Expression Profiling of lncRNAs, miRNAs, and mRNAs and Their Differential Expression in Leiomyoma Using Next-Generation RNA Sequencing
Expression Profiling of lncRNAs, miRNAs, and mRNAs and Their Differential Expression in Leiomyoma Using Next-Generation RNA Sequencing
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DOI：
10.1177/1933719117711265
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发表时间：
2018-02-01
影响因子：
2.9
通讯作者：
Khorram, Omid
中科院分区：
文献类型：
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作者：
Chuang, Tsai-Der;Khorram, Omid
本研究的目的是确定长链非编码RNA（lncRNA）的表达谱，同时使用下一代RNA测序和RNA转录本组装评估平滑肌瘤和配对子宫肌层中的microRNA（miRNA）和信使RNA（mRNA）谱。从平滑肌瘤和配对的子宫肌层（N = 8）中分离总RNA，并对来自3对的样品进行RNA测序。超过48 000个lncRNA的标准化组装导致鉴定出45 936个lncRNA。在这些lncRNA中，22 148个代表重叠、基因间、内含子和反义亚型在所有配对组织中表达，其中5941个（2813个上调和3128个下调1.5倍）在平滑肌瘤中差异表达。同步RNA测序结果显示2588个miRNAs和21814个mRNAs表达，其中392个miRNAs和16559个mRNAs在所有配对组织中均有表达。在这些转录本中，56和92个miRNA以及2030和1825个mRNA在子宫肌瘤中分别上调或下调1.5倍。使用定量逆转录-聚合酶链反应（QRT-PCR），我们证实了平滑肌瘤和匹配的子宫肌层（N = 8）中肝细胞癌上调（HULC）、lnc-母源表达3（MEG 3）、长基因间ncRNA 890（LINC 00890）、TSIX、长基因间ncRNA 473（LINC 00473）、lnc-KLF 9 -1和lnc-POTEM-3（lncRNA-ATB）的表达。总的来说，这里呈现的结果提供了一个全面的表达谱的lncRNA在平滑肌瘤与并行的整合表达的miRNA和mRNA，并暗示潜在的调控功能的lncRNA通过与特定的miRNA和mRNA的相互作用，这是已知的在平滑肌瘤的发病机制是至关重要的。
The objective of this study was to identify the expression profile of long noncoding RNAs (lncRNAs) with concurrent assessment of microRNA (miRNA) and messenger RNA (mRNA) profiles in leiomyomas and paired myometrium using next-generation RNA sequencing and assembly of RNA transcripts. Total RNA was isolated from leiomyoma and paired myometrium (N = 8) and samples from 3 pairs were subjected to RNA sequencing. Normalized assembly of over 48 000 lncRNAs resulted in identification of 45 936 lncRNAs. Of these lncRNAs, 22 148 representing overlapping, intergenic, intronic, and antisense subtypes were expressed in all paired tissues, with 5941 (2813 up- and 3128 downregulated at 1.5 fold) differentially expressed in leiomyomas. Concurrent RNA sequencing revealed the expression of 2588 miRNAs and 21 814 mRNAs, of which 392 miRNAs and 16 559 mRNAs were expressed in all paired tissues. Of these transcripts, 56 and 92 miRNAs and 2030 and 1825 mRNAs were up- or downregulated at 1.5 fold, respectively, in leiomyoma as compared to myometrium. Using quantitative reverse transcription-polymerase chain reaction (QRT-PCR), we confirmed the expression of hepatocellular carcinoma upregulated (HULC), lnc-maternally expressed 3 (MEG3), long intergenic ncRNA 890 (LINC00890), TSIX, long intergenic ncRNA 473 (LINC00473), lnc-KLF9-1, and lnc-POTEM-3 (lncRNA-ATB) in leiomyoma and matched myometrium (N = 8). Collectively, the results presented here provide a comprehensive expression profile of lncRNAs in leiomyomas with concurrent integrated expression of miRNAs and mRNAs and implicate potential regulatory functions of lncRNAs through interactions with specific miRNAs and mRNAs which are known to be critical in the pathogenesis of leiomyoma.