Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNAs in Failing Human Heart and Remodeling With Mechanical Circulatory Support

Abstract

Background: 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) Methods and Results: 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. Conclusions: 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.

Long non-coding RNAs link extracellular matrix gene expression to ischemic cardiomyopathy

“…P < 0.01) might lead to loss of some true positive, novel lncRNAs. Comparing these 145 differentially expressed lncRNAs to 679 lncRNAs differentially expressed in ICM patients in an earlier study, 13 we found that 19 were dysregulated in both studies. Genome browser views of representative differentially expressed lncRNAs are shown in Figure 2C.…”

“…In that study, the investigators profiled lncRNA expression from paired non-ischemic and ischemic human failing left ventricles before and after left ventricular assist device (LVAD). 13,31 The authors suggested that lncRNAs could be used to discriminate failing hearts of different pathologies. Interestingly, another recent study identified a novel circulating lncRNA, LIPCAR, as a molecular marker for HF.…”

“…The results of our analysis are consistent with a recently reported similar study. 13 We inspected the expression of signature marker genes that are associated with HF in the two groups. Indeed, many marker genes were found to be differentially expressed.…”

“…11 Another study documented dysregulated lncRNAs in infarcted mouse hearts. 12 Interestingly, Yang et al, 13 performed RNA deep sequencing and they identified HF associated lncRNAs in human patients. Together, these studies suggest that lncRNAs participate in cardiac disease pathogenesis.…”

Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers

“…S1) were shown to contribute to muscle or myocardial function (8, 9). miRNAs and other classes of RNA have been profiled in failing human myocardium (10)(11)(12)(13)(14)(15)(16)(17), and a selected subset was also investigated as circulating biomarkers in HF (18)(19)(20)(21)(22)(23)(24). However, in these studies heart tissue and circulating miRNA abundance changes were not acquired simultaneously to correlate changes in tissue versus circulating miRNA composition.…”