Characterization and analysis of long non-coding rna (lncRNA) in In Vitro- and Ex Vivo-derived cardiac progenitor cells.

Baron Arnone,Jake Y Chen,Gangjian Qin,Kishore K Wary

doi:10.1371/journal.pone.0180096

Abstract

Recent advancements in cell-based therapies for the treatment of cardiovascular disease (CVD) show continuing promise for the use of transplanted stem and cardiac progenitor cells (CPCs) to promote cardiac restitution. However, a detailed understanding of the molecular mechanisms that control the development of these cells remains incomplete and is critical for optimizing their use in such therapy. Long non-coding (lnc) RNA has recently emerged as a crucial class of regulatory molecules involved in directing a variety of critical biological processes including development, homeostasis and disease. As such, a rising body of evidence suggests that they also play key regulatory roles in CPC development, though many questions remain regarding the expression landscape and specific identity of lncRNA involved in this process. To address this, we performed whole transcriptome sequencing of two murine CPC populations–Nkx2-5 EmGFP reporter-sorted embryonic stem (ES) cell-derived and ex vivo, cardiosphere-derived–in an effort to characterize their lncRNA profiles and potentially identify novel CPC regulators. The resulting sequencing data revealed an enrichment in both CPC populations for a panel of previously-identified lncRNA genes associated with cardiac differentiation. Additionally, a total of 1,678 differentially expressed and as-of-yet unannotated, putative lncRNA genes were found to be enriched for in the two CPC populations relative to undifferentiated ES cells.

Highlights

Cardiovascular disease (CVD) is the leading cause of morbidity and mortality both in the US and worldwide [1]
A slight modification was made to the conventional in vitro approach to initiating cardiac differentiation from embryonic stem (ES) cells which typically utilizes a gravity-based hanging drop method to promote the formation of embryoid bodies (EBs) that are plated onto an adherence matrix
When RNA-seq data from the two cardiac progenitor cells (CPCs) populations was compared to a panel of 195 previously-identified lncRNAs implicated in a variant model of cardiac-directed, ES cell-based differentiation, over half (108) were determined to be differentially expressed when compared to undifferentiated ES cells

Summary

Introduction

Cardiovascular disease (CVD) is the leading cause of morbidity and mortality both in the US and worldwide [1]. The pathological endpoint for CVD is heart failure, which is characterized by significant loss of the myocardium due to acute or chronic cardiac injury, myocardial infarction (MI), leading to a progressive reduction in cardiac function and, death. Though multiple animal [2,3,4] and human [5, 6] studies have provided clear evidence for myocardial cell renewal throughout adulthood, this renewal capacity is vastly insufficient for the purposes of restoring cardiac mass and function for patients with chronic heart failure. LncRNA in cardiac progenitor cells design, data collection and analysis, decision to publish, or preparation of the manuscript

Methods

Results

Conclusion