Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.
College of Life Sciences, Chongqing Normal University, Chongqing, China.
Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa088.
Effective and safe implementation of precision oncology for breast cancer is a vital strategy to improve patient outcomes, which relies on the application of reliable biomarkers. As 'liquid biopsy' and novel resource for biomarkers, exosomes provide a promising avenue for the diagnosis and treatment of breast cancer. Although several exosome-related databases have been developed, there is still lacking of an integrated database for exosome-based biomarker discovery. To this end, a comprehensive database ExoBCD (https://exobcd.liumwei.org) was constructed with the combination of robust analysis of four high-throughput datasets, transcriptome validation of 1191 TCGA cases and manual mining of 950 studies. In ExoBCD, approximately 20 900 annotation entries were integrated from 25 external sources and 306 exosomal molecules (49 potential biomarkers and 257 biologically interesting molecules). The latter could be divided into 3 molecule types, including 121 mRNAs, 172 miRNAs and 13 lncRNAs. Thus, the well-linked information about molecular characters, experimental biology, gene expression patterns, overall survival, functional evidence, tumour stage and clinical use were fully integrated. As a data-driven and literature-based paradigm proposed of biomarker discovery, this study also demonstrated the corroborative analysis and identified 36 promising molecules, as well as the most promising prognostic biomarkers, IGF1R and FRS2. Taken together, ExoBCD is the first well-corroborated knowledge base for exosomal studies of breast cancer. It not only lays a foundation for subsequent studies but also strengthens the studies of probing molecular mechanisms, discovering biomarkers and developing meaningful clinical use.
精准肿瘤学在乳腺癌中的有效和安全实施是改善患者预后的重要策略，这依赖于可靠生物标志物的应用。作为“液体活检”和新型生物标志物资源，外泌体为乳腺癌的诊断和治疗提供了有前途的途径。尽管已经开发了几个外泌体相关数据库，但仍然缺乏基于外泌体的生物标志物发现的综合数据库。为此，我们构建了一个全面的数据库 ExoBCD（https://exobcd.liumwei.org），该数据库结合了对四个高通量数据集的稳健分析、对 1191 个 TCGA 病例的转录组验证以及对 950 项研究的手动挖掘。在 ExoBCD 中，大约 20900 个注释条目从 25 个外部来源和 306 个外泌体分子（49 个潜在生物标志物和 257 个具有生物学意义的分子）中整合而来。后者可以分为 3 种分子类型，包括 121 个 mRNAs、172 个 miRNAs 和 13 个 lncRNAs。因此，分子特征、实验生物学、基因表达模式、总生存期、功能证据、肿瘤分期和临床应用等方面的关联信息得到了充分整合。作为一种基于数据驱动和文献的生物标志物发现范式，本研究还进行了相互印证分析，并确定了 36 个有前途的分子，以及最有前途的预后生物标志物 IGF1R 和 FRS2。总之，ExoBCD 是第一个乳腺癌外泌体研究的充分印证知识库。它不仅为后续研究奠定了基础，而且加强了对分子机制的研究、生物标志物的发现以及有意义的临床应用的研究。
