Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension

Ran Miao; Xingbei Dong; Juanni Gong; Yidan Li; Xiaojuan Guo; Jianfeng Wang; Qiang Huang; Ying Wang; Jifeng Li; Suqiao Yang; Tuguang Kuang; Min Liu; Jun Wan; Zhenguo Zhai; Jiuchang Zhong; Yuanhua Yang

doi:10.3389/fcvm.2022.900353

Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension

Front Cardiovasc Med. 2022 Nov 10:9:900353. doi: 10.3389/fcvm.2022.900353. eCollection 2022.

Authors

Ran Miao^{1

2}, Xingbei Dong³, Juanni Gong², Yidan Li⁴, Xiaojuan Guo⁵, Jianfeng Wang⁶, Qiang Huang⁶, Ying Wang⁷, Jifeng Li², Suqiao Yang², Tuguang Kuang², Min Liu⁸, Jun Wan⁹, Zhenguo Zhai¹⁰, Jiuchang Zhong¹¹, Yuanhua Yang²

Affiliations

¹ Medical Research Center, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
² Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
³ Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
⁴ Department of Echocardiography, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
⁵ Department of Radiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
⁶ Department of Interventional Radiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
⁷ Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
⁸ Department of Radiology, China-Japan Friendship Hospital, Beijing, China.
⁹ Department of Respiration, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
¹⁰ Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Beijing, China.
¹¹ Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.

Abstract

Objective: The present study aimed to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension (CTEPH) using a gene chip array and single-cell RNA-sequencing (scRNA-seq).

Materials and methods: The mRNA expression profile GSE130391 was downloaded from the Gene Expression Omnibus database. The peripheral blood samples of five CTEPH patients and five healthy controls were used to prepare the Affymetrix microRNA (miRNA) chip and the Agilent circular RNA (circRNA) chip. The pulmonary endarterectomized tissues from five CTEPH patients were analyzed by scRNA-seq. Cells were clustered and annotated, followed by the identification of highly expressed genes. The gene chip data were used to identify disease-related mRNAs and differentially expressed miRNAs and circRNAs. The protein-protein interaction (PPI) network and the circRNA-miRNA-mRNA network were constructed for each cell type.

Results: A total of 11 cell types were identified. Intersection analysis of highly expressed genes in each cell type and differentially expressed mRNAs were performed to obtain disease-related genes in each cell type. TP53, ICAM1, APP, ITGB2, MYC, and ZYX showed the highest degree of connectivity in the PPI network of different types of cells. In addition, the circRNA-miRNA-mRNA network for each cell type was constructed.

Conclusion: For the first time, the key mRNAs, miRNAs, and circRNAs, as well as their possible regulatory relationships, during the progression of CTEPH were analyzed using both gene chip and scRNA-seq data. These findings may contribute to a better understanding of the pathological mechanisms of CTEPH.

Keywords: chronic thromboembolic pulmonary hypertension; circRNA; mRNA; miRNA; microarray; single-cell RNA-sequencing.