| Literature DB >> 34093788 |
Chuxiang Lei1, Wenlin Chen2, Yuekun Wang2, Binghao Zhao2, Penghao Liu2, Ziren Kong2, Delin Liu2, Congxin Dai2, Yaning Wang2, Yu Wang2, Wenbin Ma2.
Abstract
Background: Glioblastoma (GBM) is the most common primary malignant intracranial tumor and closely related to metabolic alteration. However, few accepted prognostic models are currently available, especially models based on metabolic genes.Entities:
Keywords: GEO; TCGA; glioblastoma; metabolic gene; prognostic model
Year: 2021 PMID: 34093788 PMCID: PMC8176239 DOI: 10.7150/jca.53827
Source DB: PubMed Journal: J Cancer ISSN: 1837-9664 Impact factor: 4.207
Figure 1Flow chart presenting the entire design of the study.
Figure 2Univariate Cox regression of all of the differentially expressed genes.
Genes with log2FC, FDR and their coefficients in the prognostic model after LASSO regression
| Gene symbol | Training cohort | Coefficients† | Validation cohort | ||
|---|---|---|---|---|---|
| Log2FC‡ | FDR¶ | Log2FC‡ | FDR¶ | ||
| -0.28 | <0.001* | -0.006377627 | 0.18 | 0.030* | |
| -0.26 | <0.001* | -0.002879681 | -0.43 | <0.001* | |
| -0.29 | <0.001* | -0.002808587 | 0.17 | 0.017* | |
| -0.67 | <0.001* | -0.002396644 | -0.72 | 0.3 | |
| -0.48 | <0.001* | -0.001860585 | -0.51 | <0.001* | |
| -0.44 | <0.001* | -0.001453787 | 0.26 | 0.016* | |
| -0.51 | 0.046* | -0.001408588 | -0.55 | <0.001* | |
| -0.76 | 0.002* | -0.001196549 | -0.13 | 0.3 | |
| -0.65 | 0.011* | -0.001020503 | -0.65 | <0.001* | |
| -0.34 | 0.1 | -0.000394242 | -0.29 | 0.1 | |
| 0.97 | <0.001* | -0.000262491 | 0.03 | 0.4 | |
| 0.15 | 0.1 | 0.000358099 | 0.08 | 0.4 | |
| 0.48 | 0.002* | 0.000502893 | -0.19 | <0.001* | |
| 0.60 | <0.001* | 0.001414345 | 0.66 | <0.001* | |
| 0.50 | <0.001* | 0.002176092 | 0.44 | <0.001* | |
| 0.28 | 0.003* | 0.002265462 | 0.47 | <0.001* | |
| 0.75 | <0.001* | 0.003109864 | 0.85 | <0.001* | |
| 0.60 | 0.002* | 0.004181019 | 0.36 | <0.001* | |
‡ log2FC=log2(mean expression of high-risk group/mean expression of low-risk group)
¶ FDR was calculated by the P value from the Wilcoxon test.
† Coefficients were calculated by Lasso regression.
* marked significant differences.
log2FC: log2 fold change; FDR: false discovery rate.
Figure 3Kaplan-Meier survival curve for the training cohort (A) and validation cohort (B). P value from the log-rank test.
Figure 4Risk plot of the training and validation cohorts. A heatmap of 18 metabolic genes showed the different expression patterns between high-risk and low-risk patients in the training (A) and validation (D) cohorts. (B and E) plotted the risk score of each patient and presented the cut-off value that defined high- and low-risk patients in the 2 cohorts, respectively. The OS of patients in the training (C) and validation (F) cohorts was plotted according to the value of the risk score. OS: overall survival.
Figure 5Cox regression, ROC analysis, and nomograms for patients in the training and validation cohorts. (A) Multivariate Cox regression of the training cohort. (B) Multivariate Cox regression of the validation cohort. The hazard ratios of age and risk score were 1.031 (95% CI 1.013-1.049) and 1.251 (95% CI 1.019-1.534), respectively, with P values less than 0.05. (C and D) ROC analysis of age, sex, and risk score of patients in the training (C) and validation (D) cohorts. (E and F) Nomograms predicted the 1-, 2-, and 3-year survival of patients in the training (E) and validation (F) cohorts. # Female=0; Male=1. ROC: receiver operating characteristic.
Univariate Cox regression of training and validation cohorts
| Training cohort | Validation cohort | |||||
|---|---|---|---|---|---|---|
| HR | 95% CI | HR | 95% CI | |||
| Age | 1.049 | (1.017, 1.081) | 0.002* | 1.035 | (1.017, 1.053) | <0.001* |
| Gender† | 1.415 | (0.746, 2.683) | 0.3 | 0.824 | (0.555, 1.224) | 0.3 |
| Risk score | 7.782 | (2.268, 26.704) | 0.001* | 1.336 | (1.102, 1.620) | 0.003* |
† Female=0, Male=1; HR: hazard ratio; CI: confidence interval. *Marked significant differences.
Figure 6Multiple GSEA of the enriched KEGG pathways in the training (A) and validation (B) cohorts. GSEA: gene set enrichment analysis.
Figure 7Validation of the crucial genes in the prognostic model. A. Quantitative real-time polymerase chain reaction (qRT-PCR) of the 5 crucial genes. B&C. Representative figures and statistical analysis of immunohistochemical staining. D&E. Representative figures and statistical analysis of western blot. *P<0.05, **P<0.01, ***P<0.001 vs. respective normal tissues.