1
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Sun J, Wang P, Yi Z, Wu Y, Wei Y, Fang H, Song D, Chen Y, Du H, Huang J, Li Q, Yang D, Ren G, Li H. Blocking WNT7A Enhances MHC-I Antigen Presentation and Enhances the Effectiveness of Immune Checkpoint Blockade Therapy. Cancer Immunol Res 2025; 13:400-416. [PMID: 39602462 PMCID: PMC11876963 DOI: 10.1158/2326-6066.cir-24-0484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 09/09/2024] [Accepted: 11/26/2024] [Indexed: 11/29/2024]
Abstract
The limited infiltration of CD8+ T cells in tumors hampers the effectiveness of T cell-based immunotherapy, yet the mechanisms that limit tumor infiltration by CD8+ T cells remain unclear. Through bulk RNA sequencing of human tumors, we identified a strong correlation between WNT7A expression and reduced CD8+ T-cell infiltration. Further investigation demonstrated that inhibiting WNT7A substantially enhanced MHC-I expression on tumor cells. Mechanistically, WNT7A inhibition inactivated the Wnt/β-catenin signaling pathway and thus resulted in reduced physical interaction between β-catenin and p65 in the cytoplasm, which increased the nuclear translocation of p65 and activated the NF-κB pathway, ultimately promoting the transcription of genes encoding MHC-I molecules. We found that our lead compound, 1365-0109, disrupted the protein-protein interaction between WNT7A and its receptor FZD5, resulting in the upregulation of MHC-I expression. In murine tumor models, both genetic and pharmaceutical suppression of WNT7A led to increased MHC-I levels on tumor cells, and consequently enhanced the infiltration and functionality of CD8+ T cells, which bolstered antitumor immunity and improved the effectiveness of immune checkpoint blockade therapy. These findings have elucidated the intrinsic mechanisms of WNT7A-induced immune suppression, suggesting that therapeutic interventions targeting WNT7A hold promise for enhancing the efficacy of immunotherapy.
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Affiliation(s)
- Jiazheng Sun
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Pin Wang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of General Surgery, The Third People’s Hospital of Chengdu, Chengdu, China
- Center of Breast and Thyroid Surgery, The Third People’s Hospital of Chengdu, Chengdu, China
| | - Ziying Yi
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast and Thyroid Surgery, Chongqing General Hospital, Chongqing University, Chongqing, China
| | - Yushen Wu
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuxian Wei
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huiying Fang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast Disease, Chongqing University Cancer Hospital, Chongqing, China
| | - Daqiang Song
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuru Chen
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huimin Du
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Huang
- Department of Respiratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qin Li
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Dejuan Yang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongzhong Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zhao Z, Sang M, Li Q, Zhang H, Luo Z, Zhang Y, Li H, Ma Y, Cheng Y, Zhuang D, Ju W, Guo Q. Targeted FTO knockout in endothelial cells Boosts adhesion and lowers inflammatory infiltration to alleviate pulmonary arterial hypertension. Biochem Biophys Res Commun 2025; 749:151339. [PMID: 39869947 DOI: 10.1016/j.bbrc.2025.151339] [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: 01/09/2025] [Accepted: 01/13/2025] [Indexed: 01/29/2025]
Abstract
Pulmonary arterial hypertension (PAH) is a syndrome characterized by increased pulmonary vascular resistance and elevated pulmonary artery pressure, ultimately leading to right heart failure and even death. Increasing evidence implicates the fat mass and obesity-associated protein (FTO) in various metabolic and inflammatory pathways; however, its role in pulmonary endothelial function and PAH remains largely unexplored. In this study, we examined the effects of endothelial cell-specific FTO knockout on PAH development. Our results indicate that the absence of FTO in endothelial cells mitigates hypoxia-induced PAH. Mechanistically, FTO deletion reduces endothelial cell adhesion and inflammatory cell infiltration. Single-cell RNA sequencing revealed disruptions in key inflammatory and adhesion pathways, including TNF-α/NF-κB signaling and VCAM1 expression. These findings suggest that targeting endothelial FTO could be a novel therapeutic strategy for PAH by modulating endothelial adhesion and inflammatory responses.
