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Buschur KL, Pottinger TD, Vogel-Claussen J, Powell CA, Aguet F, Allen NB, Ardlie K, Bluemke DA, Durda P, Hermann EA, Hoffman EA, Lima JA, Liu Y, Malinsky D, Manichaikul A, Motahari A, Post WS, Prince MR, Rich SS, Rotter JI, Smith BM, Tracy RP, Watson K, Winther HB, Lappalainen T, Barr RG. Peripheral Blood Mononuclear Cell Gene Expression Associated with Pulmonary Microvascular Perfusion: The Multi-Ethnic Study of Atherosclerosis Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2024; 21:884-894. [PMID: 38335160 PMCID: PMC11160125 DOI: 10.1513/annalsats.202305-417oc] [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: 05/08/2023] [Accepted: 02/09/2024] [Indexed: 02/12/2024] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) and emphysema are associated with endothelial damage and altered pulmonary microvascular perfusion. The molecular mechanisms underlying these changes are poorly understood in patients, in part because of the inaccessibility of the pulmonary vasculature. Peripheral blood mononuclear cells (PBMCs) interact with the pulmonary endothelium. Objectives: To test the association between gene expression in PBMCs and pulmonary microvascular perfusion in COPD. Methods: The Multi-Ethnic Study of Atherosclerosis (MESA) COPD Study recruited two independent samples of COPD cases and controls with ⩾10 pack-years of smoking history. In both samples, pulmonary microvascular blood flow, pulmonary microvascular blood volume, and mean transit time were assessed on contrast-enhanced magnetic resonance imaging, and PBMC gene expression was assessed by microarray. Additional replication was performed in a third sample with pulmonary microvascular blood volume measures on contrast-enhanced dual-energy computed tomography. Differential expression analyses were adjusted for age, gender, race/ethnicity, educational attainment, height, weight, smoking status, and pack-years of smoking. Results: The 79 participants in the discovery sample had a mean age of 69 ± 6 years, 44% were female, 25% were non-White, 34% were current smokers, and 66% had COPD. There were large PBMC gene expression signatures associated with pulmonary microvascular perfusion traits, with several replicated in the replication sets with magnetic resonance imaging (n = 47) or dual-energy contrast-enhanced computed tomography (n = 157) measures. Many of the identified genes are involved in inflammatory processes, including nuclear factor-κB and chemokine signaling pathways. Conclusions: PBMC gene expression in nuclear factor-κB, inflammatory, and chemokine signaling pathways was associated with pulmonary microvascular perfusion in COPD, potentially offering new targetable candidates for novel therapies.
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Affiliation(s)
| | | | - Jens Vogel-Claussen
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Norrina B. Allen
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David A. Bluemke
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | | | - Eric A. Hoffman
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - João A.C. Lima
- Division of Cardiology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Amin Motahari
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Wendy S. Post
- Division of Cardiology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | | | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Benjamin M. Smith
- Department of Medicine
- Research Institute, McGill University Health Center, Montreal, Québec, Canada
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Karol Watson
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California; and
| | - Hinrich B. Winther
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
| | - Tuuli Lappalainen
- Department of Biostatistics
- Department of Systems Biology, Columbia University Medical Center, New York, New York
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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Yu D, Zhang T, Zhou G, Wu Z, Xiao R, Zhang H, Liu B, Li X, Ruiz M, Dupuis J, Zhu L, Hu Q. Co-profiling reveals distinct patterns of genomic chromatin accessibility and gene expression in pulmonary hypertension caused by chronic hypoxia. Respir Res 2023; 24:104. [PMID: 37031175 PMCID: PMC10082509 DOI: 10.1186/s12931-023-02389-3] [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: 02/01/2023] [Accepted: 03/08/2023] [Indexed: 04/10/2023] Open
Abstract
INTRODUCTION Aberrant gene expression is a key mechanism underlying pulmonary hypertension (PH) development. The alterations of genomic chromatin accessibility and their relationship with the aberrant gene expressions in PH are poorly understood. We used bulk Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) in pulmonary artery smooth muscle cells (PASMCs) of chronic hypoxia-exposed rats mimicking group 3 human PH. METHODS Adult Sprague Dawley rats were commercially obtained from Hunan SJA (Hunan SJA Laboratory Animal Co., Changsha, China) and randomizedly allocated into four groups exposing to nomobaric hypoxia or normoxia for 1 or 28 days respectively. After the assessment of pulmonary hemodynamics, smooth muscle cells were isolated from intralobular arteries and simultaneously subjected to bulk Assay of ATAC-seq and RNA-seq. RESULTS Hypoxic exposure for continuous 28-days, but not for 1-day, induced established PH phenotypes in rats. ATAC-seq revealed a major distribution of differential accessibility regions (DARs) annotated to the genome in out-of-promoter regions, following 1-day or 28-days hypoxia. 1188 DAR-associated genes and 378 differentially expressed genes (DEGs) were identified in rats after exposure to 1-day hypoxia, while 238 DAR-associated genes and 452 DEGs for 28-days hypoxia. Most of the DAR-associated genes or DEGs in 1-day did not overlap with that of 28-days hypoxia. A Pearson correlation analysis indicated no significant correlation between ATAC-seq and RNA-seq. CONCLUSIONS The alterations in genomic chromatin accessibility and genes expression of PASMCs in the initial stage of hypoxia are distinct from the established stage of hypoxia-induced PH. The genomic differential accessibility regions may not be the main mechanisms directly underlying the differentially expressed genes observed either in the initial or established stages of PH. Thus the time-course alterations of gene expression and their possible indirect link with genomic chromatin accessibility warrant more attention in mechanistic study of pulmonary hypertension.
