1
|
Zhou X, Liang B, Lin W, Zha L. Identification of MACC1 as a potential biomarker for pulmonary arterial hypertension based on bioinformatics and machine learning. Comput Biol Med 2024; 173:108372. [PMID: 38552277 DOI: 10.1016/j.compbiomed.2024.108372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/13/2024] [Accepted: 03/24/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a life-threatening disease characterized by abnormal early activation of pulmonary arterial smooth muscle cells (PASMCs), yet the underlying mechanisms remain to be elucidated. METHODS Normal and PAH gene expression profiles were obtained from the Gene Expression Omnibus (GEO) database and analyzed using gene set enrichment analysis (GSEA) to uncover the underlying mechanisms. Weighted gene co-expression network analysis (WGCNA) and machine learning methods were deployed to further filter hub genes. A number of immune infiltration analysis methods were applied to explore the immune landscape of PAH. Enzyme-linked immunosorbent assay (ELISA) was employed to compare MACC1 levels between PAH and normal subjects. The important role of MACC1 in the progression of PAH was verified through Western blot and real-time qPCR, among others. RESULTS 39 up-regulated and 7 down-regulated genes were identified by 'limma' and 'RRA' packages. WGCNA and machine learning further narrowed down the list to 4 hub genes, with MACC1 showing strong diagnostic capacity. In vivo and in vitro experiments revealed that MACC1 was highsly associated with malignant features of PASMCs in PAH. CONCLUSIONS These findings suggest that targeting MACC1 may offer a promising therapeutic strategy for treating PAH, and further clinical studies are warranted to evaluate its efficacy.
Collapse
Affiliation(s)
- Xinyi Zhou
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Benhui Liang
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Wenchao Lin
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Lihuang Zha
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| |
Collapse
|
2
|
Li MH, Liu X, Xie YL, Tang XG, Song LF, Zhao FR, Chen YJ, Guo C, Zhang WF, Zhu TT. Sodium butyrate alleviates right ventricular hypertrophy in pulmonary arterial hypertension by inhibiting H19 and affecting the activation of let-7g-5p/IGF1 receptor/ERK. Eur J Pharmacol 2024; 965:176315. [PMID: 38176636 DOI: 10.1016/j.ejphar.2024.176315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
Pulmonary arterial hypertension (PAH) is a complex and fatal cardio-pulmonary vascular disease. Decompensated right ventricular hypertrophy (RVH) caused by cardiomyocyte hypertrophy often leads to fatal heart failure, the leading cause of mortality among patients. Sodium butyrate (SB), a compound known to reduce cardiac hypertrophy, was examined for its potential effect and the underlying mechanism of SB on PAH-RVH. The in vivo study showed that SB alleviated RVH and cardiac dysfunction, as well as improved life span and survival rate in MCT-PAH rats. The in vivo and in vitro experiments showed that SB could attenuate cardiomyocyte hypertrophy by reversing the expressions of H19, let-7g-5p, insulin-like growth factor 1 receptor (IGF1 receptor), and pERK. H19 inhibition restored the level of let-7g-5p and prevented the overexpression of IGF1 receptor and pERK in hypertrophic cardiomyocytes. In addition, dual luciferase assay revealed that H19 demonstrated significant binding with let-7g-5p, acting as its endogenous RNA. Briefly, SB attenuated PAH-RVH by inhibiting the H19 overexpression, restoring the level of let-7g-5p, and hindering IGF1 receptor/ERK activation.
Collapse
Affiliation(s)
- Ming-Hui Li
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Department of Pharmacy, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Xu Liu
- Department of Pharmacy, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yu-Liang Xie
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Xiao-Guang Tang
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Liao-Fan Song
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Fan-Rong Zhao
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Yu-Jing Chen
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Chao Guo
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China
| | - Wei-Fang Zhang
- Departments of Pharmacy, The Second Affiliated Hospital, Nanchang University, Nanchang, China.
| | - Tian-Tian Zhu
- College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China; Department of Pharmacy, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, 453003, China; Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, 453003, China.
