| Literature DB >> 31710183 |
Yan Zhou1, Xuan Wang1, Xing Huang1, Xu-Dong Li1, Kai Cheng1, Hao Yu1, Yu-Jie Zhou1, Peng Lv1, Xiao-Bing Jiang1.
Abstract
AIMS: To evaluate the clinical significance of coatomer protein complex subunit beta 2 (COPB2) in patients with glioma using a bioinformatics analysis.Entities:
Keywords: zzm321990COPB2zzm321990; biomarker; gene set enrichment analysis; gene set variation analysis; glioma
Mesh:
Substances:
Year: 2019 PMID: 31710183 PMCID: PMC7081167 DOI: 10.1111/cns.13254
Source DB: PubMed Journal: CNS Neurosci Ther ISSN: 1755-5930 Impact factor: 5.243
Figure 1A, COPB2’ expression level in cancers in Oncomine Database: the left box in red indicated the number of datasets with COPB2 hyperexpression and the right box in blue indicated the number of datasets with COPB2 hypo expression after comparing cancerous and normal tissues. B, C, TCGA cohort and GSE16011 dataset from GEO support the findings that indicate COPB2 upregulation in glioma
The Cancer Genome Atlas glioma patient characteristics
| Clinical characteristics | No. of patients | Percentage (%) | |
|---|---|---|---|
| Age (y) | 9‐89 | Median 52 | |
| Sex | Male | 651 | 58.4 |
| Female | 460 | 41.3 | |
| Missing | 3 | 0.270 | |
| Vital status | Alive | 570 | 51.2 |
| Dead | 539 | 48.4 | |
| Missing | 5 | 0.450 | |
| WHO grade | G2 | 249 | 22.4 |
| G3 | 265 | 23.8 | |
| G4 | 596 | 53.5 | |
| Missing | 4 | 3.60 | |
| Histology | Astrocytoma | 194 | 17.4 |
| Oligodendroglioma | 191 | 17.2 | |
| Oligoastrocytoma | 130 | 11.7 | |
| Glioblastoma | 596 | 53.5 | |
| Missing | 3 | 0.270 | |
| KPS | <80 | 151 | 13.6 |
| ≥80 | 584 | 52.4 | |
| Missing | 379 | 34.0 | |
| Tumor status | Tumor‐free | 209 | 18.8 |
| With tumor | 783 | 70.3 | |
| Missing | 122 | 11.0 | |
|
| Yes | 91 | 8.17 |
| No | 34 | 3.05 | |
| Missing | 989 | 88.8 | |
| Family history of cancer | Yes | 132 | 11.9 |
| No | 210 | 18.9 | |
| Missing | 772 | 69.3 | |
| Ethnicity | Hispanic or Latino | 45 | 4.04 |
| Not Hispanic or Latino | 939 | 84.3 | |
| Missing | 130 | 11.7 | |
Figure 2Associations between COPB2 expression and clinicopathologic variables in TCGA cohort, including (A): age, (B): WHO Grade, (C): histological type, (D): KPS, (E): IDH1 mutation, (F): tumor status, (G): family history of cancer, (H): vital status, and (I): influence of COPB2 expression on overall survival of glioma patients in TCGA cohort
COPB2 expression associated with clinical‐pathological characteristics (logistic regression)
| Clinical characteristics | Total (N) | Odds ratio in |
|
|---|---|---|---|
| Age (≥52 vs <52) | 670 | 2.35 (1.71‐3.23) | <.001 |
| Sex (male vs female) | 670 | 1.10 (0.81‐1.50) | .530 |
| Vital status (dead vs alive) | 670 | 2.89 (2.07‐4.07) | <.001 |
| Grade (III vs II) | 509 | 1.92 (1.35‐2.76) | <.001 |
| (IV vs II) | 409 | 8.00 (5.07‐12.89) | <.001 |
| Histological type | |||
| (GBM vs astrocytoma) | 352 | 4.20 (2.70‐6.61) | <.001 |
| (GBM vs oligoastrocytoma) | 288 | 6.08 (3.67‐10.29) | <.001 |
| (GBM vs oligodendroglioma) | 350 | 5.54 (3.52‐8.85) | <.001 |
| Tumor status (with tumor vs tumor‐free) | 591 | 3.11 (2.17‐4.50) | <.001 |
|
| 126 | 0.510 (0.220‐1.12) | .100 |
| KPS (<80 vs ≥80) | 413 | 1.80 (1.07‐3.07) | .0300 |
