Blood DNA methylation and breast cancer risk: a prospective nested case–control study

BACKGROUND: Blood tests that predict breast cancer (BC) risk before diagnosis could complement mammography screening. Whole-blood DNA methylation is stable and may capture early systemic changes related to tumour development. METHODS: We conducted a prospective matched case-control study nested within Sweden's mammography screening programme, profiling whole-blood DNA methylation on the Illumina MethylationEPIC array in 377 female participants who later developed BC and 378 age-matched female controls. We identified methylation sites (CpG sites) in Stockholm and validated them in Skåne, after stringent quality control and adjustment for technical and epidemiological confounders. We then constructed a methylation risk score (MRS). FINDINGS: We identified 87 CpG sites in Stockholm (FDR < 0.05; |β| > 0.015), of which 22 validated in Skåne (P < 0.05; concordant direction) and formed the MRS. The MRS demonstrated significant associations with BC risk, was consistent across different BC subtypes, and independent of established risk factors. The association of MRS with BC remained relatively stable over a pre-diagnostic window of up to five years. MRS exhibited predictive performance comparable to a polygenic risk score, and it significantly improved the 3-5-year prediagnosis discrimination of established BC risk models (P < 0.05, DeLong's test). Several CpG sites correlated with immune-related genes, suggesting mechanisms involving immune modulation and tumour progression. INTERPRETATION: Our methylation signature was significantly associated with BC risk and may complement existing risk models, particularly for estimating 3-5-year risk. These findings suggest that blood DNA methylation may support BC risk stratification, although further validation and assessment of clinical utility are needed. FUNDING: Swedish Research Council; Swedish Cancer Society; Stockholm County Council; Cancerföreningen i Stockholm; Erling-Persson Foundation; Sjöberg Foundation; and EU funds via ILB.