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Zhao F, Chen Y, Xie Y, Kong S, Song L, Li H, Guo C, Yin Y, Zhang W, Zhu T. Identification of Zip8-correlated hub genes in pulmonary hypertension by informatic analysis. PeerJ 2023; 11:e15939. [PMID: 37663293 PMCID: PMC10470448 DOI: 10.7717/peerj.15939] [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: 04/13/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Background Pulmonary hypertension (PH) is a syndrome characterized by marked remodeling of the pulmonary vasculature and increased pulmonary vascular resistance, ultimately leading to right heart failure and even death. The localization of Zrt/Irt-like Protein 8 (ZIP8, a metal ion transporter, encoded by SLC39A8) was abundantly in microvasculature endothelium and its pivotal role in the lung has been demonstrated. However, the role of Zip8 in PH remains unclear. Methods Bioinformatics analysis was employed to identify SLC39A8 expression patterns and differentially expressed genes (DEGs) between PH patients and normal controls (NC), based on four datasets (GSE24988, GSE113439, GSE117261, and GSE15197) from the Biotechnology Gene Expression Omnibus (NCBI GEO) database. Gene set enrichment analysis (GSEA) was performed to analyze signaling pathways enriched for DEGs. Hub genes were identified by cytoHubba analysis in Cytoscape. Reverse transcriptase-polymerase chain reaction was used to validate SLC39A8 and its correlated metabolic DEGs expression in PH (SU5416/Hypoxia) mice. Results SLC39A8 expression was downregulated in PH patients, and this expression pattern was validated in PH (SU5416/Hypoxia) mouse lung tissue. SLC39A8-correlated genes were mainly enriched in the metabolic pathways. Within these SLC39A8-correlated genes, 202 SLC39A8-correlated metabolic genes were screened out, and seven genes were identified as SLC39A8-correlated metabolic hub genes. The expression patterns of hub genes were analyzed between PH patients and controls and further validated in PH mice. Finally, four genes (Fasn, Nsdhl, Acat2, and Acly) were downregulated in PH mice. However, there were no significant differences in the expression of the other three hub genes between PH mice and controls. Of the four genes, Fasn and Acly are key enzymes in fatty acids synthesis, Nsdhl is involved in cholesterol synthesis, and Acat2 is implicated in cholesterol metabolic transformation. Taken together, these results provide novel insight into the role of Zip8 in PH.
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Affiliation(s)
- FanRong Zhao
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - Yujing Chen
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - Yuliang Xie
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - Shuang Kong
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - LiaoFan Song
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - Hanfei Li
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - Chao Guo
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
| | - Yanyan Yin
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Weifang Zhang
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Departments of Pharmacy, The Second Affiliated Hospital, Nanchang, China
| | - Tiantian Zhu
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
- Xinxiang Key Laboratory of Vascular Remodeling Intervention and Molecular Targeted Therapy Drug Development, Xinxiang, China
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, Xinxiang, China
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Identification of Signal Pathways and Hub Genes of Pulmonary Arterial Hypertension by Bioinformatic Analysis. Can Respir J 2022; 2022:1394088. [PMID: 36072642 PMCID: PMC9444450 DOI: 10.1155/2022/1394088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive and complex pulmonary vascular disease with poor prognosis. The aim of this study was to provide a new understanding of the pathogenesis of disease and potential treatment targets for patients with PAH based on multiple-microarray analysis.Two microarray datasets (GSE53408 and GSE113439) downloaded from the Gene Expression Omnibus (GEO) database were analysed. All the raw data were processed by R, and differentially expressed genes (DEGs) were screened out by the “limma” package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed and visualized by R and Cytoscape software. Protein-protein interactions (PPI) of DEGs were analysed based on the NetworkAnalyst online tool. A total of 442 upregulated DEGs and 84 downregulated DEGs were identified. GO enrichment analysis showed that these DEGs were mainly enriched in mitotic nuclear division, organelle fission, chromosome segregation, nuclear division, and sister chromatid segregation. Significant KEGG pathway enrichment included ribosome biogenesis in eukaryotes, RNA transport, proteoglycans in cancer, dilated cardiomyopathy, rheumatoid arthritis, vascular smooth muscle contraction, focal adhesion, regulation of the actin cytoskeleton, and hypertrophic cardiomyopathy. The PPI network identified 10 hub genes including HSP90AA1, CDC5L, MDM2, LRRK2, CFTR, IQGAP1, CAND1, TOP2A, DDX21, and HIF1A. We elucidated potential biomarkers and therapeutic targets for PAH by bioinformatic analysis, which provides a theoretical basis for future study.
