三阴性乳腺癌（TNBC）包括临床行为不同的多种癌症。DNA 甲基化是一种有用的工具，用于分类各种癌症。本研究通过DNA 甲基化分析和突变分析对TNBC进行了分析。在44例未治疗的TNBC中，我们进行了DNA 甲基化分析（Illumina Infinium MethylationEPIC芯片）和50个基因面板的定向DNA测序。我们确定了三个独特的DNA甲基化簇，具有特定的临床病理学和分子特征。簇1（PI3K / AKT富集簇; n=9）患者的年龄显著较大（平均年龄：71岁，p=0.008），肿瘤更可能表现为乳腺分泌极性（78％；p< 0.001），较低等级（44％为2级），增殖指数（中值ki-67：15％，p= 0.002）和较低的肿瘤浸润淋巴细胞比例（TILs）（中值：15％，p=0.0142）。肿瘤携带了反复发生的PIK3CA和AKT1突变，并且有更高百分比的低HER-2表达（89％；p=0.033）。簇3（染色体不稳定簇; n=28）患者显著较年轻（中位年龄：57岁）。肿瘤为高等级（3级：93％），更高的增殖指数（中值ki-67：75％），以及高比例的TILs（中值：30％）。91％的胚系BRCA 1/2突变携带者位于簇3中，并且这些肿瘤显示了最高水平的拷贝数改变。簇2代表具有中间临床病理学特征和无特定分子特征的个案（NSMP簇; n=7）。与阶段、复发和生存率相关的差异。总之，DNA甲基化分析是一种有前景的工具，用于将TNBC患者分为生物学相关的群体，这可能导致更好的疾病表征并揭示新型治疗的潜在靶点。版权所有© 2023。Elsevier Inc.出版。

Triple-negative breast cancers (TNBC) include diverse carcinomas with heterogeneous clinical behavior. DNA methylation is a useful tool in classifying a variety of cancers. In this study, we analyzed TNBC using DNA methylation profiling and compared results to mutational analysis. DNA methylation profiling (Illumina Infinium MethylationEPIC array) and 50-gene panel targeted DNA sequencing were performed in 44 treatment-naïve TNBC. We identified three distinct DNA methylation clusters with specific clinicopathologic and molecular features. Cluster 1 (PI3K/AKT-enriched cluster; n=9) patients were significantly older (mean age: 71 years; p=0.008) with tumors that were more likely to exhibit apocrine differentiation (78%; p< 0.001), lower grade (44% were grade 2), proliferation index (median ki-67: 15%; p= 0.002) and lower tumor-infiltrating lymphocyte fraction (TILs) (median: 15%; p=0.0142). Tumors carried recurrent PIK3CA and AKT1 mutations and a higher percentage of low HER-2 expression (89%; p=0.033). Cluster 3 (Chromosomal Instability cluster; n=28) patients were significantly younger (median age: 57 years). Tumors were higher grade (grade 3: 93%), higher proliferation index (median ki-67: 75%), and with a high fraction of TILs (median: 30%). Ninety-one percent of the germline BRCA 1/2 mutation carriers were in Cluster 3, and these tumors showed the highest level of copy-number alterations. Cluster 2 represented cases with intermediate clinicopathologic characteristics and no specific molecular profile (NSMP cluster; n=7). There were no differences in relation to stage, recurrence, and survival. In conclusion, DNA methylation profiling is a promising tool to classify TNBC patients into biologically relevant groups, which may result in better disease characterization and reveal potential targets for emerging therapies.Copyright © 2023. Published by Elsevier Inc.