MethMarkerDB: a comprehensive cancer DNA methylation biomarker database

被引：5
|
作者：
Zhu, Zhixian [1 ,2 ]
Zhou, Qiangwei [1 ,2 ]
Sun, Yuanhui [1 ,2 ]
Lai, Fuming [1 ,2 ]
Wang, Zhenji [1 ,2 ]
Hao, Zhigang [1 ,2 ]
Li, Guoliang [1 ,2 ]
机构：
[1] Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Hubei Hongshan Lab, Wuhan 430070, Peoples R China
[2] Huazhong Agr Univ, Hubei Engn Technol Res Ctr Agr Big Data, 3D Genom Res Ctr, Agr Bioinformat Key Lab Hubei Prov,Coll Informat,K, Wuhan 430070, Peoples R China
来源：
NUCLEIC ACIDS RESEARCH | 2023年
关键词：
PROMOTER METHYLATION; MOLECULAR-DETECTION; PROSTATE-CANCER; PROGNOSIS; UPDATE; METASTASIS; ANNOTATION; ENHANCERS; DIAGNOSIS; ARCHIVE;
D O I：
10.1093/nar/gkad923
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
DNA methylation plays a crucial role in tumorigenesis and tumor progression, sparking substantial interest in the clinical applications of cancer DNA methylation biomarkers. Cancer-related whole-genome bisulfite sequencing (WGBS) data offers a promising approach to precisely identify these biomarkers with differentially methylated regions (DMRs). However, currently there is no dedicated resource for cancer DNA methylation biomarkers with WGBS data. Here, we developed a comprehensive cancer DNA methylation biomarker database (MethMarkerDB, https://methmarkerdb.hzau.edu.cn/), which integrated 658 WGBS datasets, incorporating 724 curated DNA methylation biomarker genes from 1425 PubMed published articles. Based on WGBS data, we documented 5.4 million DMRs from 13 common types of cancer as candidate DNA methylation biomarkers. We provided search and annotation functions for these DMRs with different resources, such as enhancers and SNPs, and developed diagnostic and prognostic models for further biomarker evaluation. With the database, we not only identified known DNA methylation biomarkers, but also identified 781 hypermethylated and 5245 hypomethylated pan-cancer DMRs, corresponding to 693 and 2172 genes, respectively. These novel potential pan-cancer DNA methylation biomarkers hold significant clinical translational value. We hope that MethMarkerDB will help identify novel cancer DNA methylation biomarkers and propel the clinical application of these biomarkers. Graphical Abstract
引用
收藏
页码：D1380 / D1392
页数：13
相关论文
共 50 条
  • [31] Cell-Free DNA as a Biomarker in the Context of Cancer, Viruses, and Methylation
    Stebbing, Justin
    Bower, Mark
    JOURNAL OF INFECTIOUS DISEASES, 2012, 205 (07): : 1032 - 1034
  • [32] DNA methylation as a cancer-specific biomarker - From molecules to populations
    Patel, A
    Groopman, JD
    Umar, A
    EPIGENETICS IN CANCER PREVENTION: EARLY DETECTION AND RISK ASSESSMENT, 2003, 983 : 286 - 297
  • [33] DNA methylation of GSTP1 as biomarker in diagnosis of prostate cancer
    Hopkins, Tom G.
    Burns, Philip A.
    Routledge, Michael N.
    UROLOGY, 2007, 69 (01) : 11 - 16
  • [34] Septin9 DNA methylation as a promising biomarker for cervical cancer
    Bu, Qiaowen
    Luo, Xiping
    He, Lulu
    Ma, Jian
    He, Shaoyi
    Lei, Wen
    Zhou, Weiping
    Deng, Hua
    Lin, Yu
    Zhang, Liang
    Hong, Xiaoshan
    JOURNAL OF OBSTETRICS AND GYNAECOLOGY, 2023, 43 (01)
  • [35] The DNA methylation of LGALS3 gene as a prostate cancer biomarker
    Abramovic, I.
    Pezelj, I.
    Kulis, T.
    Ulamec, M.
    Bulimbasic, S.
    Bojanac, A. Katusic
    Sincic, N.
    FEBS OPEN BIO, 2022, 12 : 86 - 87
  • [36] A DNA methylation biomarker of alcohol consumption
    Liu, C.
    Marioni, R. E.
    Hedman, A. K.
    Pfeiffer, L.
    Tsai, P-C
    Reynolds, L. M.
    Just, A. C.
    Duan, Q.
    Boer, C. G.
    Tanaka, T.
    Elks, C. E.
    Aslibekyan, S.
    Brody, J. A.
    Kuehnel, B.
    Herder, C.
    Almli, L. M.
    Zhi, D.
    Wang, Y.
    Huan, T.
    Yao, C.
    Mendelson, M. M.
    Joehanes, R.
    Liang, L.
    Love, S-A
    Guan, W.
    Shah, S.
    Mcrae, A. F.
    Kretschmer, A.
    Prokisch, H.
    Strauch, K.
    Peters, A.
    Visscher, P. M.
    Wray, N. R.
    Guo, X.
    Wiggins, K. L.
    Smith, A. K.
    Binder, E. B.
    Ressler, K. J.
    Irvin, M. R.
    Absher, D. M.
    Hernandez, D.
    Ferrucci, L.
    Bandinelli, S.
    Lohman, K.
    Ding, J.
    Trevisi, L.
    Gustafsson, S.
    Sandling, J. H.
    Stolk, L.
    Uitterlinden, A. G.
    MOLECULAR PSYCHIATRY, 2018, 23 (02) : 422 - 433
  • [37] A DNA methylation biomarker of alcohol consumption
    C Liu
    R E Marioni
    Å K Hedman
    L Pfeiffer
    P-C Tsai
    L M Reynolds
    A C Just
    Q Duan
    C G Boer
    T Tanaka
    C E Elks
    S Aslibekyan
    J A Brody
    B Kühnel
    C Herder
    L M Almli
    D Zhi
    Y Wang
    T Huan
    C Yao
    M M Mendelson
    R Joehanes
    L Liang
    S-A Love
    W Guan
    S Shah
    A F McRae
    A Kretschmer
    H Prokisch
    K Strauch
    A Peters
    P M Visscher
    N R Wray
    X Guo
    K L Wiggins
    A K Smith
    E B Binder
    K J Ressler
    M R Irvin
    D M Absher
    D Hernandez
    L Ferrucci
    S Bandinelli
    K Lohman
    J Ding
    L Trevisi
    S Gustafsson
    J H Sandling
    L Stolk
    A G Uitterlinden
    Molecular Psychiatry, 2018, 23 : 422 - 433
  • [38] DNA Methylation as a Biomarker for Neuropsychiatric Diseases
    Ai, Sanxi
    Shen, Lu
    Guo, Jifeng
    Feng, Xiang
    Tang, Beisha
    INTERNATIONAL JOURNAL OF NEUROSCIENCE, 2012, 122 (04) : 165 - 176
  • [39] A Comprehensive Database for DNA Adductomics
    La Barbera, Giorgia
    Nommesen, Katrine Dalmo
    Cuparencu, Catalina
    Stanstrup, Jan
    Dragsted, Lars Ove
    FRONTIERS IN CHEMISTRY, 2022, 10
  • [40] A comprehensive database for DNA adductomics
    La Barbera, Giorgia
    Nommesen, Katrine D.
    Cuparencu, Catalina
    Stanstrup, Jan
    Dragsted, Lars O.
    ENVIRONMENTAL AND MOLECULAR MUTAGENESIS, 2023, 64 : 27 - 28
12345