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MethMarkerDB：一个全面的癌症 DNA 甲基化生物标志物数据库。

MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.

机构信息

National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.

Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.

出版信息

Nucleic Acids Res. 2024 Jan 5;52(D1):D1380-D1392. doi: 10.1093/nar/gkad923.

DOI:10.1093/nar/gkad923
PMID:37889076
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10767949/
Abstract

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.

摘要

DNA 甲基化在肿瘤发生和肿瘤进展中起着至关重要的作用，这激发了人们对癌症 DNA 甲基化生物标志物临床应用的浓厚兴趣。癌症相关的全基因组亚硫酸氢盐测序（WGBS）数据为精确识别这些具有差异甲基化区域（DMR）的生物标志物提供了一种很有前途的方法。然而，目前还没有专门针对癌症 DNA 甲基化生物标志物与 WGBS 数据的资源。在这里，我们开发了一个综合的癌症 DNA 甲基化生物标志物数据库（MethMarkerDB，https://methmarkerdb.hzau.edu.cn/），该数据库整合了 658 个 WGBS 数据集，包含了从 1425 篇已发表在 PubMed 上的文章中精选出的 724 个 DNA 甲基化生物标志物基因。基于 WGBS 数据，我们从 13 种常见类型的癌症中记录了 540 万个 DMR，作为候选的 DNA 甲基化生物标志物。我们为这些 DMR 提供了基于不同资源（如增强子和 SNPs）的搜索和注释功能，并为进一步的生物标志物评估开发了诊断和预后模型。通过该数据库，我们不仅鉴定了已知的 DNA 甲基化生物标志物，还鉴定了 781 个高甲基化和 5245 个低甲基化的泛癌症 DMR，分别对应 693 个和 2172 个基因。这些新的潜在泛癌症 DNA 甲基化生物标志物具有重要的临床转化价值。我们希望 MethMarkerDB 将有助于鉴定新的癌症 DNA 甲基化生物标志物，并推动这些生物标志物的临床应用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/dbb0d60a0088/gkad923fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/e97540b813ba/gkad923figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/0d7da58bc67a/gkad923fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/3452d9e8780d/gkad923fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/88748ad5120d/gkad923fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/6eecac418fc0/gkad923fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/dbb0d60a0088/gkad923fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/e97540b813ba/gkad923figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/0d7da58bc67a/gkad923fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/3452d9e8780d/gkad923fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/88748ad5120d/gkad923fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/6eecac418fc0/gkad923fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9669/10767949/dbb0d60a0088/gkad923fig5.jpg

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