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

ObjectiveThe 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 methodsThe mRNA expression profile GSE130391 was downloaded from the Gene Expression Omnib...

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Main Authors: 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
Format: Article
Language:English
Published: Frontiers Media S.A. 2022-11-01
Series:Frontiers in Cardiovascular Medicine
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fcvm.2022.900353/full
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author Ran Miao
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
author_facet Ran Miao
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
author_sort Ran Miao
collection DOAJ
description ObjectiveThe 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 methodsThe 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.ResultsA 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.ConclusionFor 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.
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spelling doaj.art-522aec24df3340699bd05f09fdd2e2ff2022-12-22T03:35:44ZengFrontiers Media S.A.Frontiers in Cardiovascular Medicine2297-055X2022-11-01910.3389/fcvm.2022.900353900353Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertensionRan Miao0Ran Miao1Xingbei Dong2Juanni Gong3Yidan Li4Xiaojuan Guo5Jianfeng Wang6Qiang Huang7Ying Wang8Jifeng Li9Suqiao Yang10Tuguang Kuang11Min Liu12Jun Wan13Zhenguo Zhai14Jiuchang Zhong15Yuanhua Yang16Medical Research Center, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaChinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaDepartment of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Echocardiography, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Radiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Interventional Radiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Interventional Radiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Radiology, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Respiration, Beijing Anzhen Hospital, Capital Medical University, Beijing, China0Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Beijing, China1Heart Center and Beijing Key Laboratory of Hypertension, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaDepartment of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, ChinaObjectiveThe 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 methodsThe 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.ResultsA 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.ConclusionFor 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.https://www.frontiersin.org/articles/10.3389/fcvm.2022.900353/fullchronic thromboembolic pulmonary hypertensionsingle-cell RNA-sequencingmicroarraycircRNAmiRNAmRNA
spellingShingle Ran Miao
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
Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
Frontiers in Cardiovascular Medicine
chronic thromboembolic pulmonary hypertension
single-cell RNA-sequencing
microarray
circRNA
miRNA
mRNA
title Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
title_full Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
title_fullStr Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
title_full_unstemmed Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
title_short Single-cell RNA-sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
title_sort single cell rna sequencing and microarray analyses to explore the pathological mechanisms of chronic thromboembolic pulmonary hypertension
topic chronic thromboembolic pulmonary hypertension
single-cell RNA-sequencing
microarray
circRNA
miRNA
mRNA
url https://www.frontiersin.org/articles/10.3389/fcvm.2022.900353/full
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