A Ranking-Based Meta-Analysis Reveals Let-7 Family as a Meta-Signature for Grade Classification in Breast Cancer

Breast cancer is one of the most important causes of cancer-related deaths worldwide in women. In addition to gene expression studies, the progressing work in the miRNA area including miRNA microarray studies, brings new aspects to the research on the cancer development and progression. Microarray technology has been widely used to find new biomarkers in research and many transcriptomic microarray studies are available in public databases. In this study, the breast cancer miRNA and mRNA microarray studies were collected according to the availability of their data and clinical information, and combined by a newly developed ranking-based meta-analysis approach to find out candidate miRNA biomarkers (meta-miRNAs) that classify breast cancers according to their grades and explain the relation between miRNAs and mRNAs. This approach provided meta-miRNAs specific to breast cancer grades, pointing out let-7 family members as grade classifiers. The qRT-PCR studies performed with independent breast tumors confirmed the potential biomarker role of let-7 family members (meta-miRNAs). The concordance between the meta-mRNAs and miRNA target genes specific to tumor grade (common genes) supported the idea of mRNAs as miRNA targets. The pathway analysis results showed that most of the let-7 family miRNA targets, and also common genes, were significantly taking part in cancer-related pathways. The qRT-PCR studies, together with bioinformatic analyses, confirmed the results of meta-analysis approach, which is dynamic and allows combining datasets from different platforms.

乳腺癌是全球女性癌症相关死亡的首要诱因之一。除基因表达研究外，微小RNA（microRNA, miRNA）领域的相关研究进展——包括miRNA微阵列研究——为癌症发生与发展的研究提供了全新视角。微阵列技术已被广泛应用于科研中新生物标志物的发掘，且大量转录组微阵列研究数据可在公共数据库中获取。本研究依据数据与临床信息的可获得性，收集了乳腺癌miRNA与信使RNA（messenger RNA, mRNA）微阵列研究数据集，并通过全新开发的基于排序的荟萃分析方法进行整合，旨在筛选可根据肿瘤分级对乳腺癌进行分类、且能阐明miRNA与mRNA调控关系的候选miRNA生物标志物（meta-miRNAs）。该方法筛选出了与乳腺癌分级特异性相关的meta-miRNAs，并指出let-7家族成员可作为肿瘤分级分类标志物。采用独立乳腺癌肿瘤样本开展的实时定量逆转录聚合酶链反应（quantitative reverse transcription polymerase chain reaction, qRT-PCR）实验，验证了let-7家族成员（meta-miRNAs）作为潜在生物标志物的功能。荟萃分析得到的mRNA与肿瘤分级特异性miRNA靶基因（即共调控基因）之间的一致性，验证了mRNA作为miRNA靶标的假说。通路分析结果显示，绝大多数let-7家族miRNA靶基因以及共调控基因均显著富集于癌症相关通路中。实时定量逆转录聚合酶链反应实验与生物信息学分析共同验证了本荟萃分析方法的结果——该方法具备动态适配性，可整合不同平台的数据集。