Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by DIA proteomics

Triple negative breast cancer (TNBC) accounts for 15-20% of all breast carcinomas and it is clinically characterized by an aggressive phenotype and bad prognosis. TNBC does not benefit from any targeted therapy, so further characterization is needed to define subgroups with potential therapeutic value. In this work, the proteomes of one hundred twenty-five formalin-fixed paraffin-embedded samples from patients diagnosed with triple negative breast cancer were analyzed by mass spectrometry using data-independent acquisition. Hierarchical clustering, probabilistic graphical models and Significance Analysis of Microarrays were used to characterize molecular groups. Additionally, a predictive signature related with relapse was defined. Two molecular groups with differences in several biological processes as glycolysis, translation and immune response, were defined in this cohort, and a prognostic signature based on the abundance of proteins RBM3 and NIPSNAP1 was defined. This predictor split the population into low-risk and high-risk groups. The differential processes identified between the two molecular groups may serve to design new therapeutic strategies in the future and the prognostic signature could be useful to identify a population at high-risk of relapse that could be directed to clinical trials.

三阴性乳腺癌（Triple negative breast cancer, TNBC）约占所有乳腺癌的15%-20%，临床上以侵袭性表型与不良预后为特征。三阴性乳腺癌尚无获批的靶向治疗方案，因此亟需进一步解析其分子分型，以挖掘具有潜在治疗价值的亚群。本研究采用数据非依赖采集质谱技术，对125例确诊三阴性乳腺癌患者的福尔马林固定石蜡包埋组织样本的蛋白质组进行了分析。研究采用层级聚类、概率图模型以及微阵列显著性分析等方法对分子分型进行解析。此外，本研究还构建了与肿瘤复发相关的预测特征集。本队列中共鉴定出两类分子亚型，二者在糖酵解、蛋白质翻译以及免疫应答等多种生物学过程中存在显著差异；同时基于RBM3与NIPSNAP1蛋白的表达丰度，构建了预后特征集。该预测特征集可将患者群体划分为低复发风险组与高复发风险组。两类分子亚型间的差异生物学过程可为未来新型治疗策略的开发提供理论依据，而该预后特征集则可用于筛选高复发风险人群，以指导其参与临床试验。