Decrease of RNA editing in the failing heart leads to induction of circRNAs

Background and purpose

Adenosine-to-Inosine (A-to-I) RNA editing is a post-transcriptional modification process that affects the secondary structure of RNAs. Changes in RNA editing have been associated with human diseases. We therefore aimed to analyze editing in the healthy and failing human heart.

Methods and results

Transcriptome sequencing of human heart samples of heart failure (HF) patients (n=20) and controls (n=10) revealed A-to-I editing as the major type of editing (>80%). In HF patients, RNA editing was reduced, which was primarily attributable to Alu elements in introns of protein-coding genes. We identified 166 upregulated circRNAs in HF, with the majority showing reduced RNA editing in their parental host gene (88.3%). CircRNA expression did not correlate with their corresponding host gene (R=0.07, P<0.05), suggesting that an alternative splicing mechanism gives rise to the elevated circRNA levels in HF. The RNA editing enzyme ADAR2, which binds to RNA regions that are edited from adenosine to inosine, was decreased in failing human hearts (−68.2%). In vitro, reduction of ADAR2 increased circRNA levels suggesting a causal effect of reduced ADAR2 levels on increased circRNAs in the failing human heart. To gain mechanistic insight, we examined the formation of circRNAs on one exemplary candidate. AKAP13 was among the top edited mRNAs in the human heart and gave rise to a circular transcript, which was elevated in HF. ADAR2 reduced the formation of double-stranded structures in AKAP13 pre-mRNA, thereby reducing the stability of Alu elements and the circularization of the resulting circRNA. Overexpression of circAKAP13 impaired the sarcomere regularity of human induced pluripotent stem cell-derived cardiomyocytes (−31.0%).

Conclusion

Our study shows that ADAR2 mediates A-to-I RNA editing in the human heart. We describe an alternative splicing mechanism of circRNAs in the human heart. In the healthy human heart, A-to-I RNA editing represses the formation of dsRNA structures of Alu elements thereby favoring linear mRNA splicing. Our results contribute to a better mechanistic understanding into the human-specific regulation of circRNA formation and are relevant to diseases with reduced RNA editing and increased circRNA levels.

Funding Acknowledgement

Type of funding sources: None.

The long non-coding RNA Heat4 is upregulated in heart failure and decreases the immune response of non-classical monocytes

Background and purpose

Activation of the immune system correlates with the severity and the prognosis of patients with heart failure (HF). This study aims to identify and characterize long non-coding RNAs (lncRNAs) as a potential mechanistic link between the pathophysiology of HF and the activation of the immune system.

Methods and results

Next-generation sequencing (NGS) studies identified a 2.05-fold increase of the lncRNA Heat4 in the blood of patients with HF compared to controls, which was validated in a larger cohort (HF: N=63; Controls: N=38; p<0.05). Interestingly, the lncRNA Heat4 is encoded in the well-known immune receptor locus CD300, together with 8 CD300-receptors which are associated with activation of the immune system. To determine the cellular origin of Heat4 in blood, we performed MACS and identified Heat4 to be enriched in non-classical monocytes compared to classical monocytes (3.37-fold, p<0.05). The expression of Heat4 in non-classical monocytes was further validated by single-cell RNA sequencing. Overexpression of Heat4 in monocytes decreased levels of pro-inflammatory cytokines such as TNFα (38.6% reduction, p<0.05). Conversely, the knockdown of Heat4 resulted in elevated levels of pro-inflammatory cytokines, including IL6 (10.83-fold, p<0.05) and TNFα (4.14-fold, p<0.05). In a larger cohort including patients with HF, Heat4 was able to determine the prevalence of heart failure by AUC=0.734 (p<0.05). Moreover, in a 4-year follow-up of the same cohort, Heat4 predicted mortality by AUC=0.789 (HF: N=63, Dead=32; Controls: N=38, Dead=0; p<0.05).

Conclusion

The long non-coding RNA Heat4 is elevated in the blood of HF patients. Mechanistically, Heat4 limits the extent of the inflammatory response of non-classical monocytes. Therefore, Heat4 may provide a regulatory link between inflammation and HF.

Funding Acknowledgement

Type of funding sources: None.

Reduced RNA editing in the failing human heart mediates alternative circular RNA splicing

Background and purpose

Post-transcriptional RNA editing is an important mechanism in the development of human diseases. RNA editing can affect RNA stability and alternative splicing. The aim of our study was to characterize RNA editing and its impact on alternative RNA splicing in the healthy and failing human heart.

Methods and results

Human heart samples of heart failure (HF) patients (n=20) and controls (n=10) were analyzed using RNA sequencing with subsequent analysis of RNA editing. We identified adenosine-to-inosine (A-to-I) editing as the major form of RNA editing in human hearts, being reduced in HF patients. Consistently, we found the editing enzyme ADAR2 reduced in HF patients. A-to-I RNA editing predominantly occurred in intronic regions of protein-coding genes, specifically in repetitive, primate-specific Alu elements which can affect RNA splicing. Indeed, we found 173 circular RNAs (circRNAs) regulated by alternative mRNA splicing in the failing heart.

Loss of ADAR2 led to reduced RNA editing concomitant with an increase of circRNA, while overexpression reduced circRNA expression and enhanced RNA editing.

Conclusion

A-to-I editing is the major type of RNA editing in the human heart, being reduced in HF. We demonstrate a primate-specific alternative RNA splicing mechanism mediated by RNA editing in human hearts. The findings may be relevant to diseases with reduced RNA editing such as cancer, neurological and cardiac diseases.

Funding Acknowledgement

Type of funding sources: None.