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Liu X, Zhang L, Zhang W. Metabolic reprogramming: A novel metabolic model for pulmonary hypertension. Front Cardiovasc Med 2022; 9:957524. [PMID: 36093148 PMCID: PMC9458918 DOI: 10.3389/fcvm.2022.957524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
Pulmonary arterial hypertension, or PAH, is a condition that is characterized by pulmonary artery pressures above 20 mmHg (at rest). In the treatment of PAH, the pulmonary vascular system is regulated to ensure a diastolic and contraction balance; nevertheless, this treatment does not prevent or reverse pulmonary vascular remodeling and still causes pulmonary hypertension to progress. According to Warburg, the link between metabolism and proliferation in PAH is similar to that of cancer, with a common aerobic glycolytic phenotype. By activating HIF, aerobic glycolysis is enhanced and cell proliferation is triggered. Aside from glutamine metabolism, the Randle cycle is also present in PAH. Enhanced glutamine metabolism replenishes carbon intermediates used by glycolysis and provides energy to over-proliferating and anti-apoptotic pulmonary vascular cells. By activating the Randle cycle, aerobic oxidation is enhanced, ATP is increased, and myocardial injury is reduced. PAH is predisposed by epigenetic dysregulation of DNA methylation, histone acetylation, and microRNA. This article discusses the abnormal metabolism of PAH and how metabolic therapy can be used to combat remodeling.
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Mprah R, Adzika GK, Gyasi YI, Ndzie Noah ML, Adu-Amankwaah J, Adekunle AO, Duah M, Wowui PI, Weili Q. Glutaminolysis: A Driver of Vascular and Cardiac Remodeling in Pulmonary Arterial Hypertension. Front Cardiovasc Med 2021; 8:667446. [PMID: 33996951 PMCID: PMC8113389 DOI: 10.3389/fcvm.2021.667446] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/08/2021] [Indexed: 12/30/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a decimating ailment described by chronic precapillary pulmonary hypertension, an elevated mean pulmonary arterial pressure with a normal pulmonary capillary wedge pressure, and a raised pulmonary vascular resistance resulting in increased right ventricular afterload culminating in heart failure and death. Current PAH treatments regulate the vasodilatory/vasoconstrictory balance of pulmonary vessels. However, these treatment options are unable to stop the progression of, or reverse, an already established disease. Recent studies have advanced a metabolic dysregulation, featuring increased glutamine metabolism, as a mechanism driving PAH progression. Metabolic dysregulation in PAH leads to increased glutaminolysis to produce substrate to meet the high-energy requirement by hyperproliferative and apoptosis-resistant pulmonary vascular cells. This article explores the role of glutamate metabolism in PAH and how it could be targeted as an anti-remodeling therapeutic strategy.
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Affiliation(s)
- Richard Mprah
- Department of Physiology, Xuzhou Medical University, Xuzhou, China
| | | | - Yusif I. Gyasi
- Department of Chemistry & Biochemistry, Central Michigan University, Mount Pleasant, TX, United States
| | | | | | | | - Maxwell Duah
- Haematology Department, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | | | - Qiao Weili
- Department of Physiology, Xuzhou Medical University, Xuzhou, China
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Stearman RS, Bui QM, Speyer G, Handen A, Cornelius AR, Graham BB, Kim S, Mickler EA, Tuder RM, Chan SY, Geraci MW. Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome. Am J Respir Cell Mol Biol 2020; 60:637-649. [PMID: 30562042 DOI: 10.1165/rcmb.2018-0368oc] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is characterized by increased pulmonary artery pressure and vascular resistance, typically leading to right heart failure and death. Current therapies improve quality of life of the patients but have a modest effect on long-term survival. A detailed transcriptomics and systems biology view of the PAH lung is expected to provide new testable hypotheses for exploring novel treatments. We completed transcriptomics analysis of PAH and control lung tissue to develop disease-specific and clinical data/tissue pathology gene expression classifiers from expression datasets. Gene expression data were integrated into pathway analyses. Gene expression microarray data were collected from 58 PAH and 25 control lung tissues. The strength of the dataset and its derived disease classifier was validated using multiple approaches. Pathways and upstream regulators analyses was completed with standard and novel graphical approaches. The PAH lung dataset identified expression patterns specific to PAH subtypes, clinical parameters, and lung pathology variables. Pathway analyses indicate the important global role of TNF and transforming growth factor signaling pathways. In addition, novel upstream regulators and insight into the cellular and innate immune responses driving PAH were identified. Finally, WNT-signaling pathways may be a major determinant underlying the observed sex differences in PAH. This study provides a transcriptional framework for the PAH-diseased lung, supported by previously reported findings, and will be a valuable resource to the PAH research community. Our investigation revealed novel potential targets and pathways amenable to further study in a variety of experimental systems.