| |
Collapse
|
3
|
Zhao H, Duan R, Wang Q, Hu X, Zhao Q, Wu W, Jiang R, Gong S, Wang L, Liu J, Deng J, Liang H, Miao Y, Yuan P. MiR-122-5p as a potential regulator of pulmonary vascular wall cell in idiopathic pulmonary arterial hypertension. Heliyon 2023; 9:e22922. [PMID: 38144299 PMCID: PMC10746431 DOI: 10.1016/j.heliyon.2023.e22922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
MicroRNAs (miRNAs) are versatile regulators of pulmonary arterial remodeling in idiopathic pulmonary arterial hypertension (IPAH). We herein aimed to characterize miRNAs in peripheral blood mononuclear cell (PBMC) and plasma exosomes, and investigate specific miRNA expression in pulmonary artery cells and lung tissues in IPAH. A co-dysregulated miRNA was identified from the miRNA expression profiles of PBMC and plasma exosomes in IPAH. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the potential function of differentially expressed miRNAs. Real-time quantitative reverse transcription polymerase chain reaction was used to validate the expression of specific miRNAs in hypoxia-induced pulmonary microvascular endothelial cells (PMECs), pulmonary artery smooth muscle cells (PASMCs), pericyte cells (PCs), and lung tissues of patients with IPAH and rats. Finally, the miRNA-mRNA mechanisms of miR-122-5p were predicted. MiR-122-5p was the only co-upregulated miRNA in PBMC and plasma exosomes in patients with IPAH. Functional analysis of differentially expressed miRNAs revealed associations with the GO terms "transcription, DNA-templated," "cytoplasm," and "metal ion binding" in both PBMC and plasma exosomes, KEGG pathway MAPK signaling in PBMC, and KEGG-pathway human papillomavirus infection in plasma exosomes. Hypoxic PMECs and PCs, lung tissue of patients with IPAH, and rats showed increased expression of miR-122-5p, but hypoxic PASMCs showed decreased expression. And miR-122-5p mimics and inhibitor affected cell proliferation. Finally, miR-122-5p was found to potentially target DLAT (in lung tissue) and RIMS1 (in PMECs) in IPAH. According to the dual-luciferase assay, miR-122-5p bound to DLAT or RIMS1. In studies, DLAT imbalance was associated with cell proliferation and migration, RIMS1 is differentially expressed in cancer and correlated with cancer prognosis. Our findings suggest that the miR-122-5p is involved in various biological functions in the adjacent vascular wall cells in IPAH.
Collapse
Affiliation(s)
- Hui Zhao
- School of Materials and Chemistry & Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Ruowang Duan
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Qian Wang
- School of Materials and Chemistry & Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Xiaoyi Hu
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Qinhua Zhao
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Wenhui Wu
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Rong Jiang
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Sugang Gong
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Lan Wang
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Jinming Liu
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Jie Deng
- Southern Medical University, Guangzhou, 510000, China
| | - Huazheng Liang
- Monash Suzhou Research Institute, Suzhou, Jiangsu Province, 215125, China
| | - Yuqing Miao
- School of Materials and Chemistry & Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ping Yuan
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| |
Collapse
|
4
|
Chen YX, Deng ZH, Xue-Gao, Qiang-Du, Juan-Yin, Chen GH, Li JG, Zhao YM, Zhang HT, Zhang GX, Qian JX. Exosomes derived from mesenchymal stromal cells exert a therapeutic effect on hypoxia-induced pulmonary hypertension by modulating the YAP1/SPP1 signaling pathway. Biomed Pharmacother 2023; 168:115816. [PMID: 37918254 DOI: 10.1016/j.biopha.2023.115816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/22/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
OBJECTIVE Hypoxic pulmonary hypertension (HPH) is a progressive and life-threatening disease characterized by perivascular inflammation, pulmonary vascular remodeling, and occlusion. Mesenchymal stromal cell-derived exosomes (MSC-exo) have emerged as potential therapeutic agents due to their role in cell communication and the transportation of bioactive molecules. In this study, we aimed to investigate the therapeutic effects of MSC-exo against HPH and elucidate the underlying molecular mechanism. METHODS Exosomes were isolated from conditioned media of human bone mesenchymal stromal cells using ultracentrifugation and characterized through western blotting, transmission electron microscopy (TEM), and nanoparticle tracking analysis (NTA). An HPH animal model was established in male SD rats, and MSC-exo or phosphate-buffered saline (PBS) were administered via the tail vein for three weeks. Subsequently, right ventricular systolic pressure (RVSP), right ventricular hypertrophy index (RVHI), and pulmonary vascular remodeling were evaluated. Lung tissues from HPH rats and normal rats underwent high-throughput sequencing and