Cargando…
Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data
Purpose: Alternative splicing (AS) was reported to play a vital role in development and progression of glioblastoma (GBM), the most common and fatal brain tumor. Systematic analysis of survival-associated AS event profiles and prognostic prediction model based on multiple AS events in GBM was needed...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7387698/ https://www.ncbi.nlm.nih.gov/pubmed/32793502 http://dx.doi.org/10.3389/fonc.2020.01257 |
_version_ | 1783564179203948544 |
---|---|
author | Wang, Zihao Gao, Lu Guo, Xiaopeng Feng, Chenzhe Lian, Wei Deng, Kan Xing, Bing |
author_facet | Wang, Zihao Gao, Lu Guo, Xiaopeng Feng, Chenzhe Lian, Wei Deng, Kan Xing, Bing |
author_sort | Wang, Zihao |
collection | PubMed |
description | Purpose: Alternative splicing (AS) was reported to play a vital role in development and progression of glioblastoma (GBM), the most common and fatal brain tumor. Systematic analysis of survival-associated AS event profiles and prognostic prediction model based on multiple AS events in GBM was needed. Methods: Genome-wide AS and RNA sequencing profiles were generated in 152 patients with GBM in the cancer genome atlas (TCGA). Prognosis-associated AS events were screened by integrated Cox regression analysis to construct the prognostic risk score model in the training cohort (n = 101). The AS-based signature and clinicopathologic parameters were applied to construct a prognostic nomogram for 0.5-, 1-, and 3-year OS prediction. Finally, the regulatory networks between prognostic AS events and splicing factors (SFs) were constructed. Results: A total of 1,598 prognosis-related AS events from 1,183 source genes were determined. Eight prognostic risk score model based on integrated AS events and 7 AS types were established, respectively. Concordance index (C-index) and receiver operating characteristic (ROC) curve analysis demonstrated powerful ability in distinguishing patients' outcomes. Only Alternate Donor site (AD) and Exon Skip (ES) signature out of the eight types of AS signature were identified as independent prognostic factors for GBM, which was validated in the internal validation cohort. The nomogram with age, new event, pharmaceutical therapy, radiation therapy, AD signature and ES signature were constructed, with C-index of 0.892 (95% CI, 0.853–0.931; P = 5.13 × 10(−15)). Calibration plots, ROC, and decision curve analysis suggested excellent predictive performance for the nomogram in both TCGA training cohort and validation cohort. Splicing network indicated distinguished correlations between prognostic AS events and SFs in GBM patients. Conclusions: AS-based prediction model could serve as a promising prognostic predictor and potential therapeutic target for GBM, facilitating better treatment strategies in clinical practice. |
format | Online Article Text |
id | pubmed-7387698 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-73876982020-08-12 Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data Wang, Zihao Gao, Lu Guo, Xiaopeng Feng, Chenzhe Lian, Wei Deng, Kan Xing, Bing Front Oncol Oncology Purpose: Alternative splicing (AS) was reported to play a vital role in development and progression of glioblastoma (GBM), the most common and fatal brain tumor. Systematic analysis of survival-associated AS event profiles and prognostic prediction model based on multiple AS events in GBM was needed. Methods: Genome-wide AS and RNA sequencing profiles were generated in 152 patients with GBM in the cancer genome atlas (TCGA). Prognosis-associated AS events were screened by integrated Cox regression analysis to construct the prognostic risk score model in the training cohort (n = 101). The AS-based signature and clinicopathologic parameters were applied to construct a prognostic nomogram for 0.5-, 1-, and 3-year OS prediction. Finally, the regulatory networks between prognostic AS events and splicing factors (SFs) were constructed. Results: A total of 1,598 prognosis-related AS events from 1,183 source genes were determined. Eight prognostic risk score model based on integrated AS events and 7 AS types were established, respectively. Concordance index (C-index) and receiver operating characteristic (ROC) curve analysis demonstrated powerful ability in distinguishing patients' outcomes. Only Alternate Donor site (AD) and Exon Skip (ES) signature out of the eight types of AS signature were identified as independent prognostic factors for GBM, which was validated in the internal validation cohort. The nomogram with age, new event, pharmaceutical therapy, radiation therapy, AD signature and ES signature were constructed, with C-index of 0.892 (95% CI, 0.853–0.931; P = 5.13 × 10(−15)). Calibration plots, ROC, and decision curve analysis suggested excellent predictive performance for the nomogram in both TCGA training cohort and validation cohort. Splicing network indicated distinguished correlations between prognostic AS events and SFs in GBM patients. Conclusions: AS-based prediction model could serve as a promising prognostic predictor and potential therapeutic target for GBM, facilitating better treatment strategies in clinical practice. Frontiers Media S.A. 2020-07-22 /pmc/articles/PMC7387698/ /pubmed/32793502 http://dx.doi.org/10.3389/fonc.2020.01257 Text en Copyright © 2020 Wang, Gao, Guo, Feng, Lian, Deng and Xing. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Oncology Wang, Zihao Gao, Lu Guo, Xiaopeng Feng, Chenzhe Lian, Wei Deng, Kan Xing, Bing Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data |
title | Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data |
title_full | Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data |
title_fullStr | Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data |
title_full_unstemmed | Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data |
title_short | Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data |
title_sort | development of a nomogram with alternative splicing signatures for predicting the prognosis of glioblastoma: a study based on large-scale sequencing data |
topic | Oncology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7387698/ https://www.ncbi.nlm.nih.gov/pubmed/32793502 http://dx.doi.org/10.3389/fonc.2020.01257 |
work_keys_str_mv | AT wangzihao developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata AT gaolu developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata AT guoxiaopeng developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata AT fengchenzhe developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata AT lianwei developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata AT dengkan developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata AT xingbing developmentofanomogramwithalternativesplicingsignaturesforpredictingtheprognosisofglioblastomaastudybasedonlargescalesequencingdata |