Datasheet1_Genome-wide profiling of miRNA-gene regulatory networks in mouse postnatal heart development—implications for cardiac regeneration.pdf

BackgroundAfter birth, mammalian cardiomyocytes substantially lose proliferative capacity with a concomitant switch from glycolytic to oxidative mitochondrial energy metabolism. Micro-RNAs (miRNAs) regulate gene expression and thus control various cellular processes. Their roles in the postnatal loss of cardiac regeneration are however still largely unclear. Here, we aimed to identify miRNA-gene regulatory networks in the neonatal heart to uncover role of miRNAs in regulation of cell cycle and metabolism.
Methods and resultsWe performed global miRNA expression profiling using total RNA extracted from mouse ventricular tissue samples collected on postnatal day 1 (P01), P04, P09, and P23. We used the miRWalk database to predict the potential target genes of differentially expressed miRNAs and our previously published mRNA transcriptomics data to identify verified target genes that showed a concomitant differential expression in the neonatal heart. We then analyzed the biological functions of the identified miRNA-gene regulatory networks using enriched Gene Ontology (GO) and KEGG pathway analyses. Altogether 46 miRNAs were differentially expressed in the distinct stages of neonatal heart development. For twenty miRNAs, up- or downregulation took place within the first 9 postnatal days thus correlating temporally with the loss of cardiac regeneration. Importantly, for several miRNAs, including miR-150-5p, miR-484, and miR-210-3p there are no previous reports about their role in cardiac development or disease. The miRNA-gene regulatory networks of upregulated miRNAs negatively regulated biological processes and KEGG pathways related to cell proliferation, while downregulated miRNAs positively regulated biological processes and KEGG pathways associated with activation of mitochondrial metabolism and developmental hypertrophic growth.
ConclusionThis study reports miRNAs and miRNA-gene regulatory networks with no previously described role in cardiac development or disease. These findings may help in elucidating regulatory mechanism of cardiac regeneration and in the development of regenerative therapies.

背景
出生后，哺乳动物心肌细胞的增殖能力会显著丧失，同时伴随能量代谢方式从糖酵解向氧化磷酸化线粒体代谢的转变。微小RNA（micro-RNAs，miRNAs）可调控基因表达，进而控制多种细胞进程。然而，miRNAs在出生后心肌再生能力丧失过程中所发挥的作用，目前仍尚未完全明晰。本研究旨在鉴定新生小鼠心脏中的miRNA-基因调控网络，以揭示miRNAs在细胞周期与代谢调控中的作用。
方法与结果
本研究利用采集自出生后第1天（P01）、第4天（P04）、第9天（P09）及第23天（P23）的小鼠心室组织样本提取的总RNA，开展全基因组miRNA表达谱分析。本研究借助miRWalk数据库预测差异表达miRNAs的潜在靶基因，并结合本团队此前发表的mRNA转录组学数据，筛选出在新生小鼠心脏中伴随差异表达的验证靶基因。随后，通过富集基因本体（Gene Ontology，GO）分析与京都基因与基因组百科全书（KEGG）通路分析，对鉴定得到的miRNA-基因调控网络的生物学功能进行解析。
最终共鉴定出46个在新生小鼠心脏发育不同阶段呈现差异表达的miRNAs。其中20个miRNAs的表达上调或下调发生在出生后的前9天内，该时序与心肌再生能力丧失的过程高度相关。值得注意的是，包括miR-150-5p、miR-484及miR-210-3p在内的数种miRNAs，此前尚无关于其在心脏发育或疾病中作用的相关报道。上调表达miRNAs所构建的miRNA-基因调控网络，可负向调控与细胞增殖相关的生物学过程及KEGG通路；而下调表达miRNAs则可正向调控与线粒体代谢激活及发育性肥厚生长相关的生物学过程和KEGG通路。
结论
本研究首次报道了此前未被阐明在心脏发育或疾病中发挥作用的miRNAs及其对应的miRNA-基因调控网络。本研究结果可为阐明心肌再生的调控机制以及开发再生治疗策略提供理论支撑。