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Affiliation(s)
- Dongdong Yu
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Oncology, Renmin Hospital, Wuhan University, Wuhan, China
| | - Ting Zhang
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Guangyuan Zhou
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zeang Wu
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Xiao
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Han Zhang
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bingxun Liu
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiangpan Li
- Department of Oncology, Renmin Hospital, Wuhan University, Wuhan, China
| | - Matthieu Ruiz
- Department of Nutrition, Université de Montréal, Montreal, Canada
- Montreal Heart Institute, Montreal, QC, Canada
| | - Jocelyn Dupuis
- Montreal Heart Institute, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Liping Zhu
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qinghua Hu
- Department of Pathophysiology, School of Basic Medicine, Wuhan, China.
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Abstract
Pulmonary arterial hypertension forms the first and most severe of the 5 categories of pulmonary hypertension. Disease pathogenesis is driven by progressive remodeling of peripheral pulmonary arteries, caused by the excessive proliferation of vascular wall cells, including endothelial cells, smooth muscle cells and fibroblasts, and perivascular inflammation. Compelling evidence from animal models suggests endothelial cell dysfunction is a key initial trigger of pulmonary vascular remodeling, which is characterised by hyperproliferation and early apoptosis followed by enrichment of apoptosis-resistant populations. Dysfunctional pulmonary arterial endothelial cells lose their ability to produce vasodilatory mediators, together leading to augmented pulmonary arterial smooth muscle cell responses, increased pulmonary vascular pressures and right ventricular afterload, and progressive right ventricular hypertrophy and heart failure. It is recognized that a range of abnormal cellular molecular signatures underpin the pathophysiology of pulmonary arterial hypertension and are enhanced by loss-of-function mutations in the BMPR2 gene, the most common genetic cause of pulmonary arterial hypertension and associated with worse disease prognosis. Widespread metabolic abnormalities are observed in the heart, pulmonary vasculature, and systemic tissues, and may underpin heterogeneity in responsivity to treatment. Metabolic abnormalities include hyperglycolytic reprogramming, mitochondrial dysfunction, aberrant polyamine and sphingosine metabolism, reduced insulin sensitivity, and defective iron handling. This review critically discusses published mechanisms linking metabolic abnormalities with dysfunctional BMPR2 (bone morphogenetic protein receptor 2) signaling; hypothesized mechanistic links requiring further validation; and their relevance to pulmonary arterial hypertension pathogenesis and the development of potential therapeutic strategies.
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Affiliation(s)
- Iona Cuthbertson
- Department of Medicine, University of Cambridge School of Clinical Medicine, Heart and Lung Research Institute, United Kingdom
| | - Nicholas W Morrell
- Department of Medicine, University of Cambridge School of Clinical Medicine, Heart and Lung Research Institute, United Kingdom
| | - Paola Caruso
- Department of Medicine, University of Cambridge School of Clinical Medicine, Heart and Lung Research Institute, United Kingdom
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Wang J, Uddin MN, Wang R, Gong YH, Wu Y. Comprehensive analysis and validation of novel immune and vascular remodeling related genes signature associated with drug interactions in pulmonary arterial hypertension. Front Genet 2022; 13:922213. [PMID: 36147486 PMCID: PMC9486302 DOI: 10.3389/fgene.2022.922213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Previous studies revealed that the gene signatures are associated with the modulation and pathogenesis of pulmonary arterial hypertension (PAH). However, identifying critical transcriptional signatures in the blood of PAH patients remains lacking.Methods: The differentially expressed transcriptional signatures in the blood of PAH patients were identified by a meta-analysis from four microarray datasets. Then we investigated the enrichment of gene ontology and KEGG pathways and identified top hub genes. Besides, we investigated the correlation of crucial hub genes with immune infiltrations, hallmark gene sets, and blood vessel remodeling genes. Furthermore, we investigated the diagnostic efficacy of essential hub genes and their expression validation in an independent cohort of PAH, and we validate the expression level of hub genes in monocrotaline (MCT) induced PAH rats’ model. Finally, we have identified the FDA-approved drugs that target the hub genes and their molecular docking.Results: We found 1,216 differentially expressed genes (DEGs), including 521 up-regulated and 695 down-regulated genes, in the blood of the PAH patients. The up-regulated DEGs are significantly associated with the enrichment of KEGG pathways mainly involved with immune regulation, cellular signaling, and metabolisms. We identified 13 master transcriptional regulators targeting the dysregulated genes in PAH. The STRING-based investigation identified the function of hub genes associated with multiple immune-related pathways in PAH. The expression levels of RPS27A, MAPK1, STAT1, RPS6, FBL, RPS3, RPS2, and GART are positively correlated with ssGSEA scores of various immune cells as positively correlated with the hallmark of oxidative stress. Besides, we found that these hub genes also regulate the vascular remodeling in PAH. Furthermore, the expression levels of identified hub genes showed good diagnostic efficacy in the blood of PAH, and we validated most of the hub genes are consistently dysregulated in an independent PAH cohort. Validation of hub genes expression level in the monocrotaline (MCT)-induced lung tissue of rats with PAH revealed that 5 screened hub genes (MAPK1, STAT1, TLR4, TLR2, GART) are significantly highly expressed in PAH rats, and 4 screened hub genes (RPS6, FBL, RPS3, and RPS2) are substantially lowly expressed in rats with PAH. Finally, we analyzed the interaction of hub proteins and FDA-approved drugs and revealed their molecular docking, and the results showed that MAPK1, TLR4, and GART interact with various drugs with appropriate binding affinity.Conclusion: The identified blood-derived key transcriptional signatures significantly correlate with immune infiltrations, hypoxia, glycolysis, and blood vessel remodeling genes. These findings may provide new insight into the diagnosis and treatment of PAH patients.
