Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma
Background Lower grade glioma (LGG) are a heterogeneous tumor that may develop into high-grade malignant glioma seriously shortens patient survival time. The clinical prognostic biomarker of lower-grade glioma is still lacking. The aim of our study is to explore novel biomarkers for LGG that contrib...
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PeerJ Inc.
2020-01-01
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| Online Access: | https://peerj.com/articles/8312.pdf |
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| author | Kai Xiao Qing Liu Gang Peng Jun Su Chao-Ying Qin Xiang-Yu Wang |
| author_facet | Kai Xiao Qing Liu Gang Peng Jun Su Chao-Ying Qin Xiang-Yu Wang |
| author_sort | Kai Xiao |
| collection | DOAJ |
| description | Background Lower grade glioma (LGG) are a heterogeneous tumor that may develop into high-grade malignant glioma seriously shortens patient survival time. The clinical prognostic biomarker of lower-grade glioma is still lacking. The aim of our study is to explore novel biomarkers for LGG that contribute to distinguish potential malignancy in low-grade glioma, to guide clinical adoption of more rational and effective treatments. Methods The RNA-seq data for LGG was downloaded from UCSC Xena and the Chinese Glioma Genome Atlas (CGGA). By a robust likelihood-based survival model, least absolute shrinkage and selection operator regression and multivariate Cox regression analysis, we developed a three-gene signature and established a risk score to predict the prognosis of patient with LGG. The three-gene signature was an independent survival predictor compared to other clinical parameters. Based on the signature related risk score system, stratified survival analysis was performed in patients with different age group, gender and pathologic grade. The prognostic signature was validated in the CGGA dataset. Finally, weighted gene co-expression network analysis (WGCNA) was carried out to find the co-expression genes related to the member of the signature and enrichment analysis of the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were conducted for those co-expression network. To prove the efficiency of the model, time-dependent receiver operating characteristic curves of our model and other models are constructed. Results In this study, a three-gene signature (WEE1, CRTAC1, SEMA4G) was constructed. Based on the model, the risk score of each patient was calculated with LGG (low-risk vs. high-risk, hazard ratio (HR) = 0.198 (95% CI [0.120–0.325])) and patients in the high-risk group had significantly poorer survival results than those in the low-risk group. Furthermore, the model was validated in the CGGA dataset. Lastly, by WGCNA, we constructed the co-expression network of the three genes and conducted the enrichment of GO and KEGG. Our study identified a three-gene model that showed satisfactory performance in predicting the 1-, 3- and 5-year survival of LGG patients compared to other models and may be a promising independent biomarker of LGG. |
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| language | English |
| last_indexed | 2024-03-09T06:37:51Z |
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| spelling | doaj.art-16272e82bbcb4152a53f64e437e6a9712023-12-03T10:55:08ZengPeerJ Inc.PeerJ2167-83592020-01-018e831210.7717/peerj.8312Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade gliomaKai XiaoQing LiuGang PengJun SuChao-Ying QinXiang-Yu WangBackground Lower grade glioma (LGG) are a heterogeneous tumor that may develop into high-grade malignant glioma seriously shortens patient survival time. The clinical prognostic biomarker of lower-grade glioma is still lacking. The aim of our study is to explore novel biomarkers for LGG that contribute to distinguish potential malignancy in low-grade glioma, to guide clinical adoption of more rational and effective treatments. Methods The RNA-seq data for LGG was downloaded from UCSC Xena and the Chinese Glioma Genome Atlas (CGGA). By a robust likelihood-based survival model, least absolute shrinkage and selection operator regression and multivariate Cox regression analysis, we developed a three-gene signature and established a risk score to predict the prognosis of patient with LGG. The three-gene signature was an independent survival predictor compared to other clinical parameters. Based on the signature related risk score system, stratified survival analysis was performed in patients with different age group, gender and pathologic grade. The prognostic signature was validated in the CGGA dataset. Finally, weighted gene co-expression network analysis (WGCNA) was carried out to find the co-expression genes related to the member of the signature and enrichment analysis of the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were conducted for those co-expression network. To prove the efficiency of the model, time-dependent receiver operating characteristic curves of our model and other models are constructed. Results In this study, a three-gene signature (WEE1, CRTAC1, SEMA4G) was constructed. Based on the model, the risk score of each patient was calculated with LGG (low-risk vs. high-risk, hazard ratio (HR) = 0.198 (95% CI [0.120–0.325])) and patients in the high-risk group had significantly poorer survival results than those in the low-risk group. Furthermore, the model was validated in the CGGA dataset. Lastly, by WGCNA, we constructed the co-expression network of the three genes and conducted the enrichment of GO and KEGG. Our study identified a three-gene model that showed satisfactory performance in predicting the 1-, 3- and 5-year survival of LGG patients compared to other models and may be a promising independent biomarker of LGG.https://peerj.com/articles/8312.pdfLow-grade gliomaPrognosisWGCNARisk scoreRobust likelihood-based survival modelBiomarker |
| spellingShingle | Kai Xiao Qing Liu Gang Peng Jun Su Chao-Ying Qin Xiang-Yu Wang Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma PeerJ Low-grade glioma Prognosis WGCNA Risk score Robust likelihood-based survival model Biomarker |
| title | Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma |
| title_full | Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma |
| title_fullStr | Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma |
| title_full_unstemmed | Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma |
| title_short | Identification and validation of a three-gene signature as a candidate prognostic biomarker for lower grade glioma |
| title_sort | identification and validation of a three gene signature as a candidate prognostic biomarker for lower grade glioma |
| topic | Low-grade glioma Prognosis WGCNA Risk score Robust likelihood-based survival model Biomarker |
| url | https://peerj.com/articles/8312.pdf |
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