An Chung-Il, Ichihashi Yasunori, Peng Jie, Sinha Neelima R, Hagiwara Nobuko
Division of Cardiovascular Medicine, Department of Internal Medicine, University of California Davis, Davis, California, United States of America.
Department of Plant Biology, University of California Davis, Davis, California, United States of America.
PLoS One. 2016 Nov 10;11(11):e0166574. doi: 10.1371/journal.pone.0166574. eCollection 2016.
The postnatal heart undergoes highly coordinated developmental processes culminating in the complex physiologic properties of the adult heart. The molecular mechanisms of postnatal heart development remain largely unexplored despite their important clinical implications. To gain an integrated view of the dynamic changes in gene expression during postnatal heart development at the organ level, time-series transcriptome analyses of the postnatal hearts of neonatal through adult mice (P1, P7, P14, P30, and P60) were performed using a newly developed bioinformatics pipeline. We identified functional gene clusters by principal component analysis with self-organizing map clustering which revealed organized, discrete gene expression patterns corresponding to biological functions associated with the neonatal, juvenile and adult stages of postnatal heart development. Using weighted gene co-expression network analysis with bootstrap inference for each of these functional gene clusters, highly robust hub genes were identified which likely play key roles in regulating expression of co-expressed, functionally linked genes. Additionally, motivated by the role of the transcription factor Sox6 in the functional maturation of skeletal muscle, the role of Sox6 in the postnatal maturation of cardiac muscle was investigated. Differentially expressed transcriptome analyses between Sox6 knockout (KO) and control hearts uncovered significant upregulation of genes involved in cell proliferation at postnatal day 7 (P7) in the Sox6 KO heart. This result was validated by detecting mitotically active cells in the P7 Sox6 KO heart. The current report provides a framework for the complex molecular processes of postnatal heart development, thus enabling systematic dissection of the developmental regression observed in the stressed and failing adult heart.
出生后的心脏经历高度协调的发育过程，最终形成成体心脏复杂的生理特性。尽管出生后心脏发育的分子机制具有重要的临床意义，但在很大程度上仍未被探索。为了在器官水平上全面了解出生后心脏发育过程中基因表达的动态变化，我们使用新开发的生物信息学流程对新生小鼠至成年小鼠（P1、P7、P14、P30和P60）出生后的心脏进行了时间序列转录组分析。我们通过主成分分析和自组织映射聚类确定了功能基因簇，揭示了与出生后心脏发育的新生儿、幼年和成年阶段相关的生物学功能相对应的有组织、离散的基因表达模式。对于这些功能基因簇中的每一个，我们使用加权基因共表达网络分析和自举推理，确定了高度稳健的中心基因，这些基因可能在调节共表达、功能相关基因的表达中起关键作用。此外，受转录因子Sox6在骨骼肌功能成熟中的作用的启发，我们研究了Sox6在心肌出生后成熟中的作用。Sox6基因敲除（KO）心脏与对照心脏之间的差异表达转录组分析发现，在出生后第7天（P7），Sox6基因敲除心脏中参与细胞增殖的基因显著上调。通过检测P7 Sox6基因敲除心脏中有丝分裂活跃的细胞，验证了这一结果。本报告为出生后心脏发育的复杂分子过程提供了一个框架，从而能够系统地剖析在应激和衰竭的成体心脏中观察到的发育衰退。
