Discovery of Novel miRNAs and isomiRs and Use in Sub-typing TCGA Cancers

 描述(由申请人提供)：microRNAs(MiRNAs)是发育和动态平衡的关键角色，也是许多转录本的有效转录后调节因子。尽管在过去的二十年里取得了巨大的进步，但关键的问题仍然在很大程度上是悬而未决的，例如“人类基因组中有多少miRNAs被编码”，“有多少不同的miRNA产物来自一个miRNA基因座”，以及“每个成熟的miRNA产物有多少转录本”。他们的答案直接关系到社区试图解开和理解疾病转录后调控的复杂性。我们最近报告了我们对1,323个个体的深度测序转录数据(短RNA-seq)的分析，并发现了3,707个新的人类miRNAs，这些miRNAs是组织特异的和Pri Mate特异的，有效地使目前miRBase储存库中的人类miRNA前体的数量增加了两倍。我们还报告了一项平行研究的结果，该研究来自452名健康个体的短RNA-SEQ数据，在该研究中，我们发现miRNA前体臂产生多种异构体，即异构体，并且异构体的丰度分布意外地依赖于个人的性别、人口和种族。对于许多新的miRNAs和异构体，我们证明它们是负载在ArgAerte上的，因此它们在RNA干扰途径中发挥作用。最后，我们分析了来自“癌症基因组图谱”(TCGA)的乳腺癌(BRCA)数据集，并表明这些观察结果在疾病背景下也是正确的。这些结果表明，许多活跃在转录后调节层的分子已经躲避了我们，就像它们对疾病亚型、性别、人口和种族的意外依赖一样。这些分子和它们所调节的相互作用有待发现和表征。值得注意的是，由于它们是人类/灵长类动物特有的，许多新发现的新miRNAs及其靶向效应器在癌症小鼠模型中缺失，因此不能被捕获。在这个项目中，我们将把我们的TCGA BRCA分析扩展到另外四种TCGA癌症。在这四个案例中的每一个案例中，我们都将寻找新的miRNAs，为已知和新的miRNAs建立异构体图谱，并表征它们对癌症亚型、性别和种族的依赖性。根据我们的初步发现，我们预计在这些癌症中发现的一些新的miRNAs将是组织特异性和人类特异性的。这将有助于为这些癌症及其亚型产生新的高度特异的签名。通过在我们的分析中包括长RNA-seq数据集，我们将对miRNAs/isomiRs对其信使-RNA/lncRNA靶标的调控效应进行建模。该项目将产生目前不存在的丰富知识，这些知识将有助于为社区铺平新的探索途径，并产生最终可能导致新的治疗方法的见解。

 DESCRIPTION (provided by applicant): MicroRNAs (miRNAs) are critical players in development and homeostasis and potent post-transcriptional regulators of numerous transcripts. Despite tremendous progress during the last two decades, key questions such as "how many miRNAs are encoded in the human genome," "how many distinct miRNA products arise from a single miRNA locus," and "how many transcripts are targeted by each mature miRNA product" remain largely open. Their answers directly bear upon the community's attempts to unravel and understand the complexity of post-transcriptional regulation in disease. We recently reported our analyses of deep-sequencing transcriptomic data (short RNA-seq) from 1,323 individuals and the discovery of 3,707 novel human miRNAs that are tissue-specific and pri-mate-specific, effectively tripling the number of human miRNA precursors currently in the miRBase repository. We also reported results from a parallel study of short RNA-seq data from 452 healthy in-dividuals where we found that miRNA precursor arms produce multiple isoforms, the isomiRs, and that the isomiRs' abundance profiles have an unexpected dependency on an individual's gender, population, and race. For many of the novel miRNAs and the isomiRs we showed that they are loaded on Argonaute, thus they function in the RNA interference pathway. Lastly, we analyzed breast cancer (BRCA) datasets from "The Cancer Genome Atlas" (TCGA) and showed that these observations ex-tend to and hold true in the disease context as well. These results indicate that many molecules that are active in the post-transcriptional regulatory layer have eluded us, as has their unexpected dependency on disease subtype, gender, population, and race. These molecules and the interactions that they mediate await discovery and characterization. Notably, due to their human-/primate-specific nature, many of the newly discovered novel miRNAs and their targeted effectors are absent from and thus cannot be captured by mouse models of cancer. In this project, we will be expanding our TCGA BRCA analyses to four more TCGA cancers. In each of the four cases, we will seek novel miRNAs, establish isomiR profiles for known and novel miRNAs, and characterize their dependencies on cancer sub-type, gender, and race. Based on our preliminary findings we expect that some of the novel miRNAs to be discovered in these cancers will be tissue-specific and human-specific. This will help generate novel highly specific signatures for these cancers and their sub-types. By including in our analyses long RNA-seq datasets we will model the regulatory effects of miRNAs/isomiRs on their messenger-RNA/lncRNA targets. The project will generate a wealth of knowledge that does not currently exist and which will help pave new avenues of exploration for the community and generate insights that can eventually lead to new therapeutic approaches.