bims-dinmec 2025-10-19 papers

Issue of 2025–10–19
two papers selected by
Lorena Ancona, Humanitas Research

Genomics Proteomics Bioinformatics. 2025 Oct 14. pii: qzaf092. [Epub ahead of print]

cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers.

Yuanhui Sun, Zhixian Zhu, Qiangwei Zhou, Zhe Wang, Yuying Hou, Xionghui Zhou, Guoliang Li.

Cancer is a major global health threat, and early detection is crucial for improving patient outcomes. DNA methylation in circulating cell-free DNA (cfDNA) has emerged as a promising biomarker for non-invasive cancer diagnosis. However, the integration and utilization of existing cfDNA methylation data have been limited, hindering comprehensive research efforts, particularly in the discovery of cfDNA methylation biomarkers. To address this challenge, we introduce cfMethDB, a comprehensive database dedicated to cfDNA methylation in cancer that encompasses 4828 publicly available datasets. Through standardized analysis, we identified 1,048,770 differentially methylated cytosines (DMCs) as candidate biomarkers across seven cancer types. With cfMethDB, we not only identified known cfDNA methylation biomarkers, but also discovered several genes, such as ZIC4, that could be novel biomarkers. Moreover, cfMethDB offers a suite of user-friendly tools, including biomarker evaluation, pan-cancer search, and end motif analysis. We hope that cfMethDB will serve as a valuable platform for the discovery of novel cancer cfDNA methylation biomarkers and will facilitate cancer research and clinical applications. cfMethDB is publicly available at: https://cfmethdb.hzau.edu.cn/home.

Keywords: Biomarker; DNA methylation; Database; Pan-cancer; cfDNA

DOI: https://doi.org/10.1093/gpbjnl/qzaf092

Cancers (Basel). 2025 Sep 26. pii: 3132. [Epub ahead of print]17(19):

Impact of Epigenome-Wide Methylation and Breast Cancer Recurrence in Women Tested Negative for BRCA Genes: The Breast Methylation Risk (BREMERI) Study.

Silvia Polidoro, Harriet Johansson, Giovanni Cugliari, Aliana Guerrieri-Gonzaga, Valentina Aristarco, Debora Macis, Mariarosaria Calvello, Monica Marabelli, Irene Feroce, Davide Serrano, Sara Cagnacci, Cristina Zanzottera, Francesca Fava, Federica Bellerba, Bernardo Bonanni, Sara Gandini.

BACKGROUND AND AIM: DNA methylation may contribute to a worsening in breast cancer (BC).
METHODS: We conducted a matched case-control study to investigate the contribution of DNA methylation (DNAm) in breast cancer recurrence risk. Genome-wide DNAm profiles were generated from peripheral white blood cells (WBC) collected post-surgery from women with primary breast cancer BRCA wild-type, using Illumina Infinium HumanMethylationEPIC array. Cases had to experience recurrence of breast cancer or death and were matched to controls (subjects without recurrence, ratio 1:2) by age at diagnosis (+/- 5 years) and follow-up duration.
RESULTS: We identified three differentially methylated regions between the groups. Cases showed two hypomethylated regions, one upstream of the vtRNA2-1 gene (estimate -0.30, p-value < 0.005), and one in the 5' UTR region of the FGFR2 gene (estimate -0.34, p-value < 0.028), whereas one, upstream of the RUFY1 gene (estimate 0.32, p-value < 0.015), was hypermethylated. Additionally, we identified two methylation signals, recognised as predictors of biochemical traits. The chemokine ligand 21 (unadjusted p-value < 0.03) and insulin receptor expression (unadjusted p-value < 0.04) were higher in cases than in controls.
CONCLUSIONS: Our exploratory study suggests that specific DNA methylation patterns in WBCs, particularly in genes related to cellular proliferation, invasion, and glucose homeostasis, may be associated with the risk of breast cancer recurrence in BRCA wild-type women. If validated in larger cohorts, these circulating signatures may serve as blood-based biomarkers to improve risk stratification and guide tailored treatment strategies.

Keywords: DNA methylation; breast cancer; epigenetics; glucose homeostasis

DOI: https://doi.org/10.3390/cancers17193132