Differences in individual drug responses are obstacles in breast cancer (BRCA) treatment, so predicting responses would help to plan treatment strategies. The accumulation of cancer molecular profiling and drug response data provide opportunities and challenges to identify novel molecular signatures and mechanisms of tumor responsiveness to drugs in BRCA. This study evaluated drug responses with a multi-omics integrated system that depended on long non-coding RNAs (lncRNAs). We identified drug response-related lncRNAs (DRlncs) by combining expression data of lncRNA, microRNA, messenger RNA, methylation levels, somatic mutations, and the survival data of cancer patients treated with drugs. We constructed an integrated and computational multi-omics approach to identify DRlncs for diverse chemotherapeutic drugs in BRCA. Some DRlncs were identified with Adriamycin, Cytoxan, Tamoxifen, and all samples for BRCA patients. These DRlncs showed specific features regarding both expression and computational accuracies. The DRlnc-gene co-expression networks were constructed and analyzed. Key DRlncs, such as HOXA-AS2 (Ensembl: ENSG00000253552), in the drug Adriamycin were characterized. The experimental analysis also suggested that HOXA-AS2 (Ensembl: ENSG00000253552) was a key DRlnc in Adriamycin drug resistance in BRCA patients. Some DRlncs were associated with survival and some specific functions. A possible mechanism of DRlnc HOXA-AS2 (Ensembl: ENSG00000253552) in the Adriamycin drug response for BRCA resistance was inferred. In summary, this study provides a framework for lncRNA-based evaluation of clinical drug responses in BRCA. Understanding the underlying molecular mechanisms of drug responses will facilitate improved responses to chemotherapy and outcomes of BRCA treatment.

个体药物反应的差异是乳腺癌（BRCA）治疗的障碍，因此预测反应将有助于规划治疗策略。癌症分子分布图和药物反应数据的积累为鉴定BRCA中新颖的分子标记和肿瘤对药物反应机制提供了机遇和挑战。这项研究通过依赖长的非编码RNA（lncRNA）的多组学集成系统评估了药物反应。我们通过结合lncRNA，microRNA，信使RNA，甲基化水平，体细胞突变以及接受药物治疗的癌症患者的生存数据来鉴定与药物反应相关的lncRNA（DRlncs）。我们构建了一种集成的计算多组学方法，以识别BRCA中多种化学治疗药物的DRlncs。一些DRlncs与阿霉素，细胞毒素，他莫昔芬以及所有BRCA患者的样品一起鉴定。这些DRlncs显示了有关表达和计算精度的特定功能。构建并分析了DRlnc基因共表达网络。表征了药物阿霉素中的关键DRlncs，例如HOXA-AS2（集成：ENSG00000253552）。实验分析还表明，HOXA-AS2（Ensembl：ENSG00000253552）是BRCA患者阿霉素耐药的关键DRlnc。一些DRlncs与生存和某些特定功能有关。推断DRlnc HOXA-AS2（Ensembl：ENSG00000253552）在阿霉素对BRCA耐药的药物应答中的可能机制。总之，这项研究为BRCA中基于lncRNA的临床药物反应评估提供了框架。