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Mai H, Yang X, Xie Y, Zhou J, Wei Y, Luo T, Yang J, Cui P, Ye L, Liang H, Huang J. Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension. Sci Rep 2024; 14:7048. [PMID: 38528047 DOI: 10.1038/s41598-024-55645-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024] Open
Abstract
The close link between HIV-1 infection and the occurrence of pulmonary arterial hypertension (PAH). However, the underlying molecular mechanisms of their interrelation remain unclear. The microarray data of HIV-1 and PAH were downloaded from GEO database. We utilized WGCNA to identify shared genes between HIV-1 and PAH, followed by conducting GO and pathway enrichment analyses. Subsequently, differentially genes analysis was performed using external validation datasets to further filter hub genes. Immunoinfiltration analysis was performed using CIBERSORT. Finally, hub gene expression was validated using scRNA-seq data. We identified 109 shared genes through WGCNA, primarily enriched in type I interferon (IFN) pathways. By taking the intersection of WGCNA important module genes and DEGs, ISG15 and IFI27 were identified as pivotal hub genes. Immunoinfiltration analysis and scRNA-seq results indicated the significant role of monocytes in the shared molecular mechanisms of HIV-1 and PAH. In summary, our study illustrated the possible mechanism of PAH secondary to HIV-1 and showed that the heightened IFN response in HIV-1 might be a crucial susceptibility factor for PAH, with monocytes being pivotal cells involved in the type I IFN response pathway. This provides potential new insights for further investigating the molecular mechanisms connecting HIV-1 and PAH.
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Affiliation(s)
- Huanzhuo Mai
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Xing Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
- Guangxi Academy of Medical Sciences, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Yulan Xie
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Jie Zhou
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Yiru Wei
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Tingyan Luo
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Jing Yang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
- Life Science Institute, Guangxi Medical University, Nanning, 530021, China
| | - Li Ye
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
| | - Hao Liang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China
- Life Science Institute, Guangxi Medical University, Nanning, 530021, China
| | - Jiegang Huang
- School of Public Health, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of AIDS Prevention and Treatment, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, China.
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Liu Y, Zhu L, Ming Y, Wu Z, Zhang L, Chen Q, Qi Y. A role of TRIM59 in pulmonary hypertension: modulating the protein ubiquitylation modification. J Transl Med 2023; 21:821. [PMID: 37978515 PMCID: PMC10655329 DOI: 10.1186/s12967-023-04712-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Pulmonary hypertension (PH), an infrequent disease, is characterized by excessive pulmonary vascular remodeling and proliferation of pulmonary artery smooth muscle cells (PASMCs). However, its underlying molecular mechanisms remain unclear. Uncovering its molecular mechanisms will be beneficial to the treatment of PH. METHODS Differently expressed genes (DEGs) in the lung tissues of PH patients were analyzed with a GEO dataset GSE113439. From these DEGs, we focused on TRIM59 which was highly expressed in PH patients. Subsequently, the expression of TRIM59 in the pulmonary arteries of PH patients, lung tissues of PH rat model and PASMCs cultured in a hypoxic condition was verified by quantitative real-time PCR (qPCR), western blot and immunohistochemistry. Furthermore, the role of TRIM59 in PAMSC proliferation and pathological changes in PH rats was assessed via gain-of-function and loss-of-function experiments. In addition, the transcriptional regulation of YAP1/TEAD4 on TRIM59 was confirmed by qPCR, western blot, luciferase reporter assay, ChIP and DNA pull-down. In order to uncover the underlying mechanisms of TRIM59, a protein ubiquitomics and a CoIP- HPLC-MS/MS were companied to identify the direct targets of TRIM59. RESULTS TRIM59 was highly expressed in the pulmonary arteries of PH patients and lung tissues of PH rats. Over-expression of TRIM59 accelerated the proliferation of PASMCs, while TRIM59 silencing resulted in the opposite results. Moreover, TRIM59 silencing mitigated the injuries in heart and lung and attenuated pulmonary vascular remodeling during PH. In addition, its transcription was positively regulated by YAP1/TEAD4. Then we further explored the underlying mechanisms of TRIM59 and found that TRIM59 overexpression resulted in an altered ubiquitylation of proteins. Accompanied with the results of CoIP- HPLC-MS/MS, 34 proteins were identified as the direct targets of TRIM59. CONCLUSION TRIM59 was highly expressed in PH patients and promoted the proliferation of PASMCs and pulmonary vascular remodeling, thus contributing to the pathogenesis of PH. It is indicated that TRIM59 may become a potential target for PH treatment.
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Affiliation(s)
- Yingli Liu
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, People's Republic of China
| | - Li Zhu
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, People's Republic of China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, People's Republic of China
| | - Yue Ming
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, People's Republic of China
| | - Zhuhua Wu
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, People's Republic of China
| | - Lili Zhang
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, People's Republic of China
| | - Qi Chen
- Department of Pulmonary and Critical Care Medicine, Henan University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, People's Republic of China
| | - Yong Qi
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan University People's Hospital, Zhengzhou, People's Republic of China.
