Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Endocardial-like And Primary Cardiac Endothelial Cell Transcriptomes

Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of human primary cardiac microvascular endothelial cells and hPSC-derived endocardial endothelial cells, and compare to those of other cell lineages including hPSCs, mesoderm, cardiomcyotyes as well as mouse cardiac microvascular and endocardial endothelial cells. Six cardiac endothelial cell samples from two different hPSC lines and one donor were performed in IIIumina HiSeq2500. The resulting sequence reads (about 20 million reads per sample) were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key endocardial endothelial cell markers including CDH5, vWF, PECAM1, NFATC1 and NPR3, and the gene set enrichment analysis (GSEA) showed enrichment in angiogenesis and vasculature development. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to endocardial function. This study represents the first detailed analysis of endocardial-like endothelial cell transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into endocardium.