Chuang Tsai-Der, Khorram Omid
1 LA-Biomed Research Institute, Torrance, CA, USA.
2 Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center, Torrance, CA, USA.
Reprod Sci. 2018 Feb;25(2):246-255. doi: 10.1177/1933719117711265. Epub 2017 Jun 7.
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.
本研究的目的是通过下一代RNA测序和RNA转录本组装，在平滑肌瘤及配对的子宫肌层中同时评估微小RNA（miRNA）和信使RNA（mRNA）谱，以确定长链非编码RNA（lncRNA）的表达谱。从平滑肌瘤及配对的子宫肌层（N = 8）中分离总RNA，并对3对样本进行RNA测序。超过48000个lncRNA的标准化组装鉴定出45936个lncRNA。在这些lncRNA中，22148个代表重叠、基因间、内含子和反义亚型的lncRNA在所有配对组织中均有表达，其中5941个（2813个上调和3128个下调，倍数变化≥1.5）在平滑肌瘤中差异表达。同时进行的RNA测序揭示了2588个miRNA和21814个mRNA的表达，其中392个miRNA和16559个mRNA在所有配对组织中均有表达。在这些转录本中，与子宫肌层相比，平滑肌瘤中分别有56个和92个miRNA以及2030个和1825个mRNA上调或下调，倍数变化≥1.5。我们使用定量逆转录-聚合酶链反应（QRT-PCR），在平滑肌瘤及配对的子宫肌层（N = 8）中证实了肝细胞癌上调基因（HULC）、母系表达的lncRNA 3（MEG3）、长链基因间非编码RNA 890（LINC00890）、TSIX、长链基因间非编码RNA 473（LINC00473）、lnc-KLF9-1和lnc-POTEM-3（lncRNA-ATB）的表达。总体而言，本文给出的结果提供了平滑肌瘤中lncRNA的全面表达谱，同时整合了miRNA和mRNA的表达，并通过与已知在平滑肌瘤发病机制中起关键作用的特定miRNA和mRNA相互作用，暗示了lncRNA的潜在调控功能。