transcriptomic analysis. Gene Ontology (GO) analysis was employed to identify upregulated differentially expressed genes. Additionally, rat pulmonary artery smooth muscle cells (PASMC) exposed to platelet-derived growth factor-BB (PDGF-BB) were used to simulate HPH-related pathological behavior. In vitro cellular models were established to examine the molecular mechanism of MSC-exo in HPH. RESULTS MSC-exo administration protected rats from hypoxia-induced increases in RVSP, RVHI, and pulmonary vascular remodeling. Additionally, MSC-exo alleviated PDGF-BB-induced proliferation and migration of PASMC. Transcriptomic analysis revealed 267 upregulated genes in lung tissues of HPH rats compared to control rats. Gene Ontology analysis indicated significant differences in pathways associated with Yes Associated Protein 1 (YAP1), a key regulator of cell proliferation and organ size. RT-qPCR and western blot analysis confirmed significantly increased expression of YAP1 in HPH lung tissues and PASMC, which was inhibited by MSC-exo treatment. Furthermore, analysis of datasets demonstrated that Secreted Phosphoprotein 1 (SPP1), also known as Osteopontin (OPN), is a downstream binding protein of YAP1 and can be upregulated by PDGF-BB. MSC-exo treatment reduced the expression of both YAP1 and SPP1. Lentivirus-mediated knockdown of YAP1 inhibited PDGF-BB-induced PASMC proliferation, migration, and SPP1 protein levels. CONCLUSION Our findings demonstrate that MSC-exo exert a therapeutic effect against hypoxia-induced pulmonary hypertension by modulating the YAP1/SPP1 signaling pathway. The inhibition of YAP1 and downstream SPP1 expression by MSC-exo may contribute to the attenuation of pulmonary vascular remodeling and PASMC proliferation and migration. These results suggest that MSC-exo could serve as a potential therapeutic strategy for the treatment of HPH. Further investigations are warranted to explore the clinical applicability of MSC-exo-based therapies in HPH patients.
Collapse
Affiliation(s)
- Yao-Xin Chen
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Zhi-Hua Deng
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Xue-Gao
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Qiang-Du
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Juan-Yin
- Department of Central Laboratory, Suzhou Municipal Hospital, Suzhou, China
| | - Guang-Hua Chen
- Department of Hematology, the First Affiliated Hospital of Suzhou University, Jiangsu Hematology Institute, National Clinical Medical Research Center for Hematology, Suzhou, China
| | - Jun-Gen Li
- Department of Emergency Medicine, the First Affiliated Hospital of Suzhou University, Suzhou, China
| | - Yi-Ming Zhao
- Department of Hematology, the First Affiliated Hospital of Suzhou University, Jiangsu Hematology Institute, National Clinical Medical Research Center for Hematology, Suzhou, China
| | - Hao-Tian Zhang
- Department of Physiology and Neurosciences, Medical College of Soochow University, Suzhou, China
| | - Guo-Xing Zhang
- Department of Physiology and Neurosciences, Medical College of Soochow University, Suzhou, China.
| | - Jin-Xian Qian
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| |
Collapse
|
5
|
Liu M, He H, Fan F, Qiu L, Zheng F, Guan Y, Yang G, Chen L. Maresin-1 protects against pulmonary arterial hypertension by improving mitochondrial homeostasis through ALXR/HSP90α axis. J Mol Cell Cardiol 2023; 181:15-30. [PMID: 37244057 DOI: 10.1016/j.yjmcc.2023.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
AIMS Pulmonary arterial hypertension (PAH) is a progressive and lethal disease characterized by continuous proliferation of pulmonary arterial smooth muscle cell (PASMCs) and increased pulmonary vascular remodeling. Maresin-1 (MaR1) is a member of pro-resolving lipid mediators and exhibits protective effects on various inflammation-related diseases. Here we aimed to study the role of MaR1 in the development and progression of PAH and to explore the underlying mechanisms. METHODS AND RESULTS We evaluated the effect of MaR1 treatment on PAH in both monocrotaline (MCT)-induced rat and hypoxia+SU5416 (HySu)-induced mouse models of pulmonary hypertension (PH). Plasma samples were collected from patients with PAH and rodent PH models to examine MaR1 production. Specific shRNA adenovirus or inhibitors were used to block the function of MaR1 receptors. The data showed that MaR1 significantly prevented the development and blunted the progression of PH in rodents. Blockade of the function of MaR1 receptor ALXR, but not LGR6 or RORα, with BOC-2, abolished the protective effect of MaR1 against PAH development and reduced its therapeutic potential. Mechanistically, we demonstrated that the MaR1/ALXR axis suppressed hypoxia-induced PASMCs proliferation and alleviated pulmonary vascular remodeling by inhibiting mitochondrial accumulation of heat shock protein 90α (HSP90α) and restoring mitophagy. CONCLUSION MaR1 protects against PAH by improving mitochondrial homeostasis through ALXR/HSP90α axis and represents a promising target for PAH prevention and treatment.
