Identification of long noncoding RNAs (lncRNAs) involved in phenotypic change of vascular smooth muscle cells (VSMCs).
(A) The VSMCs with the synthetic phenotype can be differentiated into less the proliferative and contractile phenotypic by the overexpression of myocardin (MYOCD) or by treatment with transforming growth factor beta (TGFβ). The cells with the contractile phenotype can be converted into the more proliferative and synthetic phenotype by treatment with platelet-derived growth factor (PDGF). (B) Expression level of representative genes previously known to be involved in phenotypic change of VSMCs. The RNA-seq data of PDGF-treated venous smooth muscle cells, MYOCD-overexpressing human coronary artery smooth muscle (HCASM) cells, and TGFβ-treated HCASM cells were obtained from the Gene Expression Omnibus (GEO) (see Methods). The fragments per kilobase of exon model per million mapped fragments (FPKM) values of a protein-coding gene (CNN1) and a long noncoding RNA (SMILR) are depicted in the y-axis. Error bars indicate standard errors from four samples for the PDGF set, or deviation from two samples for the MYOCD and TGFβ sets. (C) Expression profiles of lncRNAs during phenotypic change of VSMCs were analyzed. The calculation of lncRNAs’ expression changes is described in Method section. The gene clusters with prominent changes between the synthetic and contractile phenotypes are indicated with boxes. Detailed expression changes of genes from those clusters are depicted in S1 and S2 Figs.