106; P = 0.383; Figures 6B, C). In our opinion, this may be due to the rapid disease progression of GBM patients, and it is difficult to show significant differences between DSS and PFI.
Construction of NCOA4 Related Nomogram
We constructed a Nomogram using NCOA4 and other clinical indicators to predict the prognosis of patients with GBM. (Figure 7A). We obtained the final Nomogram by multivariate COX regression analysis. In the Nomogram, each factor is assigned a score range, and the sum of all factor scores is the final score, corresponding to the 1-year, 2-year and 3-year survival probability of GBM patients. (Figure 7A).
To test the prediction accuracy of this Nomogram for prognosis, we calculate a C-index of 0.622(CI: 0.5900-0.653). And the calibration curve shows that our prediction and observation have a good consistency. (Figure7B).