The effects of alternative splicing on miRNA binding sites in bladder cancer

Eukaryotic organisms have developed a variety of mechanisms to regulate translation post-transcriptionally, including but not limited to the use of miRNA silencing in many species. One method of post-transcriptional regulation is through miRNAs that bind to the 3′ UTRs to regulate mRNA abundance and influence protein expression. Therefore, the diversity of mRNA 3′ UTRs mediating miRNA binding sites influence miRNA-mediated regulation. Alternative polyadenylation, by shortening mRNA isoforms, increases the diversity of 3′ UTRs; moreover, short mRNA isoforms elude miRNA-medicated repression. Because no current prediction methods for putative miRNA target sites consider whether or not 1) splicing-informed miRNA binding sites and/or 2) the use of 3′ UTRs provide higher resolution or functionality, we sought to identify not only the genome-wide impact of using exons in mRNA 3′ UTRs but also their functional connection to miRNA regulation and clinical outcomes in cancer. With a genome-wide expression of mRNA and miRNA quantified by 395 bladder cancer cases from The Cancer Genome Atlas (TCGA), we 1) demonstrate the diversity of 3′ UTRs affecting miRNA efficiency and 2) identify a set of genes clinically associated with mRNA expression in bladder cancer. Knowledge of 3′ UTR diversity will not only be a useful addition to current miRNA target prediction algorithms but also enhance the clinical utility of mRNA isoforms in the expression of mRNA in cancer. Thus, variability among cancer patient’s variability in molecular signatures based on these exon usage events in 3′ UTR along with miRNAs in bladder cancer may lead to better prognostic/treatment strategies for improved precision medicine.

真核生物已演化出多种转录后调控翻译的机制，其中包括但不限于诸多物种中采用的miRNA（microRNA）沉默策略。转录后调控的一类方式是通过miRNA结合至mRNA的3' UTR，以此调控mRNA丰度并影响蛋白质表达。因此，介导miRNA结合位点的mRNA 3' UTR多样性会对miRNA介导的基因调控产生影响。可变多聚腺苷酸化通过缩短mRNA同工型，增加了3' UTR的多样性；此外，较短的mRNA同工型可逃脱miRNA介导的基因抑制。鉴于当前尚无任何miRNA潜在靶位点预测方法会同时考虑以下两点：1）基于剪接信息的miRNA结合位点，以及2）3' UTR的使用是否能提供更高的分辨率或功能活性，本研究旨在不仅阐明外显子在mRNA 3' UTR中的使用对全基因组的影响，同时还探究其与miRNA调控以及癌症临床结局的功能关联。本研究借助来自癌症基因组图谱（The Cancer Genome Atlas, TCGA）的395例膀胱癌病例的全基因组mRNA与miRNA表达量化数据，完成了两项核心分析：1）证实3' UTR多样性会影响miRNA的调控效率；2）鉴定出一组在膀胱癌中与mRNA表达具有临床相关性的基因。对3' UTR多样性的认知不仅可为当前的miRNA靶标预测算法提供有益补充，还能增强mRNA同工型在癌症mRNA表达中的临床应用价值。综上，膀胱癌患者中基于此类3' UTR外显子使用事件及miRNA所形成的分子特征所存在的个体差异，有望催生更优化的预后与治疗策略，进一步推动精准医学的发展。