Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer
BackgroundAberrant DNA methylation is a crucial epigenetic regulator that is closely related to the occurrence and development of various cancers, including breast cancer (BC). The present study aimed to identify a novel methylation-based prognosis biomarker panel by integrally analyzing gene expres...
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Frontiers Media S.A.
2020-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00301/full |
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| author | Yanshen Kuang Ying Wang Wanli Zhai Xuning Wang Bingdong Zhang Maolin Xu Shaohua Guo Mu Ke Baoqing Jia Hongyi Liu |
| author_facet | Yanshen Kuang Ying Wang Wanli Zhai Xuning Wang Bingdong Zhang Maolin Xu Shaohua Guo Mu Ke Baoqing Jia Hongyi Liu |
| author_sort | Yanshen Kuang |
| collection | DOAJ |
| description | BackgroundAberrant DNA methylation is a crucial epigenetic regulator that is closely related to the occurrence and development of various cancers, including breast cancer (BC). The present study aimed to identify a novel methylation-based prognosis biomarker panel by integrally analyzing gene expression and methylation patterns in BC patients.MethodsDNA methylation and gene expression data of breast cancer (BRCA) were downloaded from The Cancer Genome Atlas (TCGA). R packages, including ChAMP, SVA, and MethylMix, were applied to identify the unique methylation-driven genes. Subsequently, these genes were subjected to Metascape for GO analysis. Univariant Cox regression was used to identify survival-related genes among the methylation-driven genes. Robust likelihood-based survival modeling was applied to define the prognosis markers. An independent data set (GSE72308) was used for further validation of our risk score system.ResultsA total of 879 DNA methylation-driven genes were identified from 765 BC patients. In the discovery cohort, we identified 50 survival-related methylation-driven genes. Finally, we built an eight-methylation-driven gene panel that serves as prognostic predictors.ConclusionsOur analysis of transcriptome and methylome variations associated with the survival status of BC patients provides a further understanding of basic biological processes and a basis for the genetic etiology in BC. |
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| language | English |
| last_indexed | 2024-04-13T17:31:01Z |
| publishDate | 2020-04-01 |
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| spelling | doaj.art-e5f87a0c065c418f8240607c9c4f7b222022-12-22T02:37:34ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-04-011110.3389/fgene.2020.00301523056Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast CancerYanshen Kuang0Ying Wang1Wanli Zhai2Xuning Wang3Bingdong Zhang4Maolin Xu5Shaohua Guo6Mu Ke7Baoqing Jia8Hongyi Liu9Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaState Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing, ChinaState Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing, ChinaDepartment of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaDepartment of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, ChinaDepartment of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaDepartment of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaDepartment of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaDepartment of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaDepartment of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, ChinaBackgroundAberrant DNA methylation is a crucial epigenetic regulator that is closely related to the occurrence and development of various cancers, including breast cancer (BC). The present study aimed to identify a novel methylation-based prognosis biomarker panel by integrally analyzing gene expression and methylation patterns in BC patients.MethodsDNA methylation and gene expression data of breast cancer (BRCA) were downloaded from The Cancer Genome Atlas (TCGA). R packages, including ChAMP, SVA, and MethylMix, were applied to identify the unique methylation-driven genes. Subsequently, these genes were subjected to Metascape for GO analysis. Univariant Cox regression was used to identify survival-related genes among the methylation-driven genes. Robust likelihood-based survival modeling was applied to define the prognosis markers. An independent data set (GSE72308) was used for further validation of our risk score system.ResultsA total of 879 DNA methylation-driven genes were identified from 765 BC patients. In the discovery cohort, we identified 50 survival-related methylation-driven genes. Finally, we built an eight-methylation-driven gene panel that serves as prognostic predictors.ConclusionsOur analysis of transcriptome and methylome variations associated with the survival status of BC patients provides a further understanding of basic biological processes and a basis for the genetic etiology in BC.https://www.frontiersin.org/article/10.3389/fgene.2020.00301/fullepigeneticsDNA methylationbreast cancerprognosis biomarkerintegrative analysis |
| spellingShingle | Yanshen Kuang Ying Wang Wanli Zhai Xuning Wang Bingdong Zhang Maolin Xu Shaohua Guo Mu Ke Baoqing Jia Hongyi Liu Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer Frontiers in Genetics epigenetics DNA methylation breast cancer prognosis biomarker integrative analysis |
| title | Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer |
| title_full | Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer |
| title_fullStr | Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer |
| title_full_unstemmed | Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer |
| title_short | Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer |
| title_sort | genome wide analysis of methylation driven genes and identification of an eight gene panel for prognosis prediction in breast cancer |
| topic | epigenetics DNA methylation breast cancer prognosis biomarker integrative analysis |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00301/full |
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