肿瘤亚型和绝经状态是乳腺癌（BC）预后的强预测因子。我们旨在寻找并验证肿瘤DNA甲基化（DNAm）的亚型或绝经状态特定变化，以其与全因死亡或BC进展相关联。在The Cancer Genome Atlas参与者中（n = 692），采用Illumina Infinium HumanMethylation450 BeadChip阵列数据估计了位点特定肿瘤DNAm与BC预后的关联。通过以肿瘤亚型为分层变量，调整年龄、种族、阶段、绝经状态、肿瘤纯度和细胞类型比例的Cox比例风险模型，建立了全因死亡和BC进展预测模型。通过将DNAm与乘积项进行组合评估亚型和绝经状态的效应测量修饰。使用位点特定推理来识别亚型或绝经状态特定的差异甲基化区域（DMR）和功能途径。结果的验证在独立数据集（GSE72308; n = 180）上进行。我们发现共计15个独特的CpG探针与亚型或绝经状态特异性方式的生存结局有显著关联（P≤1×10-7）。其中，7个探针与luminal A亚型女性的总生存期（OS）或无进展生存期（PFI）有关，4个探针与luminal B亚型女性的PFI有关，5个探针与绝经后的女性的PFI有关。大多数显著探针显示较高的DNAm降低了OS或BC进展的风险。我们识别出亚型或绝经状态特定的DMR和功能途径，其中前几个相关途径在亚型或绝经状态之间存在差异。尽管经验证分析中没有位点特定分析中的显著探针达到基因组范围内的显著性水平，但系数的方向和大小显示一致的模式。我们已经确定了与全因死亡或BC进展相关的亚型或绝经状态特定的DNAm生物标志物、DMR和功能途径，尽管受到限制的验证。未来研究需要对非luminal A亚型和非绝经状态的更大独立队列进行研究，以识别亚型和绝经状态特定的DNAm生物标志物，以供BC预后使用。版权所有©2023 Kim、Binder、Zhou和Jung。

Tumor subtype and menopausal status are strong predictors of breast cancer (BC) prognosis. We aimed to find and validate subtype- or menopausal-status-specific changes in tumor DNA methylation (DNAm) associated with all-cause mortality or BC progression. Associations between site-specific tumor DNAm and BC prognosis were estimated among The Cancer Genome Atlas participants (n = 692) with Illumina Infinium HumanMethylation450 BeadChip array data. All-cause mortality and BC progression were modeled using Cox proportional hazards models stratified by tumor subtypes, adjusting for age, race, stage, menopausal status, tumor purity, and cell type proportion. Effect measure modification by subtype and menopausal status were evaluated by incorporating a product term with DNAm. Site-specific inference was used to identify subtype- or menopausal-status-specific differentially methylated regions (DMRs) and functional pathways. The validation of the results was carried out on an independent dataset (GSE72308; n = 180). We identified a total of fifteen unique CpG probes that were significantly associated ( P ≤ 1 × 10 - 7 with survival outcomes in subtype- or menopausal-status-specific manner. Seven probes were associated with overall survival (OS) or progression-free interval (PFI) for women with luminal A subtype, and four probes were associated with PFI for women with luminal B subtype. Five probes were associated with PFI for post-menopausal women. A majority of significant probes showed a lower risk of OS or BC progression with higher DNAm. We identified subtype- or menopausal-status-specific DMRs and functional pathways of which top associated pathways differed across subtypes or menopausal status. None of significant probes from site-specific analyses met genome-wide significant level in validation analyses while directions and magnitudes of coefficients showed consistent pattern. We have identified subtype- or menopausal-status-specific DNAm biomarkers, DMRs and functional pathways associated with all-cause mortality or BC progression, albeit with limited validation. Future studies with larger independent cohort of non-post-menopausal women with non-luminal A subtypes are warranted for identifying subtype- and menopausal-status-specific DNAm biomarkers for BC prognosis.Copyright © 2023 Kim, Binder, Zhou and Jung.