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Mumby S, Perros F, Grynblat J, Manaud G, Papi A, Casolari P, Caramori G, Humbert M, John Wort S, Adcock IM. Differential responses of pulmonary vascular cells from PAH patients and controls to TNFα and the effect of the BET inhibitor JQ1. Respir Res 2023; 24:193. [PMID: 37516840 PMCID: PMC10386603 DOI: 10.1186/s12931-023-02499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) encompasses a group of diseases characterized by raised pulmonary vascular resistance, resulting from vascular remodelling and inflammation. Bromodomain and extra-terminal (BET) proteins are required for the expression of a subset of NF-κB-induced inflammatory genes which can be inhibited by the BET mimic JQ1+. We hypothesised that JQ+ would supress TNFα-driven inflammatory responses in human pulmonary vascular cells from PAH patients. METHODS Immunohistochemical staining of human peripheral lung tissue (N = 14 PAH and N = 12 non-PAH) was performed for the BET proteins BRD2 and 4. Human pulmonary microvascular endothelial cells (HPMEC) and pulmonary artery smooth muscle cells (HPASMC) from PAH patients (N = 4) and non-PAH controls (N = 4) were stimulated with TNFα in presence or absence of JQ1+ or its inactive isomer JQ1-. IL-6 and -8 mRNA was measured by RT-qPCR and protein levels by ELISA. Chromatin immunoprecipitation analysis was performed using EZ-ChIP™ and NF-κB p65 activation determined using a TransAm kit. MTT assay was used to measure cell viability. RESULTS Nuclear staining of BRD2 and BRD4 was significantly (p < 0.0001) increased in the lung vascular endothelial and smooth muscle cells from PAH patients compared to controls with normal lung function. TNFα-driven IL-6 release from both HPMECs and HPASMCs was greater in PAH cells than control cells. Levels of CXCL8/IL-8 protein release was higher in PAH HPASMCs than in control cells with similar release observed in HPMECs. TNFα-induced recruitment of activated NF-κB p65 to the IL-6 and CXCL8/IL-8 promoters were similar in both cell types and between subject groups. JQ1+ suppressed TNFα-induced IL-6 and CXCL8/IL-8 release and mRNA expression to a comparable extent in control and PAH HPMECs and HPASMCs. JQ1 had a greater efficacy on IL-6 release in HPMEC and on CXCL8/IL-8 release in HPASMC. CONCLUSION BET inhibition decreases TNFα driven inflammation in primary pulmonary vascular cells. The anti-inflammatory actions of JQ1 suggests distinct cell-specific regulatory control of these genes. BET proteins could be a target for future therapies for PAH.
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Affiliation(s)
- Sharon Mumby
- Respiratory Science, NHLI, Imperial College London, London, UK.
| | - Frederic Perros
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Université Claude Bernard Lyon1, Pierre-Bénite, France
| | - Julien Grynblat
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Gregoire Manaud
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
| | - Alberto Papi
- Interdepartmental Study Center for Inflammatory and Smoke-Related Airway Diseases, Cardiorespiratory and Internal Medicine Section, University of Ferrara, Ferrara, Italy
| | - Paolo Casolari
- Interdepartmental Study Center for Inflammatory and Smoke-Related Airway Diseases, Cardiorespiratory and Internal Medicine Section, University of Ferrara, Ferrara, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e Delle Immagini Morfologiche e Funzionali (BIOMORF), Università Degli Studi di Messina, Messina, Italy
| | - Marc Humbert
- Inserm UMR-S 999, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph, Université Paris-Saclay, Le Plessis-Robinson, France
- Department of Respiratory and Intensive Care Medicine, AP-HP, Hôpital Bicêtre, Pulmonary Hypertension National Referral Center, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - S John Wort
- Respiratory Science, NHLI, Imperial College London, London, UK
- National Pulmonary Hypertension Service, Royal Brompton Hospital, London, UK
| | - Ian M Adcock
- Respiratory Science, NHLI, Imperial College London, London, UK
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Wang E, Zhou S, Zeng D, Wang R. Molecular regulation and therapeutic implications of cell death in pulmonary hypertension. Cell Death Discov 2023; 9:239. [PMID: 37438344 DOI: 10.1038/s41420-023-01535-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Pulmonary hypertension (PH) is a clinical and pathophysiological syndrome caused by changes in pulmonary vascular structure or function that results in increased pulmonary vascular resistance and pulmonary arterial pressure, and it is characterized by pulmonary endothelial dysfunction, pulmonary artery media thickening, pulmonary vascular remodeling, and right ventricular hypertrophy, all of which are driven by an imbalance between the growth and death of pulmonary vascular cells. Programmed cell death (PCD), different from cell necrosis, is an active cellular death mechanism that is activated in response to both internal and external factors and is precisely regulated by cells. More than a dozen PCD modes have been identified, among which apoptosis, autophagy, pyroptosis, ferroptosis, necroptosis, and cuproptosis have been proven to be involved in the pathophysiology of PH to varying degrees. This article provides a summary of the regulatory patterns of different PCD modes and their potential effects on PH. Additionally, it describes the current understanding of this complex and interconnected process and analyzes the therapeutic potential of targeting specific PCD modes as molecular targets.
