BACKGROUND Approximately two thirds of patients with localized triple-negative breast cancer (TNBC) harbor residual disease (RD) after neoadjuvant chemotherapy (NAC) and have a high risk-of-recurrence. Targeted therapeutic development for TNBC is of primary significance as no targeted therapies are clinically indicated for this aggressive subset. In view of this, we conducted a comprehensive molecular analysis and correlated molecular features of chemorefractory RD tumors with recurrence for the purpose of guiding downstream therapeutic development. METHODS We assembled DNA and RNA sequencing data from RD tumors as well as pre-operative biopsies, lymphocytic infiltrate, and survival data as part of a molecular correlative to a phase II post-neoadjuvant clinical trial. Matched somatic mutation, gene expression, and lymphocytic infiltrate were assessed before and after chemotherapy to understand how tumors evolve during chemotherapy. Kaplan-Meier survival analyses were conducted categorizing cancers with TP53 mutations by the degree of loss as well as by the copy number of a locus of 18q corresponding to the SMAD2, SMAD4, and SMAD7 genes. RESULTS Analysis of matched somatic genomes pre-/post-NAC revealed chaotic acquisition of copy gains and losses including amplification of prominent oncogenes. In contrast, significant gains in deleterious point mutations and insertion/deletions were not observed. No trends between clonal evolution and recurrence were identified. Gene expression data from paired biopsies revealed enrichment of actionable regulators of stem cell-like behavior and depletion of immune signaling, which was corroborated by total lymphocytic infiltrate, but was not associated with recurrence. Novel characterization of TP53 mutation revealed prognostically relevant subgroups, which were linked to MYC-driven transcriptional amplification. Finally, somatic gains in 18q were associated with poor prognosis, likely driven by putative upregulation of TGFß signaling through the signal transducer SMAD2. CONCLUSIONS We conclude TNBCs are dynamic during chemotherapy, demonstrating complex plasticity in subclonal diversity, stem-like qualities, and immune depletion, but somatic alterations of TP53/MYC and TGFß signaling in RD samples are prominent drivers of recurrence, representing high-yield targets for additional interrogation.

中文翻译：

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剖析化学难治性三阴性乳腺癌的复发分子调节剂。

背景技术大约三分之二的局部三阴性乳腺癌（TNBC）患者在新辅助化疗（NAC）后出现残留疾病（RD），并且有很高的复发风险。TNBC的靶向治疗开发具有最重要的意义，因为临床上没有针对这种侵袭性亚类的靶向治疗。有鉴于此，我们进行了化学分子难治性RD肿瘤复发的综合分子分析和相关分子特征，以指导下游治疗的发展。方法我们收集了来自RD肿瘤的DNA和RNA测序数据以及术前活检，淋巴细胞浸润和生存数据，作为与新辅助治疗后II期临床相关的分子的一部分。匹配的体细胞突变，基因表达，在化疗前后评估淋巴细胞和淋巴细胞浸润的情况，以了解肿瘤在化疗过程中如何演变。进行了Kaplan-Meier生存分析，将TP53突变的癌症按丢失程度以及与SMAD2，SMAD4和SMAD7基因相对应的18q基因座的拷贝数进行了分类。结果在NAC之前/之后对匹配的体细胞基因组进行的分析表明，混沌获取了复制的得失，包括明显的癌基因的扩增。相反，未观察到有害点突变和插入/缺失的显着增加。没有发现克隆进化和复发之间的趋势。配对活检的基因表达数据显示，干细胞样行为的可调节调节剂丰富，免疫信号耗竭，总淋巴细胞浸润证实了这一点，但与复发无关。TP53突变的新型表征揭示了与预后相关的亚组，这些亚组与MYC驱动的转录扩增有关。最后，18q的体细胞增高与预后不良有关，可能是通过信号转导物SMAD2推定的TGFβ信号上调驱动的。结论我们得出结论，TNBCs在化学过程中是动态的，表明亚克隆多样性，茎样质量和免疫耗竭方面具有复杂的可塑性，但是RD样品中TP53 / MYC和TGFβ信号的体细胞改变是复发的主要驱动力，代表了高产量的靶点。额外的审讯。TP53突变的新型表征揭示了与预后相关的亚组，这些亚组与MYC驱动的转录扩增有关。最后，18q的体细胞增高与预后不良有关，可能是通过信号转导物SMAD2推定的TGFβ信号上调驱动的。结论我们得出结论，TNBCs在化学过程中是动态的，表明亚克隆多样性，茎样质量和免疫耗竭方面具有复杂的可塑性，但是RD样品中TP53 / MYC和TGFβ信号的体细胞改变是复发的主要驱动力，代表了高产量的靶点。额外的审讯。TP53突变的新型表征揭示了与预后相关的亚组，这些亚组与MYC驱动的转录扩增有关。最后，18q的体细胞增高与预后不良有关，可能是通过信号转导物SMAD2推定的TGFβ信号上调驱动的。结论我们得出结论，TNBCs在化疗过程中是动态的，表明亚克隆多样性，茎样质量和免疫耗竭方面具有复杂的可塑性，但是RD样品中TP53 / MYC和TGFβ信号的体细胞改变是复发的主要驱动力，代表了高产量的靶点。额外的审讯。可能是由通过信号传感器SMAD2的TGFβ信号的推测上调驱动的。结论我们得出结论，TNBCs在化学过程中是动态的，表明亚克隆多样性，茎样质量和免疫耗竭方面具有复杂的可塑性，但是RD样品中TP53 / MYC和TGFβ信号的体细胞改变是复发的主要驱动力，代表了高产量的靶点。额外的审讯。可能是由通过信号传感器SMAD2的TGFβ信号的推测上调驱动的。结论我们得出结论，TNBCs在化疗过程中是动态的，表明亚克隆多样性，茎样质量和免疫耗竭方面具有复杂的可塑性，但是RD样品中TP53 / MYC和TGFβ信号的体细胞改变是复发的主要驱动力，代表了高产量的靶点。额外的审讯。