Long noncoding RNA VENTHEART is required for ventricular cardiomyocyte specification and function

Abstract

Rationale: Cardiac-expressed long noncoding RNAs (lncRNAs) are important for cardiomyocyte (CM) differentiation and function. Several lncRNAs have been identified and characterized for early CM lineage commitment, however those in later CM lineage specification and maturation remain less well studied. Moreover, unique atrial / ventricular lncRNA expression has never been studied in detail.

Objectives: Here, we characterized a novel ventricular myocyte-restricted lncRNA, not expressed in atrial myocytes, and conserved only in primates.

Methods and results: First, we performed single cell RNA-seq on human pluripotent stem cell derived cardiomyocytes (hPSC-CM) at the late stages of 2, 6 and 12 weeks of differentiation. Weighted correlation network analysis identified core gene modules, including a set of lncRNAs highly abundant and predominantly expressed in the human heart. A lncRNA (we call VENTHEART, VHRT) co-expressed with cardiac maturation and ventricular-specific genes MYL2 and MYH7, and was expressed in fetal and adult human ventricles, but not atria. CRISPR-mediated deletion of the VHRT gene led to impaired CM sarcomere formation and significant disruption of the ventricular CM gene program. Indeed, a similar disruption was not observed in VHRT KO hPSC-derived atrial CM, suggesting that VHRT exhibits only ventricular myocyte subtype-specific effects. Optical recordings validated that loss of VHRT significantly prolonged action potential duration at 90 % repolarization (APD₉₀) for ventricular-like, but not atrial-like, CMs.

Conclusion: This reports the first lncRNA that is exclusively required for proper ventricular, and not atrial, CM specification and function.

Keywords: Cardiac myocyte specification and maturation; Cardiomyocyte contraction; Single cell RNAseq; Stem cell derived cardiomyocytes; Transcriptomic; lncRNA.