Integrating lncRNAs and mRNAs expression profiles in terminal hindgut of fetal rats with anorectal malformations
Integrating lncRNAs and mRNAs expression profiles in terminal hindgut of fetal rats with anorectal malformations
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DOI：
10.1007/s00383-018-4311-8
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发表时间：
2018-08
影响因子：
1.8
通讯作者：
Hui Xiao;Rui Huang;Long Chen;M. Diao;Long Li
中科院分区：
文献类型：
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作者：
Hui Xiao;Rui Huang;Long Chen;M. Diao;Long Li
研究背景直肠肛门畸形(ARMS)的胚胎病因和发病机制尚不清楚。最近的研究表明，基因表达异常是导致ARM的关键因素。据报道，长的非编码RNA(LncRNAs)是基因组中的“转录噪音”。在ARM的发病机制中，LncRNA和mRNA的表达谱特征仍然较少。此外，到目前为止，lncRNAs在这一过程中的调控功能还没有被研究过。因此，本研究旨在利用Agilents公司的lncRNA和mRNA共表达微阵列整合乙硫脲(ETU)诱导的ARM大鼠后肠末端的lncRNA和mRNA的表达谱。方法在妊娠第10天用乙硫脲(ETU)诱导ARM模型，于第20天剖宫产收集胚胎，取3只空气质量相近的胎鼠后肠末端1 cm组织，提取总RNA。结果与对照组相比，ARM组后肠末端有16 4个基因异常表达(Fc ≥ 2；P<； 0.0 5)，其中36个表达上调，12 8个表达下调；772个基因异常表达(Fc ≥ 2；P<； 0.0 5)。利用ARM和对照组的差异表达谱进行基因本体论(GO)和通径分析。这些核糖核酸中的一个子集被确定为与武器的发展进程密切相关。选取两组间差异表达的4个RNA进行定量聚合酶链式反应验证，结果与芯片数据一致。此外，根据相关性分析，建立了LncRNAs和mRNAs的共表达网络。我们通过转录因子(转录因子)来预测转录因子的功能，这些转录因子可能调节转录因子的表达。在LncRNA-Tf对的核心网络中，LncRNAs可分为Jun、c-Myc、USF1、Alf2和Stat3调控的5类途径。结论以上结果提示这些异常的LncRNAs可能参与了ARM的发病机制，我们的工作可能为今后对ARM的研究提供新的研究方向。
BackgroundThe detailed embryonic etiology and pathogenesis of anorectal malformations (ARMs) remains unclear. Recent studies have shown that gene expression abnormalities were the key factors that result in ARMs. Long non-coding RNAs (lncRNAs) were reported as the ‘transcriptional noise’ within the genome. The expression profiles of lncRNA and mRNA remain less characterized in the pathogenesis of ARMs. Furthermore, the function of lncRNAs in the regulation of this process has not been investigated so far. Therefore, this current study was aimed to integrate lncRNA and mRNA expression profiles in terminal hindgut of ethylenethiourea (ETU)-induced ARM rats using Agilents lncRNA and mRNA co-expression microarrays.MethodsARM model was induced with ethylenethiourea (ETU) on gestational day 10. Cesarean deliveries were conducted to collect the embryos on gestational day 20. For the extraction of total RNA, 1-cm terminal hindgut tissues were collected from three fetal rats with similair weights. The microarrays and quantitative RT-PCR analysis were conducted to evaluate the lncRNA and mRNA expression profiles in normal fetal rats and ARM fetal rats.ResultsCompared with control group, 164 lncRNAs were observed to be aberrantly expressed (FC ≥ 2;P< 0.05) in ARM group, including 36 upregulated and 128 downregulated, while 772 mRNAs were observed to be aberrantly expressed (FC ≥ 2;P< 0.05) in the terminal hindgut, including 350 up-regulated and 422 down-regulated. The differential expression profiles between the ARM and the control group were used for gene ontology (GO) and pathway analysis. A subset of those RNAs was identified to be closely related to the development process of ARMs. The four RNAs that were differentially expressed between the two groups were selected for qPCR validation, and the results were in line with the microarray data. In addition, the lncRNAs and mRNA co-expression network was established according to the correlation analysis. We predicted the functions of transregulatory lncRNAs by the TFs (transcription factors) which might modulate their expression. In the core network of lncRNA–TF pairs, the lncRNAs can be classified into 5 categories of pathways governed by Jun, c-Myc, Usf1, Alf2, and Stat3.ConclusionFrom the above results, it can be suggested that these aberrant lncRNAs might participate in the pathogenesis of ARM, and our present work may provide new research directions for future studies of ARMs.