| Ethnicity (Hispanic or Latino vs not Hispanic or Latino) | 609 | 1.28 (0.640‐2.61) | .490 |
| Family history of cancer (yes vs no) | 338 | 1.22 (0.790‐1.89) | .370 |
(A) Univariate analysis of clinicopathologic characteristics and overall survival in The Cancer Genome Atlas cohort. (B) Multivariate analysis postvariable selection
| Characteristics | Hazard ratio (95% CI) |
|
|---|---|---|
| A. | ||
| Age | 3.70 (2.52‐5.44) | <.001 |
| Gender | 1.08 (0.750‐1.55) | .696 |
| Grade | 5.32 (3.88‐7.31) | <.001 |
| Histological type | 1.89 (1.54‐2.30) | <.001 |
| KPS | 2.26 (1.41‐3.62) | <.001 |
| Tumor status | 39.7 (5.53‐284) | <.001 |
| Ethnicity | 0.480 (0.150‐1.51) | .209 |
|
| 1.13 (1.09‐1.18) | <.001 |
| B. | ||
| Tumor status | 4.51 (3.29‐6.18) | <.001 |
| Histological type | 1.07 (0.900‐1.27) | .452 |
|
| 1.05 (1.01‐1.08) | .00600 |
Figure 3Enrichment plots from gene set enrichment analysis (GSEA)
Gene sets enriched in high COPB2 expression phenotype
| MSigDB collection | Gene set name | NES | NOM | FDR |
|---|---|---|---|---|
| Kegg.v6.2.symbols.gmt | KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION | 1.78 | .0180 | 0.0250 |
| KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY | 1.73 | .0240 | 0.0300 | |
| KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY | 1.68 | .0250 | 0.0390 | |
| KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS | 1.80 | .00800 | 0.0220 | |
| KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY | 1.66 | .0330 | 0.0420 | |
| KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION | 1.91 | .00200 | 0.0110 | |
| KEGG_PATHWAYS_IN_CANCER | 2.14 | 0 | 0.00300 | |
| KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION | 1.73 | .0270 | 0.0300 |
Gene sets with NOM P‐value <.05 and FDR q‐value <0.05 were considered as significantly enriched.
Abbreviations: FDR, false discovery rate; NES, normalized enrichment score; NOM, nominal.
Figure 4COPB2‐related inflammatory response. Heat maps displaying COPB2 expression, the clinicopathological parameters, and seven well‐established metagenes from the TCGA datasets
Figure 5A, Correlograms were established based on GSVA enrichment scores for the seven metagenes and COPB2 expression. The circles filled clockwise in blue represented positive values and anticlockwise in red represented negative values. The color depth increased with the absolute values of the correlation. B, Correlations of COPB2 mRNA with immune cell markers. Each circle represented a single sample
Secreted and membrane immunosuppressive molecules expressed by glioma cells
| Cytokines | Type | Function | References |
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| Soluble | Suppressing T‐cell activation, proliferation and differentiation into effector cells. |
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| Membrane proteins | Inducing apoptosis of T and B cells from PBMCs. |
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| Inducing apoptosis of FAS‐expressing T cells. |
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| Inhibiting proliferation, cytotoxicity by interaction with inhibitory receptors expressed on effector lymphocytes. |
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| Inhibiting T‐cell proliferation. |
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