RNA sequencing (RNA-seq) analysis of gene expression provides new insights into hindlimb unloading-induced skeletal muscle atrophy.
RNA sequencing (RNA-seq) analysis of gene expression provides new insights into hindlimb unloading-induced skeletal muscle atrophy.
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DOI：
10.21037/atm-20-7400
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发表时间：
2020-12
影响因子：
--
通讯作者：
Zhu J
中科院分区：
文献类型：
--
作者：
Cui Q;Yang H;Gu Y;Zong C;Chen X;Lin Y;Sun H;Shen Y;Zhu J
失重引起的骨骼肌萎缩，伴随着复杂的生化和生理变化，具有潜在的损害后果。然而，仍然没有一个有效的策略来治疗骨骼肌萎缩。因此，有必要探讨骨骼肌萎缩的分子调控机制和有效的保护措施。采用RNA测序(RNA-seq)技术检测大鼠后肢卸载后12、24、36h、3d、7d比目鱼肌的差异表达基因(Deg)。应用皮尔逊相关热图和主成分分析(PCA)分析DEGS的表达谱。采用基因本体论(GO)和京都基因与基因组百科全书(KEGG)对DEG进行聚类分析。独创性路径分析(IPA)被用来进一步分析特定的生物学过程。在后肢负重后的不同时间点(12、24、36小时、3天、7天)，比目鱼肌中712、1,109、1,433、1,162和1,182个基因的表达水平分别上调，1,186，1,324，1,632，1,446和1,596个基因的表达水平分别下调。主成分分析显示，大鼠比目鱼肌在后肢卸载后7天内表现出三个不同的转录阶段。KEGG和GO注释表明，第一转录阶段主要涉及应激反应的激活，包括氧化应激，抑制细胞增殖和血管生成；第二转录阶段主要涉及蛋白水解系统的激活，并在一定程度上参与炎症反应；第三转录阶段主要涉及蛋白水解系统的广泛激活，显著抑制能量代谢，激活衰老过程和从慢到快的肌肉转换。大鼠骨骼肌在卸载后依次激活不同的生理过程。从这些被激活的生物过程来看，骨骼肌卸载后的三个转录阶段可以依次定义为应激反应阶段、萎缩起始阶段和萎缩阶段。我们的研究不仅有助于了解失重导致肌肉萎缩的分子机制，而且可能为治疗和预防失重引起的肌肉萎缩提供一个重要的时间窗口。
Weightlessness-induced skeletal muscle atrophy, accompanied by complex biochemical and physiological changes, has potentially damaged consequences. However, there is still an insufficient effective strategy to treat skeletal muscle atrophy. Therefore, exploring the molecular mechanisms regulating skeletal muscle atrophy and effective protection is necessary. RNA sequencing (RNA-seq) analysis was used to detect differentially expressed genes (DEGs) in the soleus muscle at 12, 24, 36 hours, three days, and seven days after hindlimb unloading in rats. Pearson correlation heatmaps and principal component analysis (PCA) were applied to analyze DEGs’ expression profiles. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for cluster analysis of DEGs. Ingenuity pathway analysis (IPA) was used to analyze specific biological processes further. At different time points (12, 24, 36 hours, three days, seven days) after hindlimb unloading, the expression levels of 712, 1,109, 1,433, 1,162, and 1,182 genes in rat soleus muscle were upregulated, respectively, whereas the expression levels of 1,186, 1,324, 1,632, 1,446, and 1,596 genes were downregulated, respectively. PCA revealed that rat soleus muscle showed three different transcriptional phases within seven days after hindlimb unloading. KEGG and GO annotation indicated that the first transcriptional phase primarily involved the activation of stress responses, including oxidative stress, and the inhibition of cell proliferation and angiogenesis; the second transcriptional phase primarily involved the activation of proteolytic systems and, to a certain degree, inflammatory responses; and the third transcriptional phase primarily involved extensive activation of the proteolytic system, significant inhibition of energy metabolism, and activation of the aging process and slow-to-fast muscle conversion. Different physiological processes in rat skeletal muscles were activated sequentially after unloading. From these activated biological processes, the three transcriptional phases after skeletal muscle unloading can be successively defined as the stress response phase, the atrophic initiation phase, and the atrophic phase. Our study not only helps in the understanding of the molecular mechanisms underlying weightlessness-induced muscle atrophy but may also provide an important time window for the treatment and prevention of weightlessness-induced muscle atrophy.