Dataset Information

GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.

ABSTRACT:

Motivation

Many studies have shown that IDH mutation and 1p/19q co-deletion can serve as prognostic signatures of glioma. Although these genetic variations affect the expression of one or more genes, the prognostic value of gene expression related to IDH and 1p/19q status is still unclear.

Results

We constructed an ensemble gene pair signature for the risk evaluation and survival prediction of glioma based on the prior knowledge of the IDH and 1p/19q status. First, we separately built two gene pair signatures IDH-GPS and 1p/19q-GPS and elucidated that they were useful transcriptome markers projecting from corresponding genome variations. Then, the gene pairs in these two models were assembled to develop an integrated model named Glioma Prognostic Gene Pair Signature (GPGPS), which demonstrated high area under the curves (AUCs) to predict 1-, 3- and 5-year overall survival (0.92, 0.88 and 0.80) of glioma. GPGPS was superior to the single GPSs and other existing prognostic signatures (avg AUC = 0.70, concordance index = 0.74). In conclusion, the ensemble prognostic signature with 10 gene pairs could serve as an independent predictor for risk stratification and survival prediction in glioma. This study shed light on transferring knowledge from genetic alterations to expression changes to facilitate prognostic studies.

Availability and implementation

Codes are available at https://github.com/Kimxbzheng/GPGPS.git.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Cheng L

PROVIDER: S-EPMC9843586 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.

Cheng Lixin L Wu Haonan H Zheng Xubin X Zhang Ning N Zhao Pengfei P Wang Ran R Wu Qiong Q Liu Tao T Yang Xiaojun X Geng Qingshan Q

Bioinformatics (Oxford, England) 20230101 1

<h4>Motivation</h4>Many studies have shown that IDH mutation and 1p/19q co-deletion can serve as prognostic signatures of glioma. Although these genetic variations affect the expression of one or more genes, the prognostic value of gene expression related to IDH and 1p/19q status is still unclear.<h4>Results</h4>We constructed an ensemble gene pair signature for the risk evaluation and survival prediction of glioma based on the prior knowledge of the IDH and 1p/19q status. First, we separately b ...[more]

PMID: 36637205

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Project description:BackgroundThe nuclear transport system has been proposed to be indispensable for cell proliferation and invasion in cancers. Prognostic biomarkers and molecular targets in nuclear transport systems have been developed. However, no systematic analysis of genes related to nuclear transport in gliomas has been performed. An integrated prognostic classification involving mutation and nuclear transport gene signatures has not yet been explored.MethodsIn the present study, we analyzed gliomas from a training cohort (TCGA dataset, n = 660) and validation cohort (CGGA dataset, n = 668) to develop a prognostic nuclear transport gene signature and generate an integrated classification system. Gene set enrichment analysis (GSEA) showed that glioblastoma (GBM) was mainly enriched in nuclear transport progress compared to lower-grade glioma (LGG). Then, we developed a nuclear transport risk score (NTRS) for gliomas with a training cohort. NTRS was significantly correlated with clinical and genetic characteristics, including grade, age, histology, IDH status and 1p/19q codeletion, in the training and validation cohorts.ResultsSurvival analysis revealed that patients with a higher NTRS exhibited shorter overall survival. NTRS showed better prognostic value compared to classical molecular markers, including IDH status and 1p/19q codeletion. Furthermore, univariate and multivariate analyses indicated that NTRS was an independent prognostic factor for gliomas. Enrichment map and Gene Ontology analysis demonstrated that signaling pathways related to the cell cycle were enriched in the NTRSHigh group. Subgroup survival analysis revealed that NTRS could differentiate the outcomes of low- and high-risk patients with wild-type IDH or mutant IDH and 1p/19q non-codeletion.ConclusionsNTRS is associated with poor outcomes and could be an independent prognostic marker in diffuse gliomas. Prognostic classification combined with IDH mutation, 1p/19q codeletion and NTRS could better predict the survival of glioma patients.

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Dataset Information

GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.

Motivation

Results

Availability and implementation

Supplementary information

Publications

GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.

Similar Datasets

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