Collapse
Affiliation(s)
- Min Liu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Huixiang He
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Fenling Fan
- Division of Pulmonary Vascular Disease, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Lejia Qiu
- Health Science Center, East China Normal University, Shanghai 200241, China
| | - Feng Zheng
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Youfei Guan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Guangrui Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Lihong Chen
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China; Health Science Center, East China Normal University, Shanghai 200241, China.
| |
Collapse
|
6
|
Mamazhakypov A, Maripov A, Sarybaev AS, Schermuly RT, Sydykov A. Osteopontin in Pulmonary Hypertension. Biomedicines 2023; 11:biomedicines11051385. [PMID: 37239056 DOI: 10.3390/biomedicines11051385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Pulmonary hypertension (PH) is a pathological condition with multifactorial etiology, which is characterized by elevated pulmonary arterial pressure and pulmonary vascular remodeling. The underlying pathogenetic mechanisms remain poorly understood. Accumulating clinical evidence suggests that circulating osteopontin may serve as a biomarker of PH progression, severity, and prognosis, as well as an indicator of maladaptive right ventricular remodeling and dysfunction. Moreover, preclinical studies in rodent models have implicated osteopontin in PH pathogenesis. Osteopontin modulates a plethora of cellular processes within the pulmonary vasculature, including cell proliferation, migration, apoptosis, extracellular matrix synthesis, and inflammation via binding to various receptors such as integrins and CD44. In this article, we provide a comprehensive overview of the current understanding of osteopontin regulation and its impact on pulmonary vascular remodeling, as well as consider research issues required for the development of therapeutics targeting osteopontin as a potential strategy for the management of PH.
Collapse
Affiliation(s)
- Argen Mamazhakypov
- Department of Internal Medicine, Excellence Cluster Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Abdirashit Maripov
- Department of Mountain and Sleep Medicine and Pulmonary Hypertension, National Center of Cardiology and Internal Medicine, Bishkek 720040, Kyrgyzstan
| | - Akpay S Sarybaev
- Department of Mountain and Sleep Medicine and Pulmonary Hypertension, National Center of Cardiology and Internal Medicine, Bishkek 720040, Kyrgyzstan
| | - Ralph Theo Schermuly
- Department of Internal Medicine, Excellence Cluster Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus Liebig University of Giessen, 35392 Giessen, Germany
| | - Akylbek Sydykov
- Department of Internal Medicine, Excellence Cluster Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus Liebig University of Giessen, 35392 Giessen, Germany
| |
Collapse
|
7
|
Liu W, Sun X, Huang J, Zhang J, Liang Z, Zhu J, Chen T, Zeng Y, Peng M, Li X, Zeng L, Lei W, Cheng J. Development and validation of a genomic nomogram based on a ceRNA network for comprehensive analysis of obstructive sleep apnea. Front Genet 2023; 14:1084552. [PMID: 36968605 PMCID: PMC10036397 DOI: 10.3389/fgene.2023.1084552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/13/2023] [Indexed: 03/12/2023] Open
Abstract
Objectives: Some ceRNA associated with lncRNA have been considered as possible diagnostic and therapeutic biomarkers for obstructive sleep apnea (OSA). We intend to identify the potential hub genes for the development of OSA, which will provide a foundation for the study of the molecular mechanism underlying OSA and for the diagnosis and treatment of OSA.Methods: We collected plasma samples from OSA patients and healthy controls for the detection of ceRNA using a chip. Based on the differential expression of lncRNA, we identified the target genes of miRNA that bind to lncRNAs. We then constructed lncRNA-related ceRNA networks, performed functional enrichment analysis and protein-protein interaction analysis, and performed internal and external validation of the expression levels of stable hub genes. Then, we conducted LASSO regression analysis on the stable hub genes, selected relatively significant genes to construct a simple and easy-to-use nomogram, validated the nomogram, and constructed the core ceRNA sub-network of key genes.Results: We successfully identified 282 DElncRNAs and 380 DEmRNAs through differential analysis, and we constructed an OSA-related ceRNA network consisting of 292 miRNA-lncRNAs and 41 miRNA-mRNAs. Through PPI and hub gene selection, we obtained 7 additional robust hub genes, CCND2, WT1, E2F2, IRF1, BAZ2A, LAMC1, and DAB2. Using LASSO regression analysis, we created a nomogram with four predictors (CCND2, WT1, E2F2, and IRF1), and its area under the curve (AUC) is 1. Finally, we constructed a core ceRNA sub-network composed of 74 miRNA-lncRNA and 7 miRNA-mRNA nodes.Conclusion: Our study provides a new foundation for elucidating the molecular mechanism of lncRNA in OSA and for diagnosing and treating OSA.
