PROMISE, a clonal promoter methylation signature capturing early epigenetic evolution and prognostic programs across epithelial cancers

Epigenetic remodeling is a hallmark of tumor evolution, yet the timing and clonality of promoter methylation events remain poorly defined. We investigated the spatial architecture of promoter DNA methylation in multiregion lung adenocarcinoma (LUAD) to identify clonal epigenetic alterations and evaluate their prognostic and translational relevance across cancers. Reduced representation bisulfite sequencing (RRBS) was performed on 151 tumor regions from 32 TRACERx LUAD patients with matched normal tissue. Differentially methylated regions (DMRs) were quantified for intratumor (ITH) and intertumor (ITeH) heterogeneity. Clonality was evaluated through three complementary metrics of methylation ubiquity, followed by univariate and LASSO Cox modeling. The resulting 30DMR panel, termed PROMISE, was derived through clustering concordance with TCGA LUAD and independently validated in CPTAC 3. PROMISE was subsequently tested for pancancer specificity across 18 tumor types from several publicly available sources.We identified 21,358 promoter DMRs showing a continuum of ITH and ITeH patterns. Promoters with low ITH but high ITeH, ubiquitously hypermethylated within tumors yet variable across patients, represented early clonal events significantly associated with poor survival. LASSO Cox selection yielded a 30-DMR signature encompassing genes involved in immune regulation, epithelial polarity, and TGFbeta signaling. PROMISE robustly stratified patients into high and low risk groups in both TCGA LUAD and CPTAC 3 cohorts (logrank P < 0.01) and remained independent of clinicopathologic variables. Cross-cancer analyses revealed strong prognostic associations in kidney, thyroid, liver, and colorectal cancers, but minimal signal in squamous, stromal rich, or hematologic malignancies.PROMISE captures a panepithelial program of early, clonal promoter hypermethylation recurrent across multiple carcinomas and predictive of outcome in selected epithelial tumors. These findings highlight clonal methylation remodeling as an early determinant of tumor evolution and nominate PROMISE as a clinically actionable biomarker for cancer risk stratification.