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Affiliation(s)
- Robert S Stearman
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Quan M Bui
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Gil Speyer
- 2 Quantitative Medicine and Systems Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona.,3 Research Computing, Arizona State University, Tempe, Arizona
| | - Adam Handen
- 4 Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Amber R Cornelius
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Brian B Graham
- 5 Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado; and
| | - Seungchan Kim
- 6 Department of Electrical and Computer Engineering, Center for Computational Systems Biology, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, Texas
| | - Elizabeth A Mickler
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Rubin M Tuder
- 5 Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado; and
| | - Stephen Y Chan
- 4 Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mark W Geraci
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
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Elinoff JM, Mazer AJ, Cai R, Lu M, Graninger G, Harper B, Ferreyra GA, Sun J, Solomon MA, Danner RL. Meta-analysis of blood genome-wide expression profiling studies in pulmonary arterial hypertension. Am J Physiol Lung Cell Mol Physiol 2019; 318:L98-L111. [PMID: 31617731 DOI: 10.1152/ajplung.00252.2019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Inflammatory cell infiltrates are a prominent feature of aberrant vascular remodeling in pulmonary arterial hypertension (PAH), suggesting that immune effector cells contribute to disease progression. Genome-wide blood expression profiling studies have attempted to better define this inflammatory component of PAH pathobiology but have been hampered by small sample sizes, methodological differences, and very little gene-level reproducibility. The current meta-analysis (seven studies; 156 PAH patients/110 healthy controls) was performed to assess the comparability of data across studies and to possibly derive a generalizable transcriptomic signature. Idiopathic (IPAH) compared with disease-associated PAH (APAH) displayed highly similar expression profiles with no differentially expressed genes, even after substantially relaxing selection stringency. In contrast, using a false discovery rate of ≤1% and I2 < 40% (low-to-moderate heterogeneity across studies) both IPAH and APAH differed markedly from healthy controls with the combined PAH cohort yielding 1,269 differentially expressed, unique gene transcripts. Bioinformatic analyses, including gene-set enrichment, which uses all available data independent of gene selection thresholds, identified interferon, mammalian target of rapamycin/p70S6K, stress kinase, and Toll-like receptor signaling as enriched mechanisms within the PAH gene signature. Enriched biological functions and diseases included tumorigenesis, autoimmunity, antiviral response, and cell death consistent with prevailing theories of PAH pathogenesis. Although otherwise indistinguishable, APAH (predominantly PAH due to systemic sclerosis) had a somewhat stronger interferon profile than IPAH. Meta-analysis defined a robust and generalizable transcriptomic signature in the blood of PAH patients that can help inform the identification of biomarkers and therapeutic targets.
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Affiliation(s)
- Jason M Elinoff
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Adrien J Mazer
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Rongman Cai
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Mengyun Lu
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Grace Graninger
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Bonnie Harper
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Gabriela A Ferreyra
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Junfeng Sun
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
| | - Michael A Solomon
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland.,Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Robert L Danner
- Critical Care Medicine Department, Clinical Center, and National Institutes of Health, Bethesda, Maryland
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A Combined Targeted and Whole Exome Sequencing Approach Identified Novel Candidate Genes Involved in Heritable Pulmonary Arterial Hypertension. Sci Rep 2019; 9:753. [PMID: 30679663 PMCID: PMC6345742 DOI: 10.1038/s41598-018-37277-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 11/29/2018] [Indexed: 01/08/2023] Open
Abstract
The pathogenesis of idiopathic and heritable forms of pulmonary arterial hypertension is still not completely understood, even though several causative genes have been proposed, so that a third of patients remains genetically unresolved. Here we applied a multistep approach to extend identification of the genetic bases of such a disease by searching for novel candidate genes/pathways. Twenty-eight patients belonging to 18 families were screened for BMPR2 mutations and BMPR2-negative samples were tested for 12 additional candidate genes by means of a specific massive parallel sequencing-based assay. Finally, whole exome sequencing was performed on four patients showing no mutations at known disease genes, as well as on their unaffected parents. In addition to EIF2AK4, which has been already suggested to be associated with pulmonary veno-occlusive disease, we identified the novel candidate genes ATP13A3, CD248, EFCAB4B, involved in lung vascular remodeling that represent reliable drivers contributing to the disease according to their biological functions/inheritance patterns. Therefore, our results suggest that combining gene panel and whole exome sequencing provides new insights useful for the genetic diagnosis of familial and idiopathic pulmonary arterial hypertension, as well as for the identification of biological pathways that will be potentially targeted by new therapeutic strategies.
