Distinct Circulating Expression Profiles of Long Noncoding RNAs in Heart Failure Patients With Ischemic and Nonischemic Dilated Cardiomyopathy

Abstract

Ischemic cardiomyopathy (ICM) and dilated cardiomyopathy (DCM), with distinct long-term prognosis and responses to treatment, are two major problems that lead to heart failure (HF) ultimately. In this study, we investigated the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expressions in the plasma of patients with DCM and ICM and analyzed the different lncRNA profile between the two groups. The microarray analysis identified 3,222 and 1,911 significantly differentially expressed lncRNAs and mRNAs between DCM and ICM group. The most enriched upregulated functional terms included positive regulation of I-kappaB kinase/nuclear factor-kappaB signaling and regulation of cellular localization, while the top 10 downregulated genes mainly consisted of acid secretion and myosin heavy chain binding. Furthermore, the Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differentially expressed lncRNA-coexpressed mRNAs between DCM and ICM group were significantly enriched in the natural killer cell mediated cytotoxicity and ras signaling pathway respectively. Quantitative real-time PCR confirmed 8 of 12 lncRNAs were upregulated in DCM group compared to ICM group which was consistent with the initial microarray results. The lncRNA/mRNA coexpression network indicated the possible functions of the validated lncRNAs. These findings revealed for the first time the specific expression pattern of both protein-coding RNAs and lncRNAs in plasma of HF patients due to DCM and ICM which may provide some important evidence to conveniently identify the etiology of myocardial dysfunctions and help to explore a better strategy for future HF prognosis evaluation.

Keywords: dilated cardiomyopathy; expression profile; ischemic cardiomyopathy; long noncoding RNA; messenger RNA; microarray.

Figure 1

The heat map and hierarchical clustering analysis of long noncoding RNAs (lncRNAs) (A) and messenger RNAs (mRNAs) (B) that were differentially expressed between the peripheral plasma samples from dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) patients. Top 20 upregulated and top 20 downregulated results were filtered with fold change (FC) ≥ 2.0 and p 0.05. Expression values are represented in shades of red and green, indicating expression above and below the relative expression respectively. −3.0, 0, and 3.0 are FCs in the corresponding spectrum. The magnitude of deviation from the median is represented by the color saturation.

Figure 2

The volcano plots and scatter plots of long noncoding RNA (lncRNA) (A, C) and messenger RNA (mRNA) (B, D) expression variation between the dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) patients. Expression values of 11,784 lncRNA and 7,473 mRNA in DCM and ICM patients were converted to log₂ (fold change) and were compared to −log₁₀ (p-value) using a volcano plot. A threshold of p 0.05 and fold change ≥2.0 (The red dots represented upregulated, the green dots represented downregulated). Scatter plots indicated the normalized signal values of the plasma sample (log₂ scaled).The red dots represented upregulation and fold change ≥ 2.0, the green dots represented downregulation and fold change ≥ 2.0.

Figure 3

Chromosome distribution of long noncoding RNAs (lncRNAs) differentially expressed in plasma between the DCM and ICM patients. chr, chromosome; M, mitochondrial.

Figure 4

Top 20 GO terms for the differences in coexpressed long noncoding RNA (lncRNA) genes in the dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) patients. The top 10 Gene Ontology (GO) terms that upregulated genes correlated with (A). The top 10 GO terms that downregulated genes correlated with (B). The bar plot shows the top 10 enrichment score [−log10(p-value)] value of the significant enrichment GO terms.

Figure 5

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. Top 20 pathways for the differences in long noncoding RNA (lncRNA) genes coexpressed in the dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) patients. The red bars are associated with upregulated pathways, the green bars are associated with downregulated pathways. The bar plot shows the top 20 enrichment score [−log10(p-value)] value of the significant enrichment gene ontology terms.

Figure 6

Validation of the differential expression of long noncoding RNAs (lncRNAs) by quantitative real-time PCR (qRT-PCR) (A–L). Levels of the lncRNA (T226011, ENST00000554552, T201134, T023556, T109935, NR_109994, NR_046647, NR_029376, ENST00000494340, T191270, T207073, uc004bsl.1) in plasma of patients with dilated cardiomyopathy (DCM) or ischemic cardiomyopathy (ICM). DCM group, n = 11; ICM group, n = 9. *p 0.05 versus control, **p 0.01 versus control.

Figure 7

Coding–noncoding gene coexpression networks network of the seven validated long noncoding RNAs (lncRNAs) and their correlated messenger RNAs (mRNAs). The network represents coexpression correlations between seven lncRNAs and their correlated mRNAs. Red nodes represent lncRNAs. Blue nodes represent correlated mRNAs. The real lines between lncRNAs and mRNAs mean positive correlation, while the dotted lines mean negative correlation.