Rahimi Azadeh, Sedighi Rina, Emadi-Baygi Modjtaba, Honardoost Mohammad-Amin, Mowla Seyed-Javad, Khanahmad Hossein, Nikpour Parvaneh
Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
Department of Genetics, Faculty of Basic Sciences, Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran.
J Cell Biochem. 2020 Feb;121(2):1307-1316. doi: 10.1002/jcb.29367. Epub 2019 Sep 6.
As a class of short noncoding RNAs, microRNAs (miRNAs) play a key role in the modulation of gene expression. Although, the regulatory roles of currently identified miRNAs in various cancer types including breast cancer have been well documented, there are many as yet undiscovered miRNAs. The aim of the current study was to bioinformatically reanalyze a list of 189 potentially new miRNAs introduced in a previously published paper (PMID: 21346806) and experimentally explore the existence and function of a candidate one: hsa-miR-B43 in breast cancer cells. The sequences of 189 potential miRNAs were re-checked in the miRbase database. Genomic location and conservation of them were assessed with the University of California Santa Cruz (UCSC) genome browser. SSC profiler, RNAfold, miRNAFold, MiPred, and FOMmiR bioinformatics tools were furthermore utilized to explore potential hairpin structures and differentiate real miRNA precursors from pseudo ones. hsa-miR-B43 was finally selected as one of the best candidates for laboratory verification. The expression and function of hsa-miR-B43 were examined by real-time polymerase chain reaction, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, and wound-healing assays. DIANA-microT, RNAhybrid and Enrichr tools were used to predict the miRNA target genes and for further enrichment analysis. We could detect the exogenous and endogenous expression of hsa-miR-B43, as a real novel miRNA, in cancer cell lines. Gene Ontology enrichment, pathway analysis and wound-healing assay results furthermore confirmed that a metastasis-related function may be assigned to hsa-miR-B43. Our results introduced hsa-miR-B43, as a novel functional miRNA, which might play a role in the metastatic process. Further studies will be necessary to completely survey the existence and function of hsa-miR-B43 in other cancer types.
作为一类短链非编码RNA，微小RNA（miRNA）在基因表达调控中发挥着关键作用。尽管目前已鉴定出的miRNA在包括乳腺癌在内的各种癌症类型中的调控作用已有充分记录，但仍有许多尚未被发现的miRNA。本研究的目的是通过生物信息学方法重新分析先前发表的一篇论文（PMID：21346806）中引入的189个潜在新miRNA列表，并通过实验探索候选miRNA之一：hsa-miR-B43在乳腺癌细胞中的存在及功能。在miRbase数据库中重新检查了189个潜在miRNA的序列。利用加利福尼亚大学圣克鲁兹分校（UCSC）基因组浏览器评估它们的基因组位置和保守性。此外，还使用了SSC profiler、RNAfold、miRNAFold、MiPred和FOMmiR生物信息学工具来探索潜在的发夹结构，并区分真正的miRNA前体和假的miRNA前体。hsa-miR-B43最终被选为实验室验证的最佳候选者之一。通过实时聚合酶链反应、3-（4,5-二甲基噻唑-2-基）-2,5-二苯基四氮唑溴盐和伤口愈合试验检测了hsa-miR-B43的表达和功能。使用DIANA-microT、RNAhybrid和Enrichr工具预测miRNA靶基因并进行进一步的富集分析。我们能够在癌细胞系中检测到hsa-miR-B43作为一种真正的新miRNA的外源和内源表达。基因本体富集、通路分析和伤口愈合试验结果进一步证实，hsa-miR-B43可能具有与转移相关的功能。我们的结果表明hsa-miR-B43是一种新型功能性miRNA，可能在转移过程中发挥作用。有必要进一步研究以全面考察hsa-miR-B43在其他癌症类型中的存在及功能。
