Systems epigenetic approach towards non-invasive breast cancer detection

Chiara M. S. Herzog, Bente Theeuwes, Allison Jones, Iona Evans, Line Bjørge, Michal Zikan, David Cibula, Nadia Harbeck, Nicoletta Colombo, Nora Pashayan and Martin Widschwendter ()
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Chiara M. S. Herzog: Universität Innsbruck
Bente Theeuwes: Universität Innsbruck
Allison Jones: University College London
Iona Evans: University College London
Line Bjørge: University of Bergen
Michal Zikan: First Faculty of Medicine and Hospital Na Bulovce
David Cibula: Charles University
Nadia Harbeck: LMU University Hospital
Nicoletta Colombo: European Institute of Oncology IRCCS
Nora Pashayan: University of Cambridge
Martin Widschwendter: Universität Innsbruck

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract No study has systematically compared the suitability of DNA methylation (DNAme) profiles in non-invasive samples for the detection of breast cancer (BC). We assess non-tumour DNAme in 1,100 cervical, buccal, and blood samples from BC cases and controls and find that cervical samples exhibit the largest nuber of differentially methylated sites, followed by buccal samples. No sites were significant in blood after FDR adjustment. Deriving DNAme-based classifiers for BC detection in each sample type (WID-buccal-, cervical-, or blood-BC), we achieve validation AUCs of 0.75, 0.66, and 0.51, respectively. Buccal and cervical BC-associated DNAme alterations distinguish between BC cases and controls in both surrogate and breast tissue (AUC > 0.88), yet individual sites and the directionality of methylation changes are not identical between these two sample types, and buccal sample DNAme aligns with breast methylation changes more closely. Pending additional validation, these insights may have the potential to improve non-invasive personalized BC prevention.

Date: 2025
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DOI: 10.1038/s41467-024-53696-2

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