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Affiliation(s)
- Enze Wang
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei, 230022, China
| | - Sijing Zhou
- Department of Occupational Disease, Hefei third clinical college of Anhui Medical University, Hefei, 230022, China
| | - Daxiong Zeng
- Department of pulmonary and critical care medicine, Dushu Lake Hospital Affiliated to Soochow University, Medical Center of Soochow University, Suzhou, 215006, China.
| | - Ran Wang
- Department of respiratory and critical care medicine, the first affiliated hospital of Anhui medical university, Hefei, 230022, China.
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Ganekal P, Vastrad B, Vastrad C, Kotrashetti S. Identification of biomarkers, pathways, and potential therapeutic targets for heart failure using next-generation sequencing data and bioinformatics analysis. Ther Adv Cardiovasc Dis 2023; 17:17539447231168471. [PMID: 37092838 PMCID: PMC10134165 DOI: 10.1177/17539447231168471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Heart failure (HF) is the most common cardiovascular diseases and the leading cause of cardiovascular diseases related deaths. Increasing molecular targets have been discovered for HF prognosis and therapy. However, there is still an urgent need to identify novel biomarkers. Therefore, we evaluated biomarkers that might aid the diagnosis and treatment of HF. METHODS We searched next-generation sequencing (NGS) dataset (GSE161472) and identified differentially expressed genes (DEGs) by comparing 47 HF samples and 37 normal control samples using limma in R package. Gene ontology (GO) and pathway enrichment analyses of the DEGs were performed using the g: Profiler database. The protein-protein interaction (PPI) network was plotted with Human Integrated Protein-Protein Interaction rEference (HiPPIE) and visualized using Cytoscape. Module analysis of the PPI network was done using PEWCC1. Then, miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed by Cytoscape software. Finally, we performed receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes. RESULTS A total of 930 DEGs, 464 upregulated genes and 466 downregulated genes, were identified in HF. GO and REACTOME pathway enrichment results showed that DEGs mainly enriched in localization, small molecule metabolic process, SARS-CoV infections, and the citric acid tricarboxylic acid (TCA) cycle and respiratory electron transport. After combining the results of the PPI network miRNA-hub gene regulatory network and TF-hub gene regulatory network, 10 hub genes were selected, including heat shock protein 90 alpha family class A member 1 (HSP90AA1), arrestin beta 2 (ARRB2), myosin heavy chain 9 (MYH9), heat shock protein 90 alpha family class B member 1 (HSP90AB1), filamin A (FLNA), epidermal growth factor receptor (EGFR), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), cullin 4A (CUL4A), YEATS domain containing 4 (YEATS4), and lysine acetyltransferase 2B (KAT2B). CONCLUSIONS This discovery-driven study might be useful to provide a novel insight into the diagnosis and treatment of HF. However, more experiments are needed in the future to investigate the functional roles of these genes in HF.
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Affiliation(s)
- Prashanth Ganekal
- Department of General Medicine, Basaveshwara Medical College, Chitradurga, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, #253, Bharthinagar, Dharwad 580001, India
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Liu J, Ke X, Wang L, Zhang Y, Yang J. Deficiency of cold-inducible RNA-binding protein exacerbated monocrotaline-induced pulmonary artery hypertension through Caveolin1 and CAVIN1. J Cell Mol Med 2021; 25:4732-4743. [PMID: 33755319 PMCID: PMC8107102 DOI: 10.1111/jcmm.16437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Cold‐inducible RNA‐binding protein (CIRP) was a crucial regulator in multiple diseases. However, its role in pulmonary artery hypertension (PAH) is still unknown. Here, we first established monocrotaline (MCT)‐induced rat PAH model and discovered that CIRP was down‐regulated predominantly in the endothelium of pulmonary artery after MCT injection. We then generated Cirp‐knockout (Cirp‐KO) rats, which manifested severer PAH with exacerbated endothelium damage in response to MCT. Subsequently, Caveolin1 (Cav1) and Cavin1 were identified as downstream targets of CIRP in MCT‐induced PAH, and the decreased expression of these two genes aggravated the injury and apoptosis of pulmonary artery endothelium. Moreover, CIRP deficiency intensified monocrotaline pyrrole (MCTP)‐induced rat pulmonary artery endothelial cells (rPAECs) injuries both in vivo and in vitro, which was counteracted by Cav1 or Cavin1 overexpression. In addition, CIRP regulated the proliferative effect of conditioned media from MCTP‐treated rPAECs on rat pulmonary artery smooth muscle cells, which partially explained the exceedingly thickened pulmonary artery intimal media in Cirp‐KO rats after MCT treatment. These results demonstrated that CIRP acts as a critical protective factor in MCT‐induced rat PAH by directly regulating CAV1 and CAVIN1 expression, which may facilitate the development of new therapeutic targets for the intervention of PAH.
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Affiliation(s)
- Jingjing Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Xianting Ke
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Luxin Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Yangyang Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiovascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jian Yang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Medical Genetics, Tongji University School of Medicine, Shanghai, China
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