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Serum cytokine profiles in patients with chronic obstructive pulmonary disease associated pulmonary hypertension identified using protein array. Cytokine 2018; 111:342-349. [PMID: 30273784 DOI: 10.1016/j.cyto.2018.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/09/2018] [Accepted: 09/11/2018] [Indexed: 11/24/2022]
Abstract
Pulmonary hypertension (PH) is a common complication of chronic obstructive pulmonary disease (COPD) and is a significant risk factor for hospitalization and shortened life expectancy. Therefore, developing new serum biomarkers for early diagnosis and prognosis of COPD associated PH is crucial. In the present study, a solid-phase antibody array simultaneously detecting multiple proteins was used to search specific COPD associated PH biomarkers, with COPD patients and healthy subjects as control groups. As a result, compared to the COPD and healthy groups, the levels of MCP-4, SDF-1 alpha, CCL28, Adipsin, IL-28A, CD40 and AgRP were uniquely altered in COPD patient serum with pulmonary hypertension. Among these proteins, CCL28, MCP-4, CD40, AgRP and IL-28A were identified to be differentially expressed in COPD patients with hypertension, indicating that these cytokines may serve as novel biomarkers for the diagnosis and prognosis of COPD associated pulmonary hypertension.
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Bertero T, Handen AL, Chan SY. Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. Int J Mol Sci 2018; 19:ijms19082289. [PMID: 30081553 PMCID: PMC6121519 DOI: 10.3390/ijms19082289] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 11/16/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is characterized by occlusion of lung arterioles, leading to marked increases in pulmonary vascular resistance. Although heritable forms of PAH are known to be driven by genetic mutations that share some commonality of function, the extent to which these effectors converge to regulate shared processes in this disease is unknown. We have causally connected extracellular matrix (ECM) remodeling and mechanotransduction to the miR-130/301 family in a feedback loop that drives vascular activation and downstream PAH. However, the molecular interconnections between factors genetically associated with PAH and this mechano-driven feedback loop remain undefined. We performed systematic manipulation of matrix stiffness, the miR-130/301 family, and factors genetically associated with PAH in primary human pulmonary arterial cells and assessed downstream and reciprocal consequences on their expression. We found that a network of factors linked to heritable PAH converges upon the matrix stiffening-miR-130/301-PPARγ-LRP8 axis in order to remodel the ECM. Furthermore, we leveraged a computational network biology approach to predict a number of additional molecular circuits functionally linking this axis to the ECM. These results demonstrate that multiple genes associated with heritable PAH converge to control the miR-130/301 circuit, triggering a self-amplifying feedback process central to pulmonary vascular stiffening and disease.
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Affiliation(s)
- Thomas Bertero
- Université Côte d'Azur, CNRS UMR7284, INSERM U1081, IRCAN, Nice 06100, France.
| | - Adam L Handen
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
| | - Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA.
