Identification of long non-coding RNAs involved in the regulation of the human cardiac rhythm

Although long non-coding RNAs (lncRNAs), a class of RNAs longer than 500 nt with limited coding potential, have been shown to be relevant in rodent cardiac development and function, their role in controlling the human cardiac rhythm remains poorly understood.
 
This study aims to identify and characterize long non-coding RNAs with functional relevance in cardiac rhythm control in humans and investigate their role in modulating life-threatening arrhythmias.
 
Human cardiac transcriptomic datasets were combined with genetic information, such as analysis of genome-wide association studies (GWAS) of arrhythmias. We validated promising candidates identified through this in silico approach in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) by delivering the RNA-targeting CRISPR system CRISPR/CasRx using adeno-associated virus serotype 6 (AAV6). We evaluated the effects of these manipulations at the transcriptomic level using qPCR and bulk RNA sequencing and investigated the functional consequences using optical action potential recordings with the voltage-sensitive dye di-8-ANEPPS.
 
Based on our in silico prediction, seven top-scoring lncRNAs were selected for further investigation in hiPSC-CMs. Transcriptomic analysis showed significant repression of the target lncRNA upon manipulation with AAV6-CasRx for all tested candidates. Four out of seven candidates showed a high number of significantly deregulated genes (log2FC > |0.6| , FDR < 0.05) in response to this treatment. For example, the knockdown of lncCM3 was associated with repression of genes related to the cardiac muscle cell action potential. In line with these data, optical action potential recordings in hiPSC-CMs revealed a significant shortening of the action potential duration upon knockdown of lncCM3 (24% vs. Control, P < 0.0005).
 
In summary, we have identified several lncRNA candidates that are involved in the regulation of human cardiac rhythm. Upon in-depth characterization of their mechanism of action, these genes may show potential as future drug targets.