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Affiliation(s)
- Ziwen Zhao
- Department of Ultrasonography, Fuwai Yunnan Hospital, Chinese Academy of Medical, Sciences/Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, 650102, China
| | - Mengmeng Sang
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Qi Li
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China
| | - Hao Zhang
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China
| | - Zhiling Luo
- Department of Ultrasonography, Fuwai Yunnan Hospital, Chinese Academy of Medical, Sciences/Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, 650102, China
| | - Yunhan Zhang
- Department of Ultrasonography, Fuwai Yunnan Hospital, Chinese Academy of Medical, Sciences/Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, 650102, China
| | - Hanlu Li
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China
| | - Yinbo Ma
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China
| | - Yuanyuan Cheng
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China
| | - Donglin Zhuang
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China.
| | - Wenhao Ju
- Department of Structural Heart Disease, National Center for Cardiovascular Disease, State Key Laboratory of Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102308, China.
| | - Qiuzhe Guo
- Department of Ultrasonography, Fuwai Yunnan Hospital, Chinese Academy of Medical, Sciences/Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, 650102, China.
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3
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Aulak KS, Mavarakis L, Tian L, Paul D, Comhair SA, Dweik RA, Tonelli AR. Characteristic disease defects in circulating endothelial cells isolated from patients with pulmonary arterial hypertension. PLoS One 2024; 19:e0312535. [PMID: 39466801 PMCID: PMC11516004 DOI: 10.1371/journal.pone.0312535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 10/08/2024] [Indexed: 10/30/2024] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disease characterized by elevated pulmonary arterial pressures that can lead to right heart failure and death. No cure exists for this disease, but therapeutic advancements have extended its median survival from 2 to 7 years. Mechanistic research in PAH has been limited by factors including that a) animal models do not fully recapitulate the disease or provide insights into its pathogenesis, and b) cellular material from PAH patients is primarily obtained from donor lungs during autopsy or transplantation, which reflect end-stage disease. Therefore, there is a need to identify tools that can elucidate the specific mechanisms of human disease in individual patients, a critical step to guide treatment decisions based on specific pathway abnormalities. Here we demonstrate a simple method to isolate and culture circulating endothelial cells (CECs) obtained at the time of right heart catheterization in PAH patients. We tested these CECs using transcriptomics and found that they have typical traits of PAH, including those involving key treatment pathways, i.e. nitric oxide, endothelin, prostacyclin and BMP/activin pathways. CECs show important gene expression changes in other central PAH disease pathways. In summary, we present a new cellular model for the ex-vivo mechanistic evaluation of critical PAH pathways that participate in the pathogenesis of the disease and may help personalized therapeutic decisions.
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Affiliation(s)
- Kulwant S. Aulak
- Department of Immunology and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Lori Mavarakis
- Department of Immunology and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Liping Tian
- Department of Immunology and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Deborah Paul
- Department of Pulmonary, Cleveland Clinic, Allergy and Critical Care Medicine, Respiratory Institute, Cleveland, Ohio, United States of America
| | - Suzy A. Comhair
- Department of Immunology and Immunity, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Raed A. Dweik
- Department of Pulmonary, Cleveland Clinic, Allergy and Critical Care Medicine, Respiratory Institute, Cleveland, Ohio, United States of America
| | - Adriano R. Tonelli
- Department of Pulmonary, Cleveland Clinic, Allergy and Critical Care Medicine, Respiratory Institute, Cleveland, Ohio, United States of America
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4
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Shi X, Ma Q, Huo Y, Su Y. 5-Aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase promotes pulmonary arterial smooth muscle cell proliferation via the Ras signaling pathway. Am J Physiol Cell Physiol 2024; 327:C901-C912. [PMID: 39129491 PMCID: PMC11481986 DOI: 10.1152/ajpcell.00262.2024] [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: 04/18/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 08/13/2024]
Abstract
