环状 RNA 在人诱导多能干细胞及其衍生心肌细胞中的特征。
Signature of circular RNAs in human induced pluripotent stem cells and derived cardiomyocytes.
机构信息
Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Soochow University, Suzhou, China.
Key Laboratory of Stem Cells and Biomedical Materials of Jiangsu Province and Chinese Ministry of Science and Technology, Soochow University, Suzhou, China.
出版信息
Stem Cell Res Ther. 2018 Mar 9;9(1):56. doi: 10.1186/s13287-018-0793-5.
BACKGROUND
Circular RNAs (circRNAs) are regarded as a novel class of noncoding RNA regulators. Although a number of circRNAs have been identified by bioinformatics analysis of RNA-seq data, tissue and disease-specific circRNAs are still to be uncovered to promote their application in basic research and clinical practice. The purpose of this study was to explore the circRNA profiles in human induced pluripotent stem cells (hiPSCs) and hiPSC-derived cardiomyocytes (hiPSC-CMs), and to identify cardiac or disease-specific circRNAs.
METHODS
hiPSCs were generated from fibroblasts, and then further differentiated to hiPSC-CMs by modulating WNT signaling in RPMI+B27 medium. Following high-throughput RNA sequencing, circRNAs were extracted and quantified by a combined strategy known as CIRCexplorer. Integrative analysis was performed to illuminate the correlation between circRNAs and their parental linear isoforms. Cardiac and disease-specific expression of circRNAs was confirmed by quantitative reverse-transcription PCR.
RESULTS
In this study, a total of 5602 circRNAs were identified in hiPSCs and hiPSC-CMs. Our data indicated, for the first time, more enriched expression of circRNAs in differentiated cardiomyocytes than in undifferentiated hiPSCs. In addition to the host gene-dependent expression, our integrative analysis also identified a number of circRNAs showing host gene-independent expression in hiPSCs and hiPSC-CMs. CircRNAs including circSLC8A1, circCACNA1D, circSPHKAP and circALPK2 showed cardiac-selective expression during cardiac differentiation and human heart-specific enrichment in fetal tissues. Furthermore, circSLC8A1 abnormally increased in heart tissues from patients suffering from dilated cardiomyopathy.
CONCLUSIONS
CircRNAs are highly enriched in hiPSC-differentiated CMs, and cardiac-specific circRNAs such as circSLC8A1, circCACNA1D, circSPHKAP and circALPK2 may serve as biomarkers of CMs. Detection of the excessive expression of circSLC8A1 provides a potential approach for pathological status indication of heart disease.
背景
环状 RNA（circRNAs）被认为是一类新的非编码 RNA 调控因子。尽管通过 RNA-seq 数据的生物信息学分析已经鉴定出许多 circRNAs，但仍需要发现组织和疾病特异性的 circRNAs，以促进它们在基础研究和临床实践中的应用。本研究旨在探索人诱导多能干细胞（hiPSCs）和 hiPSC 衍生的心肌细胞（hiPSC-CMs）中的 circRNA 谱，并鉴定心脏或疾病特异性的 circRNAs。
方法
hiPSCs 由成纤维细胞生成，然后通过在 RPMI+B27 培养基中调节 WNT 信号进一步分化为 hiPSC-CMs。在高通量 RNA 测序后，通过称为 CIRCexplorer 的组合策略提取和定量 circRNAs。整合分析用于阐明 circRNAs 与其亲本线性异构体之间的相关性。通过定量逆转录 PCR 验证 circRNAs 的心脏和疾病特异性表达。
结果
在本研究中，在 hiPSCs 和 hiPSC-CMs 中共鉴定出 5602 个 circRNAs。我们的数据首次表明，分化的心肌细胞中 circRNAs 的表达更为丰富，而未分化的 hiPSCs 中则较少。除了依赖于宿主基因的表达外，我们的整合分析还鉴定了许多在 hiPSCs 和 hiPSC-CMs 中表现出宿主基因非依赖性表达的 circRNAs。circSLC8A1、circCACNA1D、circSPHKAP 和 circALPK2 等 circRNAs在心脏分化过程中表现出心脏选择性表达，并且在胎儿组织中特异性富集于人心脏。此外，circSLC8A1 在患有扩张型心肌病的患者的心脏组织中异常增加。
结论
circRNAs 在 hiPSC 分化的 CMs 中高度富集，circSLC8A1、circCACNA1D、circSPHKAP 和 circALPK2 等心脏特异性 circRNAs可能作为 CMs 的标志物。circSLC8A1 的过度表达检测为心脏病的病理状态提供了一种潜在的指示方法。
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