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Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma
BACKGROUND: Osteosarcoma (OS) is a common malignant bone tumor in children and adolescents. DNA methylation plays a crucial role in the prognosis prediction of cancer. Identification of novel DNA methylation sites biomarkers could be beneficial for the prognosis of OS patients. In this study, we aim...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
AME Publishing Company
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798623/ https://www.ncbi.nlm.nih.gov/pubmed/35117331 http://dx.doi.org/10.21037/tcr-20-3204 |
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author | Zhang, Xijun Zheng, Yongjun Li, Gaoshan Yu, Changying Ji, Ting Miao, Shenghu |
author_facet | Zhang, Xijun Zheng, Yongjun Li, Gaoshan Yu, Changying Ji, Ting Miao, Shenghu |
author_sort | Zhang, Xijun |
collection | PubMed |
description | BACKGROUND: Osteosarcoma (OS) is a common malignant bone tumor in children and adolescents. DNA methylation plays a crucial role in the prognosis prediction of cancer. Identification of novel DNA methylation sites biomarkers could be beneficial for the prognosis of OS patients. In this study, we aim to find an efficient methylated site model for predicting survival in OS. METHODS: DNA methylation data were downloaded from the Cancer Genome Atlas database (TCGA) and the GEO database. Cox proportional hazard regression and random survival forest algorithm (RSFVH) were applied to identify DNA methylated site signature in the samples randomly assigned to the training subset and the other samples as the test subset. By randomizing 71 clinical samples into two individual groups and a series of statistical analyses between the two groups, a DNA methylation signature is verified. RESULTS: This signature comprises four methylation sites (cg04533248, cg12401425, cg13997435, and cg15075357) associated with the patient training group from the univariate Cox proportional hazards regression analysis, RSFVH, and multivariate Cox regression analysis. Kaplan-Meier survival curves showed the OS patients in the high-risk group have a poor 5-year overall survival compared with the low-risk group, and this finding was identified in the test data set. A ROC analysis was performed in the current research. The results revealed that this signature was an independent predictor of patient survival by investigating the AUC of the four methylation sites signature in the training data set (AUC =0.861) and test data set, respectively (AUC =0.920). The nomogram described in the current study placed a great guiding value for predicting 1-, 2-, 3-year survival of the OS by combining age, gender, grade, and TNM stage as covariates with the RS of patients’ methylation related signatures. CONCLUSIONS: Our study proved that this signature might be a powerful prognostic tool for survival rate evaluation and guide tailored therapy for OS patients. |
format | Online Article Text |
id | pubmed-8798623 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | AME Publishing Company |
record_format | MEDLINE/PubMed |
spelling | pubmed-87986232022-02-02 Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma Zhang, Xijun Zheng, Yongjun Li, Gaoshan Yu, Changying Ji, Ting Miao, Shenghu Transl Cancer Res Original Article BACKGROUND: Osteosarcoma (OS) is a common malignant bone tumor in children and adolescents. DNA methylation plays a crucial role in the prognosis prediction of cancer. Identification of novel DNA methylation sites biomarkers could be beneficial for the prognosis of OS patients. In this study, we aim to find an efficient methylated site model for predicting survival in OS. METHODS: DNA methylation data were downloaded from the Cancer Genome Atlas database (TCGA) and the GEO database. Cox proportional hazard regression and random survival forest algorithm (RSFVH) were applied to identify DNA methylated site signature in the samples randomly assigned to the training subset and the other samples as the test subset. By randomizing 71 clinical samples into two individual groups and a series of statistical analyses between the two groups, a DNA methylation signature is verified. RESULTS: This signature comprises four methylation sites (cg04533248, cg12401425, cg13997435, and cg15075357) associated with the patient training group from the univariate Cox proportional hazards regression analysis, RSFVH, and multivariate Cox regression analysis. Kaplan-Meier survival curves showed the OS patients in the high-risk group have a poor 5-year overall survival compared with the low-risk group, and this finding was identified in the test data set. A ROC analysis was performed in the current research. The results revealed that this signature was an independent predictor of patient survival by investigating the AUC of the four methylation sites signature in the training data set (AUC =0.861) and test data set, respectively (AUC =0.920). The nomogram described in the current study placed a great guiding value for predicting 1-, 2-, 3-year survival of the OS by combining age, gender, grade, and TNM stage as covariates with the RS of patients’ methylation related signatures. CONCLUSIONS: Our study proved that this signature might be a powerful prognostic tool for survival rate evaluation and guide tailored therapy for OS patients. AME Publishing Company 2020-11 /pmc/articles/PMC8798623/ /pubmed/35117331 http://dx.doi.org/10.21037/tcr-20-3204 Text en 2020 Translational Cancer Research. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/. |
spellingShingle | Original Article Zhang, Xijun Zheng, Yongjun Li, Gaoshan Yu, Changying Ji, Ting Miao, Shenghu Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma |
title | Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma |
title_full | Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma |
title_fullStr | Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma |
title_full_unstemmed | Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma |
title_short | Identifying four DNA methylation gene sites signature for predicting prognosis of osteosarcoma |
title_sort | identifying four dna methylation gene sites signature for predicting prognosis of osteosarcoma |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798623/ https://www.ncbi.nlm.nih.gov/pubmed/35117331 http://dx.doi.org/10.21037/tcr-20-3204 |
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