Discovering the key genes and important DNA methylation regions in breast cancer

被引：7
作者：
Cao, Yan-Ni [1 ]
Li, Qian-Zhong [1 ,2 ]
Liu, Yu-Xian [1 ]
Jin, Wen [1 ]
Hou, Rui [1 ]
机构：
[1] Inner Mongolia Univ, Sch Phys Sci & Technol, Lab Theoret Biophys, 235 West Daxue St, Hohhot 010021, Peoples R China
[2] Inner Mongolia Univ, State Key Lab Reprod Regulat & Breeding Grassland, Hohhot 010070, Peoples R China
来源：
HEREDITAS | 2022年 / 159卷 / 01期
基金：
中国国家自然科学基金;
关键词：
Breast cancer; DNA methylation; Oncogene; Tumor suppressor gene; Biomarker; HYPERMETHYLATION; PATHWAYS; RISK;
D O I：
10.1186/s41065-022-00220-5
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
Background Breast cancer is the malignant tumor with the highest incidence in women. DNA methylation has an important effect on breast cancer, but the effect of abnormal DNA methylation on gene expression in breast cancer is still unclear. Therefore, it is very important to find therapeutic targets related to DNA methylation. Results In this work, we calculated the DNA methylation distribution and gene expression level in cancer and para-cancerous tissues for breast cancer samples. We found that DNA methylation in key regions is closely related to gene expression by analyzing the relationship between the distribution characteristics of DNA methylation in different regions and the change of gene expression level. Finally, the 18 key genes (17 tumor suppressor genes and 1 oncogene) related to prognosis were confirmed by the survival analysis of clinical data. Some important DNA methylation regions in these genes that result in breast cancer were found. Conclusions We believe that 17 TSGs and 1 oncogene may be breast cancer biomarkers regulated by DNA methylation in key regions. These results will help to explore DNA methylation biomarkers as potential therapeutic targets for breast cancer.
引用
收藏
页数：13
相关论文
共 46 条
[1]   The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice [J].
Abbott, Kenneth L. ;
Nyre, Erik T. ;
Abrahante, Juan ;
Ho, Yen-Yi ;
Vogel, Rachel Isaksson ;
Starr, Timothy K. .
NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D844-D848
[2]  
Abe O, 2005, LANCET, V366, P2087, DOI 10.1016/s0140-6736(05)66544-0
[3]   Runx2 association with progression of prostate cancer in patients: mechanisms mediating bone osteolysis and osteoblastic metastatic lesions [J].
Akech, J. ;
Wixted, J. J. ;
Bedard, K. ;
van der Deen, M. ;
Hussain, S. ;
Guise, T. A. ;
van Wijnen, A. J. ;
Stein, J. L. ;
Languino, L. R. ;
Altieri, D. C. ;
Pratap, J. ;
Keller, E. ;
Stein, G. S. ;
Lian, J. B. .
ONCOGENE, 2010, 29 (06) :811-821
[4]   jvenn: an interactive Venn diagram viewer [J].
Bardou, Philippe ;
Mariette, Jerome ;
Escudie, Frederic ;
Djemiel, Christophe ;
Klopp, Christophe .
BMC BIOINFORMATICS, 2014, 15
[5]   A decade of exploring the cancer epigenome - biological and translational implications [J].
Baylin, Stephen B. ;
Jones, Peter A. .
NATURE REVIEWS CANCER, 2011, 11 (10) :726-734
[6]   Enhancer methylation dynamics contribute to cancer plasticity and patient mortality [J].
Bell, Rachel E. ;
Golan, Tamar ;
Sheinboim, Danna ;
Malcov, Hagar ;
Amar, David ;
Salamon, Avi ;
Liron, Tamar ;
Gelfman, Sahar ;
Gabet, Yankel ;
Shamir, Ron ;
Levy, Carmit .
GENOME RESEARCH, 2016, 26 (05) :601-611
[7]   DNA methylation and hormone receptor status in breast cancer [J].
Benevolenskaya, Elizaveta V. ;
Islam, Abul B. M. M. K. ;
Ahsan, Habibul ;
Kibriya, Muhammad G. ;
Jasmine, Farzana ;
Wolff, Ben ;
Al-Alem, Umaima ;
Wiley, Elizabeth ;
Kajdacsy-Balla, Andre ;
Macias, Virgilia ;
Rauscher, Garth H. .
CLINICAL EPIGENETICS, 2016, 8 :1-10
[8]   High density DNA methylation array with single CpG site resolution [J].
Bibikova, Marina ;
Barnes, Bret ;
Tsan, Chan ;
Ho, Vincent ;
Klotzle, Brandy ;
Le, Jennie M. ;
Delano, David ;
Zhang, Lu ;
Schroth, Gary P. ;
Gunderson, Kevin L. ;
Fan, Jian-Bing ;
Shen, Richard .
GENOMICS, 2011, 98 (04) :288-295
[9]   Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma [J].
Cao, Wei ;
Lee, Hayan ;
Wu, Wei ;
Zaman, Aubhishek ;
McCorkle, Sean ;
Yan, Ming ;
Chen, Justin ;
Xing, Qinghe ;
Sinnott-Armstrong, Nasa ;
Xu, Hongen ;
Sailani, M. Reza ;
Tang, Wenxue ;
Cui, Yuanbo ;
Liu, Jia ;
Guan, Hongyan ;
Lv, Pengju ;
Sun, Xiaoyan ;
Sun, Lei ;
Han, Pengli ;
Lou, Yanan ;
Chang, Jing ;
Wang, Jinwu ;
Gao, Yuchi ;
Guo, Jiancheng ;
Schenk, Gundolf ;
Shain, Alan Hunter ;
Biddle, Fred G. ;
Collisson, Eric ;
Snyder, Michael ;
Bivona, Trever G. .
NATURE COMMUNICATIONS, 2020, 11 (01)
[10]   Evaluation of Promoter Methylation of RASSF1A and ATM in Peripheral Blood of Breast Cancer Patients and Healthy Control Individuals [J].
Cao, Xue ;
Tang, Qiuqiong ;
Holland-Letz, Tim ;
Guendert, Melanie ;
Cuk, Katarina ;
Schott, Sarah ;
Heil, Joerg ;
Golatta, Michael ;
Sohn, Christof ;
Schneeweiss, Andreas ;
Burwinkel, Barbara .
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2018, 19 (03)
12345