Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support.
Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support.
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DOI：
10.1161/circulationaha.113.003863
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发表时间：
2014-03-04
期刊：
影响因子：
37.8
通讯作者：
Nerbonne JM
中科院分区：
文献类型：
--
作者：
Yang KC;Yamada KA;Patel AY;Topkara VK;George I;Cheema FH;Ewald GA;Mann DL;Nerbonne JM
微阵列已被广泛用于分析人类心脏衰竭的转录组重塑，尽管所提供的基因组覆盖范围有限，并且无法提供心肌转录组景观的详细图片。在这里，我们描述了基于测序的转录组分析，提供了心肌mRNA、microRNA （miRNA）和长链非编码RNA （lncRNA）在衰竭人类心脏中表达的全面分析，在机械支持左心室辅助装置（LVAD）前后。对LVAD前后收集的配对非缺血性（NICM,n=8）和缺血性（ICM,n=8）人类衰竭左心室样本以及非衰竭人类左心室样本（n=8）分离的RNA进行了深度测序。这些分析显示线粒体起源的mRNA（37%）和lncRNA（71%）丰度很高。miRNASeq显示，与未衰竭的左室相比，ICM和NICM中分别有160和147个差异表达的mirna。其中只有2个（ICM）和5个（NICM） mirna与LVAD归一化。RNASeq在人LV中检测到18480个lncrna，其中包括113个新的lncrna。在与心力衰竭差异表达的679 （ICM）和570 (NICM) lncrna中，约10%的lncrna在LVAD后得到改善或正常化。此外，lncrna的表达特征，而不是mirna或mrna，可以区分缺血性和非缺血性起源的心肌病。进一步分析表明，顺式基因调控是人类心脏lncRNAs的主要作用机制。心肌转录组在晚期心力衰竭和LVAD支持后是动态调节的。lncrna的表达谱，而不是mrna或mirna，可以区分不同病因的衰竭心脏，并在LVAD支持下显着改变。这些结果表明lncrna在心力衰竭的发病机制和机械支持下观察到的逆转重塑中发挥了重要作用。
Microarrays have been used extensively to profile transcriptome remodeling in failing human heart, although the genomic coverage provided is limited and fails to provide a detailed picture of the myocardial transcriptome landscape. Here, we describe sequencing-based transcriptome profiling, providing comprehensive analysis of myocardial mRNA, microRNA (miRNA) and long non-coding RNA (lncRNA) expression in failing human heart, before and after mechanical support with a left ventricular assisted device (LVAD) Deep sequencing of RNA isolated from paired non-ischemic (NICM,n=8) and ischemic (ICM,n=8) human failing LV samples collected pre- and post-LVAD, as well as from non-failing human LV (n=8), was conducted. These analyses revealed high abundance of mRNA (37%) and lncRNA (71%) of mitochondrial origin. miRNASeq revealed 160 and 147 differentially expressed miRNAs in ICM and NICM, respectively, compared with non-failing LV. Among these only 2 (ICM) and 5 (NICM) miRNAs are normalized with LVAD. RNASeq detected 18480, including 113 novel, lncRNAs in human LV. Among the 679 (ICM) and 570 (NICM) lncRNAs differentially expressed with heart failure, ~10% are improved or normalized with LVAD. In addition, the expression signature of lncRNAs, but not miRNAs or mRNAs, distinguishes cardiomyopathy of ischemic and non-ischemic origins. Further analysis suggests that cis-gene regulation represents a major mechanism of action of human cardiac lncRNAs. The myocardial transcriptome is dynamically regulated in advanced heart failure and following LVAD support. The expression profiles of lncRNAs, but not mRNAs or miRNAs, can discriminate failing hearts of different etiologies and are markedly altered in response to LVAD support. These results suggest an important role for lncRNAs in the pathogenesis of heart failure and in reverse remodeling observed with mechanical support.