Genome‑wide DNA methylation profile of thymomas and potential epigenetic regulation of thymoma subtypes

Bi,Yalan; Meng,Yunxiao; Niu,Yuchen; Li,Shanqing; Liu,Hongsheng; He,Jia; Zhang,Ye; Liang,Naixin; Liu,Lei; Mao,Xinxin; Yan,Jie; Long,Bo; Liang,Zhiyong; Wu,Zhihong

doi:10.3892/or.2019.7035

Genome‑wide DNA methylation profile of thymomas and potential epigenetic regulation of thymoma subtypes

Authors:
- Yalan Bi
- Yunxiao Meng
- Yuchen Niu
- Shanqing Li
- Hongsheng Liu
- Jia He
- Ye Zhang
- Naixin Liang
- Lei Liu
- Xinxin Mao
- Jie Yan
- Bo Long
- Zhiyong Liang
- Zhihong Wu
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Affiliations: Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China, Central Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China, Department of General Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
Published online on: February 28, 2019 https://doi.org/10.3892/or.2019.7035
Pages: 2762-2774
Copyright: © Bi et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The aim of the present study was to examine the whole‑genome DNA methylation status of thymomas and identify differences in thymoma DNA methylation profiles. DNA methylation profiles of tissues (n=12) were studied using the Infinium MethylationEPIC BeadChip microarray (850K) and analyzed in relation to gene expression data. Functional annotation analysis of DNA methylation between the different groups was performed using the online tool GeneCodis3. In order to assess the diagnostic value of candidate DNA methylation markers, receiver operation characteristic (ROC) analysis was performed using the pROC package. A total of 10,014 CpGs were found to be differentially methylated (Δβ>0.2) between two thymoma types (type A and B). Combination analysis showed that 36 genes had differentially methylated CpG sites in their promoter region. ‘Pathways in cancer’, ‘focal adhesion’ and ‘regulation of actin cytoskeleton’ were the most enriched KEGG pathways of differentially methylated genes between tumor and controls. Among the 29 genes that were hypomethylated with a high expression, zinc finger protein 396 and Fraser extracellular matrix complex subunit 1 had the largest area under the curve. The present results may provide useful insights into the tumorigenesis of thymomas and a strong basis for future research on the molecular subtyping of epigenetic regulation in thymomas.

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