The alterations in molecular markers and signaling pathways in chronic thromboembolic pulmonary hypertension, a study with transcriptome sequencing and bioinformatic analysis

Wenqing Xu; Mei Deng; Xiapei Meng; Xuebiao Sun; Xincao Tao; Dingyi Wang; Shuai Zhang; Yanan Zhen; Xiaopeng Liu; Min Liu

doi:10.3389/fcvm.2022.961305

The alterations in molecular markers and signaling pathways in chronic thromboembolic pulmonary hypertension, a study with transcriptome sequencing and bioinformatic analysis

Front Cardiovasc Med. 2022 Jul 26:9:961305. doi: 10.3389/fcvm.2022.961305. eCollection 2022.

Authors

Wenqing Xu¹, Mei Deng², Xiapei Meng¹, Xuebiao Sun¹, Xincao Tao³, Dingyi Wang⁴, Shuai Zhang³, Yanan Zhen⁵, Xiaopeng Liu⁵, Min Liu⁶

Affiliations

¹ Department of Radiology, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
² Department of Radiology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
³ Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China.
⁴ Institute of Medicine, China-Japan Friendship Hospital, Beijing, China.
⁵ Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, China.
⁶ Department of Radiology, China-Japan Friendship Hospital, Beijing, China.

Abstract

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 in vitro 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.

Keywords: ceRNA network; chronic thromboembolic pulmonary hypertension; differentially expressed lncRNAs; differentially expressed mRNAs; transcriptome sequencing.