Collapse
Affiliation(s)
- Wang Liu
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xishi Sun
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jiewen Huang
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jinjian Zhang
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhengshi Liang
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jinru Zhu
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tao Chen
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yu Zeng
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Min Peng
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiongbin Li
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Lijuan Zeng
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Wei Lei
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- *Correspondence: Junfen Cheng, ; Wei Lei,
| | - Junfen Cheng
- The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- *Correspondence: Junfen Cheng, ; Wei Lei,
| |
Collapse
|
8
|
Shikhevich S, Chadaeva I, Khandaev B, Kozhemyakina R, Zolotareva K, Kazachek A, Oshchepkov D, Bogomolov A, Klimova NV, Ivanisenko VA, Demenkov P, Mustafin Z, Markel A, Savinkova L, Kolchanov NA, Kozlov V, Ponomarenko M. Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24043996. [PMID: 36835409 PMCID: PMC9966505 DOI: 10.3390/ijms24043996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.
Collapse
Affiliation(s)
- Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Natalya V. Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arcady Markel
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI) SB RAS, Novosibirsk 630099, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
| |
Collapse
|
9
|
Yang Z, Zhou L, Ge H, Shen W, Shan L. Identification of autophagy-related biomarkers in patients with pulmonary arterial hypertension based on bioinformatics analysis. Open Med (Wars) 2022; 17:1148-1157. [PMID: 35859795 PMCID: PMC9263897 DOI: 10.1515/med-2022-0497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Autophagy participates in the regulation of pulmonary arterial hypertension (PAH). However, the role of autophagy-related genes (ARGs) in the pathogenesis of the PAH is still unclear. This study aimed to identify the ARGs in PAH via bioinformatics analysis. A microarray dataset (GSE113439) was downloaded from the Gene Expression Omnibus database to identify differentially expressed ARGs (DEARGs). Protein–protein interactions network, gene ontology, and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to screen hub genes and the underlying molecular mechanisms of PAH. Finally, the mRNA expression of the hub genes was validated using the GSE53408 dataset. Twenty-six DEARGs were identified, all of which were upregulated. Enrichment analyses revealed that these DEARGs were mainly enriched in the nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway, PI3K-Akt signaling pathway, response to hypoxia, response to nutrient levels, and autophagy. Among these hub genes, the mRNA expression levels of HSP90AA1, HIF1A, MET, IGF1, LRRK2, CLTC, DNM1L, MDM2, RICTOR, and ROCK2 were significantly upregulated in PAH patients than in healthy individuals. Ten hub DEARGs were identified and may participate in the pathogenesis of the PAH via the regulation of autophagy. The present study may provide novel therapeutic targets for PAH prevention and treatment and expand our understanding of PAH.
Collapse
Affiliation(s)
- Zhisong Yang
- Department of Emergency, Daqing Longnan Hospital, Daqing, Heilongjiang 163453, China
| | - Li Zhou
- Department of Emergency, Daqing Longnan Hospital, Daqing, Heilongjiang 163453, China
| | - Haiyan Ge
- Department of Respiratory Medicine, Shanghai Huadong Hospital, Shanghai 200040, China
| | - Weimin Shen
- Department of Respiratory Medicine, Shanghai Huadong Hospital, Shanghai 200040, China
| | - Lin Shan
- Department of Respiratory Medicine, Shanghai Huadong Hospital, Shanghai 200040, China
| |
Collapse
|
10
|
Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients. Int J Mol Sci 2022; 23:ijms23052835. [PMID: 35269977 PMCID: PMC8911431 DOI: 10.3390/ijms23052835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Although half of hypertensive patients have hypertensive parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% of hypertension heredity. Therefore, mainstream transcriptome profiling of hypertensive subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating patients according to their symptoms, individual lifestyle, and genetic background. Within this mainstream paradigm, here, we determined whether, among the known hypertension-related DEGs that we could find, there is any genome-wide hypertension theranostic molecular marker applicable to everyone, everywhere, anytime. Therefore, we sequenced the hippocampal transcriptome of tame and aggressive rats, corresponding to low and high stress reactivity, an increase of which raises hypertensive risk; we identified stress-reactivity-related rat DEGs and compared them with their known homologous hypertension-related animal DEGs. This yielded significant correlations between stress reactivity-related and hypertension-related fold changes (log2 values) of these DEG homologs. We found principal components, PC1 and PC2, corresponding to a half-difference and half-sum of these log2 values. Using the DEGs of hypertensive versus normotensive patients (as the control), we verified the correlations and principal components. This analysis highlighted downregulation of β-protocadherins and hemoglobin as whole-genome hypertension theranostic molecular markers associated with a wide vascular inner diameter and low blood viscosity, respectively.
Collapse
|