Pulmonary arterial hypertension (PAH) is a debilitating vascular disorder characterized by abnormal pulmonary artery smooth muscle cell (PASMC) proliferation and collagen synthesis, contributing to vascular remodeling and elevated pulmonary vascular resistance. This study investigated the critical role of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase (ATIC) in cell proliferation and collagen synthesis in PASMCs in PAH. Here we show that ATIC levels are significantly increased in the lungs of monocrotaline (MCT)-induced PAH rat model, hypoxia-induced PAH mouse model, and platelet-derived growth factor (PDGF)-stimulated PASMCs. Inhibition of ATIC attenuated PDGF-induced cell proliferation and collagen I synthesis in PASMCs. Conversely, overexpression or knockdown of ATIC causes a significant promotion or inhibition of Ras and ERK activation, cell proliferation, and collagen synthesis in PASMCs. Moreover, ATIC deficiency attenuated Ras activation in the lungs of hypoxia-induced PAH mice. Furthermore, Ras inhibition attenuates ATIC overexpression- and PDGF-induced collagen synthesis and PASMC proliferation. Notably, we identified that transcription factors MYC, early growth response protein 1 (EGR1), and specificity protein 1 (SP1) directly binds to promoters of Atic gene and regulate ATIC expression. These results provide the first evidence that ATIC promotes PASMC proliferation in pulmonary vascular remodeling through the Ras signaling pathway.NEW & NOTEWORTHY Our findings highlight the important role of ATIC in the PASMC proliferation of pulmonary vascular remodeling through its modulation of the Ras signaling pathway and its regulation by transcription factors MYC, EGR1, and SP1. ATIC's modulation of Ras signal pathway represents a novel mechanism contributing to PAH development.
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MESH Headings
- Animals
- Male
- Mice
- Rats
- Cell Proliferation
- Cells, Cultured
- Disease Models, Animal
- Early Growth Response Protein 1/metabolism
- Early Growth Response Protein 1/genetics
- Hydroxymethyl and Formyl Transferases/metabolism
- Hydroxymethyl and Formyl Transferases/genetics
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/chemically induced
- Hypertension, Pulmonary/genetics
- Hypertension, Pulmonary/enzymology
- Mice, Inbred C57BL
- Monocrotaline/toxicity
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/enzymology
- Muscle, Smooth, Vascular/drug effects
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/enzymology
- Platelet-Derived Growth Factor/metabolism
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/drug effects
- ras Proteins/metabolism
- ras Proteins/genetics
- Rats, Sprague-Dawley
- Signal Transduction
- Vascular Remodeling/drug effects
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Affiliation(s)
- Xiaofan Shi
- Department of Pharmacology & Toxicology, Augusta University, Augusta, Georgia, United States
| | - Qian Ma
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Yuqing Huo
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, Georgia, United States
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Yunchao Su
- Department of Pharmacology & Toxicology, Augusta University, Augusta, Georgia, United States
- Department of Medicine, Augusta University, Augusta, Georgia, United States
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
- Research Service, Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia, United States
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5
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Scimone C, Donato L, Alibrandi S, Conti A, Bortolotti C, Germanò A, Alafaci C, Vinci SL, D'Angelo R, Sidoti A. Methylome analysis of endothelial cells suggests new insights on sporadic brain arteriovenous malformation. Heliyon 2024; 10:e35126. [PMID: 39170526 PMCID: PMC11336478 DOI: 10.1016/j.heliyon.2024.e35126] [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: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
Arteriovenous malformation of the brain (bAVM) is a vascular phenotype related to brain defective angiogenesis. Involved vessels show impaired expression of vascular differentiation markers resulting in the arteriolar to venule direct shunt. In order to clarify aberrant gene expression occurring in bAVM, here we describe results obtained by methylome analysis performed on endothelial cells (ECs) isolated from bAVM specimens, compared to human cerebral microvascular ECs. Results were validated by quantitative methylation-specific PCR and quantitative realtime-PCR. Differential methylation events occur in genes already linked to bAVM onset, as RBPJ and KRAS. However, among differentially methylated genes, we identified EPHB1 and several other loci involved in EC adhesion as well as in EC/vascular smooth muscle cell (VSMC) crosstalk, suggesting that only endothelial dysfunction might not be sufficient to trigger the bAVM phenotype. Moreover, aberrant methylation pattern was reported for many lncRNA genes targeting transcription factors expressed during neurovascular development. Among these, the YBX1 that was recently shown to target the arteridin coding gene. Finally, in addition to the conventional CpG methylation, we further considered the role of impaired CHG methylation, mainly occurring in brain at embryo stage. We showed as differentially CHG methylated genes are clustered in pathways related to EC homeostasis, as well as to VSMC-EC crosstalk, suggesting as impairment of this interaction plays a prominent role in loss of vascular differentiation, in bAVM phenotype.
