Cross-cohort DNA methylation analysis shows CpG island promoter hypermethylation features associated with cervical lesion grade.

Abstract

Background: Cervical lesion progression is accompanied by epigenomic alterations, but reproducible methylation features across public cohorts require cautious re-analysis.

Study design and methods: We performed a secondary analysis of public Illumina 450K methylation cohorts: GSE46306 as discovery (20 normal, 17 CIN3, six carcinoma), GSE99511 and GSE186835 as validation, and TCGA-CESC tumors for methylation-RNA expression association. Shared autosomal CpGs were screened for monotonic grade-associated change, cross-cohort directional consistency, promoter annotation, regional aggregation, sample-level score performance, and tumor expression correlation. No intervention, dose, treatment regimen, blinding, or safety outcome was involved.

Results: Among 340, 248 shared autosomal CpGs, 3, 008 met robust cross-cohort criteria, including 2, 991 hypermethylated and 17 hypomethylated sites. Robust sites mapped to 628 promoter genes and 660 multi-CpG DMR-like regions. A fixed 200-CpG score yielded AUCs of 0.733-0.963 for CIN3 or worse versus controls and 0.971-0.988 for cancer versus non-cancer. In TCGA-CESC, 394 of 610 detectable robust promoter genes showed significant negative methylation-expression correlations.

Conclusions: The reanalysis supports reproducible CpG island and promoter hypermethylation features associated with cervical lesion grade, but processed data, cohort heterogeneity, cross-sectional tumor associations, and absence of prospective validation limit interpretation to candidate atlas generation.