BACKGROUNDS Triple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early and sensitive diagnostic signatures and potential therapeutic targets for TNBC patients. METHODS We performed an iTRAQ labeling coupled LC-MS/MS approach to explore the global proteome in tumor tissues and corresponding para-tumor tissues from 24 patients with grade I-II and grade III primary TNBC. Relative peptide quantification and protein identification were performed by Proteome Discoverer™ software with Mascot search engine. Differentially expressed proteins were analyzed by bioinformatic analyses, including GO function classification annotation and KEGG enrichment analysis. Pathway analyses for protein-protein interactions and upstream regulations of differentially expressed candidates were performed by Ingenuity Pathway Analysis (IPA) software. RESULTS Totally, 5401 unique proteins were identified and quantified in different stage of TNBCs. 845 proteins were changed in patients with grade I or II TNBC, among which 304 were up-regulated and 541 were down-regulated. Meanwhile, for patients with grade III TNBC, 358 proteins were increased and 651 proteins were decreased. Comparing to para-cancerous tissues, various signaling pathways and metabolic processes, including PPAR pathways, PI3K-Akt pathway, one-carbon metabolism, amino acid synthesis, and lipid metabolism were activated in TNBC cancer tissues. Death receptor signaling was significantly activated in grade I-II TNBCs, however, remarkably inhibited in grade III TNBCs. Western blot experiments were conducted to validate expression levels of CYCS, HMGA1 and XIAP with samples from individual patients. CONCLUSIONS Overall, our proteomic data presented precise quantification of potential signatures, signaling pathways, regulatory networks, and characteristic differences in each clinicopathological subgroup. The proteome provides complementary information for TNBC accurate subtype classification and therapeutic targets research.

中文翻译：

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定量蛋白质组学揭示了三阴性乳腺癌的阶段特异性蛋白质调控。

背景三阴性乳腺癌（TNBC）是一种异质性疾病，其临床病程比其他亚型乳腺癌更具侵袭性。在这项研究中，我们对 TNBC 临床组织标本进行了基于高分辨率质谱的定量蛋白质组学，以探索 TNBC 患者的早期和敏感诊断特征和潜在的治疗靶点。方法我们使用 iTRAQ 标记耦合 LC-MS/MS 方法来探索 24 名 I-II 级和 III 级原发性 TNBC 患者的肿瘤组织和相应的副肿瘤组织中的全局蛋白质组。相对肽定量和蛋白质鉴定由 Proteome Discoverer™ 软件和 Mascot 搜索引擎进行。通过生物信息学分析对差异表达的蛋白质进行分析，包括GO功能分类注释和KEGG富集分析。通过 Ingenuity Pathway Analysis (IPA) 软件对蛋白质-蛋白质相互作用和差异表达候选物的上游调控进行通路分析。结果在TNBC的不同阶段共鉴定和定量了5401个独特的蛋白质。I或II级TNBC患者中845个蛋白质发生变化，其中304个上调，541个下调。同时，对于 III 级 TNBC 患者，增加了 358 个蛋白质，减少了 651 个蛋白质。与癌旁组织相比，TNBC癌组织激活了多种信号通路和代谢过程，包括PPAR通路、PI3K-Akt通路、一碳代谢、氨基酸合成和脂质代谢。死亡受体信号在 I-II 级 TNBC 中显着激活，但在 III 级 TNBC 中显着抑制。进行蛋白质印迹实验以验证来自个体患者的样品的 CYCS、HMGA1 和 XIAP 的表达水平。结论 总的来说，我们的蛋白质组学数据精确量化了每个临床病理亚组的潜在特征、信号通路、调节网络和特征差异。蛋白质组为 TNBC 准确的亚型分类和治疗靶点研究提供了补充信息。我们的蛋白质组学数据精确量化了每个临床病理亚组的潜在特征、信号通路、调节网络和特征差异。蛋白质组为 TNBC 准确的亚型分类和治疗靶点研究提供了补充信息。我们的蛋白质组学数据精确量化了每个临床病理亚组的潜在特征、信号通路、调节网络和特征差异。蛋白质组为 TNBC 准确的亚型分类和治疗靶点研究提供了补充信息。