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Abou Hassan OK, Haidar W, Nemer G, Skouri H, Haddad F, BouAkl I. Clinical and genetic characteristics of pulmonary arterial hypertension in Lebanon. BMC MEDICAL GENETICS 2018; 19:89. [PMID: 29843651 PMCID: PMC5975525 DOI: 10.1186/s12881-018-0608-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/18/2018] [Indexed: 12/26/2022]
Abstract
Background Pulmonary arterial hypertension (PAH) is a rare disease with an incidence rate of 2–6 cases per million per year. Our knowledge of the disease in the Middle East and North Africa (MENA) region is limited by the small number of clinical studies and the complete absence of genetic studies. Methods Our aim was to shed light on the clinical and genetic characteristics of PAH in Lebanon and the region by using exome sequencing on PAH patients referred to the American University of Beirut Medical Center (AUBMC). Twenty-one idiopathic, hereditary and Congenital Heart Disease (CHD) PAH patients were prospectively recruited, their clinical data summarized, and sequencing performed. Results The mean age at diagnosis was 33 years with a female preponderance of 70%. The mean pulmonary artery pressure at the time of diagnosis was 55. Genetic testing showed that 5 out of 19 idiopathic and Congenital Heart Disease PAH patients had Bone Morphogenetic Protein Receptor 2 (BMPR2) mutations at 25% prevalence, with 2 of these patients exhibiting a novel mutation. It also showed the presence of 1 BMPR2 mutation with 100% penetrance in a heritable PAH family. In the remaining cases, the lack of a complete genotype/phenotype correlation entailed a multigenic inheritance; suspected interactions involved previously associated genes T-box transcription factor 4 (TBX4), Bone Morphogenic Protein 10 (BMP10) and Growth Differentiation Factor 2 (GDF2). Conclusions This is the first study that looks into the genetic causes of PAH, including known and new BMPR2 mutations, in the MENA region. It is also the first study to characterize the clinical features of the disease in Lebanon. Electronic supplementary material The online version of this article (10.1186/s12881-018-0608-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ossama K Abou Hassan
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O.Box: 11-0236, Beirut, Lebanon
| | - Wiam Haidar
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O.Box: 11-0236, Beirut, Lebanon
| | - Georges Nemer
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, P.O.Box: 11-0236, Beirut, Lebanon.
| | - Hadi Skouri
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O.Box: 11-0236, Beirut, Lebanon
| | | | - Imad BouAkl
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O.Box: 11-0236, Beirut, Lebanon.
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Abstract
“A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker or signature molecule” – Biomarker definition, National Institutes of Health, National Cancer Institute, Dictionary of Cancer Terms
Although this definition pertains to the field of cancer and cancer biology, it applies to many disciplines, including the field of pulmonary vascular disease. In the world of pulmonary hypertension (PH), biomarkers hold a special place. In the diagnosis of PH subtype, we are limited by the risk of lung biopsy1 and, further, in patients with pulmonary arterial hypertension (PAH) we are limited by the inability to frequently obtain our strongest predictors of mortality: invasive pulmonary hemodynamic assessment. Thus, biomarkers hold much promise for the field of PH. We are searching for markers of PH subtypes and endophenotypes. We are looking for predictors of mortality in all forms of PH and, critically, we are hoping to find peripheral blood markers that will help us discover which drugs are likely to benefit a particular patient. Although we have made inroads in all 3 areas, there are substantial opportunities for refinement of our current biomarkers and discovery of novel markers to improve the care of PH patients. This review will cover the state of current biomarkers in PH and discuss challenges and future directions.
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Affiliation(s)
- Anna R. Hemnes
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN
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Zhao M, Liu Y, Qu H. Expression of epithelial-mesenchymal transition-related genes increases with copy number in multiple cancer types. Oncotarget 2017; 7:24688-99. [PMID: 27029057 PMCID: PMC5029734 DOI: 10.18632/oncotarget.8371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/04/2016] [Indexed: 01/10/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a cellular process through which epithelial cells transform into mesenchymal cells. EMT-implicated genes initiate and promote cancer metastasis because mesenchymal cells have greater invasive and migration capacities than epithelial cells. In this pan-cancer analysis, we explored the relationship between gene expression changes and copy number variations (CNVs) for EMT-implicated genes. Based on curated 377 EMT-implicated genes from the literature, we identified 212 EMT-implicated genes associated with more frequent copy number gains (CNGs) than copy number losses (CNLs) using data from The Cancer Genome Atlas (TCGA). Then by correlating these CNV data with TCGA gene expression data, we identified 71 EMT-implicated genes with concordant CNGs and gene up-regulation in 20 or more tumor samples. Of those, 14 exhibited such concordance in over 110 tumor samples. These 14 genes were predominantly apoptosis regulators, which may implies that apoptosis is critical during EMT. Moreover, the 71 genes with concordant CNG and up-regulation were largely involved in cellular functions such as phosphorylation cascade signaling. This is the first observation of concordance between CNG and up-regulation of specific genes in hundreds of samples, which may indicate that somatic CNGs activate gene expression by increasing the gene dosage.