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Affiliation(s)
- Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Alfredo Conti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Via Altura 3, 40123, Bologna, Italy
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Carlo Bortolotti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Via Altura 3, 40123, Bologna, Italy
| | - Antonino Germanò
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Concetta Alafaci
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Sergio Lucio Vinci
- Neuroradiology Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., Via Michele Miraglia 20, Palermo, 90139, Italy
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6
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Zhong Z, Li K, Shen C, Ma Y, Guo L. Erythropoietin improves pulmonary hypertension by promoting the homing and differentiation of bone marrow mesenchymal stem cells in lung tissue. Hum Cell 2024; 37:214-228. [PMID: 37968533 DOI: 10.1007/s13577-023-01009-y] [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: 06/15/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a chronic disease thatultimately progresses to right-sided heart failure and death. Erythropoietin (EPO) has been shown to have therapeutic potential in cardiovascular diseases, including PAH. In this study, we aimed to investigate the improvement effect of EPO pretreated bone marrow mesenchymal stem cells (BMSCs) on PAH. BMSCs were obtained from the bone marrow of male SD rats. Female rats were randomly divided into six groups, including control group, monocrotaline (MCT)-induced group, and four groups with different doses of EPO pretreated BMSCs. Lung tissue was taken for testing at 2 weeks of treatment. Our results showed EPO promoted homing and endothelial cell differentiation of BMSCs in the lung tissues of PAH rats. EPO and BMSCs treatment attenuated pulmonary arterial pressure, polycythemia, and pulmonary artery structural remodeling. Furthermore, BMSCs inhibited pulmonary vascular endothelial-to-mesenchymal transition (EndoMT) in PAH rats, which was further suppressed by EPO in a concentration-dependent manner. Meanwhile, EPO and BMSC treatment elevated pulmonary angiogenesis in PAH rats. BMSCs inhibited TNF-α, IL-1β, IL-6, and MCP-1 in lung tissues of PAH rats, which was further decreased by EPO in a concentration-dependent manner. Thus, EPO improved pulmonary hypertension (PH) by promoting the homing and differentiation of BMSCs in lung tissue.
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Affiliation(s)
- Zhendong Zhong
- Institute for Laboratory Animal Research, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, Sichuan, China
| | - Kang Li
- Department of Gastroenterology, People's Hospital of Tibet Autonomous Region, Lhasa, 850000, Tibet, China
| | - Chongyang Shen
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 230041, Sichuan, China
| | - Yuxiao Ma
- Department of Biology, New York University, 100 Washington Square E, New York, NY, 10003, United States of America.
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, 32# W. Sec 2,1St Ring Rd., Chengdu, 610072, Sichuan, China.
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7
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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
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Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
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8
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Goncharova EA, Kudryashova TV, Pullamsetti SS. Too hot? Too cold? Wnt signalling in pulmonary arterial hypertension: can we treat it "just right"? Eur Respir J 2023; 61:2300504. [PMID: 37290809 DOI: 10.1183/13993003.00504-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Elena A Goncharova
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
| | - Tatiana V Kudryashova
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
| | - Soni Savai Pullamsetti
- Max Planck Institute for Heart and Lung Research, Department of Lung Development and Remodeling, German Center for Lung Research (DZL), Bad Nauheim, Germany
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), DZL, Justus Liebig University, member of the German Center for Lung Research (DZL), Giessen, Germany
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9
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Goncharova EA, Kudryashova TV, de Jesus Perez V, Rafikova O. UnWNTing the Heart: Targeting WNT Signaling in Pulmonary Arterial Hypertension. Circ Res 2023; 132:1486-1488. [PMID: 37228239 PMCID: PMC10213998 DOI: 10.1161/circresaha.123.322912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Elena A. Goncharova
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
| | - Tatiana V. Kudryashova
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
| | - Vinicio de Jesus Perez
- Division of Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA, USA
| | - Olga Rafikova
- Department of Medicine, Division of Endocrinology, University of Arizona College of Medicine, Tucson, AZ, USA
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