慢性血栓栓塞性肺动脉高压中分子标志物和信号通路的改变：一项转录组测序和生物信息学分析研究
The alterations in molecular markers and signaling pathways in chronic thromboembolic pulmonary hypertension, a study with transcriptome sequencing and bioinformatic analysis.
作者信息
Xu Wenqing, Deng Mei, Meng Xiapei, Sun Xuebiao, Tao Xincao, Wang Dingyi, Zhang Shuai, Zhen Yanan, Liu Xiaopeng, Liu Min
机构信息
Department of Radiology, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
Department of Radiology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
出版信息
Front Cardiovasc Med. 2022 Jul 26;9:961305. doi: 10.3389/fcvm.2022.961305. eCollection 2022.
BACKGROUND
At present, the alterations in molecular markers and signaling pathways in chronic thromboembolic pulmonary hypertension (CTEPH) remain unclear. We aimed to compare the difference of molecular markers and signaling pathways in patients with CTEPH and healthy people with transcriptome sequencing and bioinformatic analysis.
METHODS
We prospectively included 26 patients with CTEPH and 35 sex- and age-matched healthy volunteers as control. We extracted RNA from whole blood samples to construct the library. Then, qualified libraries were sequenced using PE100 strategy on BGIseq platform. Subsequently, the DESeq2 package in R was used to screen differentially expressed mRNAs (DEmRNAs) and differentially expressed long non-coding RNAs (DElncRNAs) of 7 patients with CTEPH and 5 healthy volunteers. Afterwards, we performed functional enrichment and protein-protein interaction analysis of DEmRNAs. We also performed lncRNA-mRNA co-expression analysis and lncRNA-miRNA-mRNA network construction. In addition, we performed diagnostic analysis on the GSE130391 dataset. Finally, we performed reverse transcription polymerase chain reaction (RT-PCR) of genes in 19 patients with CTEPH and 30 healthy volunteers.
RESULTS
Gender and age between patients with CTEPH and healthy controls, between sequencing group and validation group, were comparable. A total of 437 DEmRNAs and 192 DElncRNAs were obtained. Subsequently, 205 pairs of interacting DEmRNAs and 232 pairs of lncRNA-mRNA relationship were obtained. DEmRNAs were significantly enriched in chemokine signaling pathway, metabolic pathways, arachidonic acid metabolism, and MAPK signaling pathway. Only one regulation pathway of SOBP-hsa-miR-320b-LINC00472 was found through ceRNA network construction. In diagnostic analysis, the area under curve (AUC) values of LINC00472, PIK3R6, SCN3A, and TCL6, respectively, were 0.964, 0.893, 0.750, and 0.732.
CONCLUSION
The identification of alterations in molecules and pathways may provide further research directions on pathogenesis of CTEPH. Additionally, LINC00472, PIK3R6, SCN3A, and TCL6 may act as the potential gene markers in CTEPH.
背景
目前，慢性血栓栓塞性肺动脉高压（CTEPH）中分子标志物和信号通路的改变仍不清楚。我们旨在通过转录组测序和生物信息学分析比较CTEPH患者与健康人在分子标志物和信号通路上的差异。
方法
我们前瞻性纳入了26例CTEPH患者和35例年龄及性别匹配的健康志愿者作为对照。我们从全血样本中提取RNA以构建文库。然后，使用PE100策略在BGIseq平台上对合格的文库进行测序。随后，使用R中的DESeq2软件包筛选7例CTEPH患者和5例健康志愿者的差异表达mRNA（DEmRNAs）和差异表达长链非编码RNA（DElncRNAs）。之后，我们对DEmRNAs进行了功能富集和蛋白质-蛋白质相互作用分析。我们还进行了lncRNA-mRNA共表达分析和lncRNA-miRNA-mRNA网络构建。此外，我们对GSE130391数据集进行了诊断分析。最后，我们对19例CTEPH患者和30例健康志愿者的基因进行了逆转录聚合酶链反应（RT-PCR）。
结果
CTEPH患者与健康对照之间、测序组与验证组之间的性别和年龄具有可比性。共获得437个DEmRNAs和192个DElncRNAs。随后，获得了205对相互作用的DEmRNAs和232对lncRNA-mRNA关系。DEmRNAs在趋化因子信号通路、代谢途径、花生四烯酸代谢和MAPK信号通路中显著富集。通过ceRNA网络构建仅发现了一条SOBP-hsa-miR-320b-LINC00472调控通路。在诊断分析中，LINC00472、PIK3R6、SCN3A和TCL6的曲线下面积（AUC）值分别为0.964、0.893、0.750和0.732。
结论
分子和通路改变的鉴定可能为CTEPH的发病机制提供进一步的研究方向。此外，LINC00472、PIK3R6、SCN3A和TCL6可能作为CTEPH的潜在基因标志物。
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