Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene-edited cardiomyocytes
Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene-edited cardiomyocytes
复制标题
RhoE基因编辑心肌细胞信号通路和分子网络中差异表达基因的独创性通路分析
DOI：
10.3892/ijmm.2020.4661
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发表时间：
2020-09-01
影响因子：
5.4
通讯作者：
Jie, Wei
中科院分区：
文献类型：
--
作者：
Shao, Zhongming;Wang, Keke;Jie, Wei
RhoE/RND3是Rho超家族蛋白中的一个非典型成员，然而，该蛋白的全球生物学功能仍未得到解决。本研究利用CRISPR/Cas9技术建立了RhoE基因敲除的H9C2心肌细胞系，并利用全基因组表达基因芯片筛选敲除细胞系与野生型细胞系之间的差异表达基因(Deg)。使用折叠变化阈值≥1.2和P<；0.05，共鉴定出829个DEG，其中417个上调，412个下调。使用独创性通路分析系统，以-Log(P值)>；2为阈值，发现67条典型通路被丰富。许多检测到的信号通路，包括抑癌素M信号通路，被发现与炎症反应有关。后来的疾病和功能分析表明，RhoE除了参与心血管疾病和发育功能外，还可能参与其他疾病和功能，包括生物生存、癌症、生物损伤和异常、细胞间信号和相互作用以及分子运输。此外，885个上游调控因子被浓缩，包括59个被预测为强激活的分子(Z-Score；2)和60个被预测为显著抑制的分子(Z-Score<；-2)。特别是，33个监管效应和25个网络被发现与DEGS有关。其中，最显著的调节作用是“内皮细胞黏附”和“髓系细胞募集”，排名最靠前的网络是“神经疾病”、“遗传性疾病、器官损伤和异常”。综上所述，本研究利用CRISPR/Cas9技术成功地编辑了H9C2细胞中的RhoE基因，并随后分析了丰富的deg及其相关的典型信号通路、疾病和功能分类、上游调控分子、调控效应和相互作用网络。本研究的结果将有助于发现RhoE的全球生物学和功能特性，并为了解RhoE在人类疾病中的作用，特别是在心血管系统中的作用提供新的见解。
RhoE/Rnd3 is an atypical member of the Rho super-family of proteins, However, the global biological function profile of this protein remains unsolved. In the present study, a RhoE-knockout H9C2 cardiomyocyte cell line was established using CRISPR/Cas9 technology, following which differentially expressed genes (DEGs) between the knockout and wild-type cell lines were screened using whole genome expression gene chips. A total of 829 DEGs, including 417 upregulated and 412 downregulated, were identified using the threshold of fold changes ≥1.2 and P<0.05. Using the ingenuity pathways analysis system with a threshold of -Log (P-value)>2, 67 canonical pathways were found to be enriched. Many of the detected signaling pathways, including that of oncostatin M signaling, were found to be associated with the inflammatory response. Subsequent disease and function analysis indicated that apart from cardiovascular disease and development function, RhoE may also be involved in other diseases and function, including organismal survival, cancer, organismal injury and abnormalities, cell-to-cell signaling and interaction, and molecular transport. In addition, 885 upstream regulators were enriched, including 59 molecules that were predicated to be strongly activated (Z-score >2) and 60 molecules that were predicated to be significantly inhibited (Z-scores <-2). In particular, 33 regulatory effects and 25 networks were revealed to be associated with the DEGs. Among them, the most significant regulatory effects were 'adhesion of endothelial cells' and 'recruitment of myeloid cells' and the top network was 'neurological disease', 'hereditary disorder, organismal injury and abnormalities'. In conclusion, the present study successfully edited the RhoE gene in H9C2 cells using CRISPR/Cas9 technology and subsequently analyzed the enriched DEGs along with their associated canonical signaling pathways, diseases and functions classification, upstream regulatory molecules, regulatory effects and interaction networks. The results of the present study should facilitate the discovery of the global biological and functional properties of RhoE and provide new insights into role of RhoE in human diseases, especially those in the cardiovascular system.