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Affiliation(s)
- Jie Wang
- Department of Pharmacy, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Md. Nazim Uddin
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Rui Wang
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yue-hong Gong
- Department of Pharmacy, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yun Wu
- Department of General Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Yun Wu,
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Duan X, Cheng X, Yin X, Ke Z, Song J. Systematic analysis of the function and prognostic value of RNA binding protein in head and neck squamous cell carcinoma. Eur Arch Otorhinolaryngol 2021; 279:1535-1547. [PMID: 34218307 DOI: 10.1007/s00405-021-06929-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/01/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Dysregulation of RNA binding proteins (RBPs) plays an important role in controlling processes in cancer development. However, the function of RBPs has not been thoroughly and systematically documented in head and neck cancer. We aim to explore the role of RPB in the pathogenesis of HNSC. METHODS We obtained HNSC gene expression data and corresponding clinical information from The Cancer Genome Atlas (TCGA) and the GEO databases, and identified aberrantly expressed RBPs between tumors and normal tissues. Meanwhile, we performed a series of bioinformatics to explore the function and prognostic value of these RBPs. RESULTS A total of 249 abnormally expressed RBPs were identified, including 101 downregulated RBPs and 148 upregulated RBPs. Using least absolute shrinkage and selection operator (LASSO) and univariate Cox regression analysis, the 15 RPBs were identified as hub genes. With the 15 RPBS, the prognostic prediction model was constructed. Further analysis showed that the high-risk score of the patients expressed a better survival outcome. The prediction model was validated in another HNSC dataset, and similar findings were observed. CONCLUSIONS Our results provide novel insights into the pathogenesis of HNSC. The fifteen RBP gene signature exhibited the predictive value of moderate HNSC prognosis, and have potential application value in clinical decision-making and individualized treatment.
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Affiliation(s)
- Xiaofeng Duan
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Xianlin Cheng
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Zhao Ke
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
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Weiße J, Rosemann J, Krauspe V, Kappler M, Eckert AW, Haemmerle M, Gutschner T. RNA-Binding Proteins as Regulators of Migration, Invasion and Metastasis in Oral Squamous Cell Carcinoma. Int J Mol Sci 2020; 21:E6835. [PMID: 32957697 PMCID: PMC7555251 DOI: 10.3390/ijms21186835] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
Nearly 7.5% of all human protein-coding genes have been assigned to the class of RNA-binding proteins (RBPs), and over the past decade, RBPs have been increasingly recognized as important regulators of molecular and cellular homeostasis. RBPs regulate the post-transcriptional processing of their target RNAs, i.e., alternative splicing, polyadenylation, stability and turnover, localization, or translation as well as editing and chemical modification, thereby tuning gene expression programs of diverse cellular processes such as cell survival and malignant spread. Importantly, metastases are the major cause of cancer-associated deaths in general, and particularly in oral cancers, which account for 2% of the global cancer mortality. However, the roles and architecture of RBPs and RBP-controlled expression networks during the diverse steps of the metastatic cascade are only incompletely understood. In this review, we will offer a brief overview about RBPs and their general contribution to post-transcriptional regulation of gene expression. Subsequently, we will highlight selected examples of RBPs that have been shown to play a role in oral cancer cell migration, invasion, and metastasis. Last but not least, we will present targeting strategies that have been developed to interfere with the function of some of these RBPs.
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Affiliation(s)
- Jonas Weiße
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Julia Rosemann
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Vanessa Krauspe
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Matthias Kappler
- Department of Oral and Maxillofacial Plastic Surgery, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Alexander W. Eckert
- Department of Cranio Maxillofacial Surgery, Paracelsus Medical University, 90471 Nuremberg, Germany;
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
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