Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression
DNA methylation plays a critical role in tumorigenesis through regulating oncogene activation and tumor suppressor gene silencing. Although extensively analyzed, the implication of DNA methylation in gene regulatory network is less characterized. To address this issue, in this study we performed an...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00711/full |
| _version_ | 1818525277900242944 |
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| author | Jun Wu Yunzhao Gu Yawen Xiao Chao Xia Hua Li Yani Kang Jielin Sun Zhifeng Shao Zongli Lin Xiaodong Zhao |
| author_facet | Jun Wu Yunzhao Gu Yawen Xiao Chao Xia Hua Li Yani Kang Jielin Sun Zhifeng Shao Zongli Lin Xiaodong Zhao |
| author_sort | Jun Wu |
| collection | DOAJ |
| description | DNA methylation plays a critical role in tumorigenesis through regulating oncogene activation and tumor suppressor gene silencing. Although extensively analyzed, the implication of DNA methylation in gene regulatory network is less characterized. To address this issue, in this study we performed an integrative analysis on the alteration of DNA methylation patterns and the dynamics of gene regulatory network topology across distinct stages of stomach cancer. We found the global DNA methylation patterns in different stages are generally conserved, whereas some significantly differentially methylated genes were exclusively observed in the early stage of stomach cancer. Integrative analysis of DNA methylation and network topology alteration yielded several genes which have been reported to be involved in the progression of stomach cancer, such as IGF2, ERBB2, GSTP1, MYH11, TMEM59, and SST. Finally, we demonstrated that inhibition of SST promotes cell proliferation, suggesting that DNA methylation-associated SST suppression possibly contributes to the gastric cancer progression. Taken together, our study suggests the DNA methylation-associated regulatory network analysis could be used for identifying cancer-related genes. This strategy can facilitate the understanding of gene regulatory network in cancer biology and provide a new insight into the study of DNA methylation at system level. |
| first_indexed | 2024-12-11T06:07:19Z |
| format | Article |
| id | doaj.art-da0bc44915104fa59e18ea7f7cb0f729 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T06:07:19Z |
| publishDate | 2019-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-da0bc44915104fa59e18ea7f7cb0f7292022-12-22T01:18:16ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-02-01910.3389/fgene.2018.00711431167Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer ProgressionJun Wu0Yunzhao Gu1Yawen Xiao2Chao Xia3Hua Li4Yani Kang5Jielin Sun6Zhifeng Shao7Zongli Lin8Xiaodong Zhao9School of Life Sciences, East China Normal University, Shanghai, ChinaBio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, ChinaDepartment of Automation, Shanghai Jiao Tong University, Shanghai, ChinaBio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, ChinaBio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, ChinaBio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, ChinaShanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, ChinaBio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, ChinaCharles L. Brown Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA, United StatesShanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, ChinaDNA methylation plays a critical role in tumorigenesis through regulating oncogene activation and tumor suppressor gene silencing. Although extensively analyzed, the implication of DNA methylation in gene regulatory network is less characterized. To address this issue, in this study we performed an integrative analysis on the alteration of DNA methylation patterns and the dynamics of gene regulatory network topology across distinct stages of stomach cancer. We found the global DNA methylation patterns in different stages are generally conserved, whereas some significantly differentially methylated genes were exclusively observed in the early stage of stomach cancer. Integrative analysis of DNA methylation and network topology alteration yielded several genes which have been reported to be involved in the progression of stomach cancer, such as IGF2, ERBB2, GSTP1, MYH11, TMEM59, and SST. Finally, we demonstrated that inhibition of SST promotes cell proliferation, suggesting that DNA methylation-associated SST suppression possibly contributes to the gastric cancer progression. Taken together, our study suggests the DNA methylation-associated regulatory network analysis could be used for identifying cancer-related genes. This strategy can facilitate the understanding of gene regulatory network in cancer biology and provide a new insight into the study of DNA methylation at system level.https://www.frontiersin.org/article/10.3389/fgene.2018.00711/fullDNA methylationgene regulation networkstomach cancertumor stagessystem level |
| spellingShingle | Jun Wu Yunzhao Gu Yawen Xiao Chao Xia Hua Li Yani Kang Jielin Sun Zhifeng Shao Zongli Lin Xiaodong Zhao Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression Frontiers in Genetics DNA methylation gene regulation network stomach cancer tumor stages system level |
| title | Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression |
| title_full | Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression |
| title_fullStr | Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression |
| title_full_unstemmed | Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression |
| title_short | Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression |
| title_sort | characterization of dna methylation associated gene regulatory networks during stomach cancer progression |
| topic | DNA methylation gene regulation network stomach cancer tumor stages system level |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00711/full |
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