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Affiliation(s)
- Min Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, 4558, Australia
| | - Yining Liu
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, 4558, Australia
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
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Assad TR, Hemnes AR, Larkin EK, Glazer AM, Xu M, Wells QS, Farber-Eger EH, Sheng Q, Shyr Y, Harrell FE, Newman JH, Brittain EL. Clinical and Biological Insights Into Combined Post- and Pre-Capillary Pulmonary Hypertension. J Am Coll Cardiol 2017; 68:2525-2536. [PMID: 27931609 DOI: 10.1016/j.jacc.2016.09.942] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/09/2016] [Accepted: 09/19/2016] [Indexed: 12/01/2022]
Abstract
BACKGROUND Pulmonary hypertension (PH) is a common and morbid complication of left heart disease with 2 subtypes: isolated post-capillary pulmonary hypertension (Ipc-PH) and combined post-capillary and pre-capillary pulmonary hypertension (Cpc-PH). Little is known about the clinical or physiological characteristics that distinguish these 2 subphenotypes or if Cpc-PH shares molecular similarities to pulmonary arterial hypertension (PAH). OBJECTIVES The goal of this study was to test the hypothesis that the hemodynamic and genetic profile of Cpc-PH would more closely resemble PAH than Ipc-PH. METHODS Vanderbilt University's electronic medical record linked to a DNA biorepository was used to extract demographic characteristics, clinical data, invasive hemodynamic data, echocardiography, and vital status for all patients referred for right heart catheterization between 1998 and 2014. Shared genetic variants between PAH and Cpc-PH compared with Ipc-PH were identified by using pre-existing single-nucleotide polymorphism data. RESULTS A total of 2,817 patients with PH (13% Cpc-PH, 52% Ipc-PH, and 20% PAH) were identified. Patients with Cpc-PH were on average 6 years younger, with more severe pulmonary vascular disease than patients with Ipc-PH, despite similar comorbidities and prevalence, severity, and chronicity of left heart disease. After adjusting for relevant covariates, the risk of death was similar between the Cpc-PH and Ipc-PH groups (hazard ratio: 1.14; 95% confidence interval: 0.96 to 1.35; p = 0.15) when defined according to diastolic pressure gradient. We identified 75 shared exonic single-nucleotide polymorphisms between Cpc-PH and PAH enriched in pathways involving cell structure, extracellular matrix, and immune function. These genes are expressed, on average, 32% higher in lungs relative to other tissues. CONCLUSIONS Patients with Cpc-PH develop pulmonary vascular disease similar to patients with PAH, despite younger age and similar prevalence of obesity, diabetes mellitus, and left heart disease compared with patients with Ipc-PH. An exploratory genetic analysis in Cpc-PH identified genes and biological pathways in the lung known to contribute to PAH pathophysiology, suggesting that Cpc-PH may be a distinct and highly morbid PH subphenotype.
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Affiliation(s)
- Tufik R Assad
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Anna R Hemnes
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Emma K Larkin
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Andrew M Glazer
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Meng Xu
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee
| | - Quinn S Wells
- Vanderbilt Center for Translational and Clinical Cardiovascular Research, Vanderbilt University School of Medicine, Nashville, Tennessee; Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Eric H Farber-Eger
- Vanderbilt Center for Translational and Clinical Cardiovascular Research, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Quanhu Sheng
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Frank E Harrell
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee
| | - John H Newman
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Evan L Brittain
- Vanderbilt Center for Translational and Clinical Cardiovascular Research, Vanderbilt University School of Medicine, Nashville, Tennessee; Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
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Brittain EL, Chan SY. Integration of complex data sources to provide biologic insight into pulmonary vascular disease (2015 Grover Conference Series). Pulm Circ 2016; 6:251-60. [PMID: 27683602 DOI: 10.1086/686995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The application of complex data sources to pulmonary vascular diseases is an emerging and promising area of investigation. The use of -omics platforms, in silico modeling of gene networks, and linkage of large human cohorts with DNA biobanks are beginning to bear biologic insight into pulmonary hypertension. These approaches to high-throughput molecular phenotyping offer the possibility of discovering new therapeutic targets and identifying variability in response to therapy that can be leveraged to improve clinical care. Optimizing the methods for analyzing complex data sources and accruing large, well-phenotyped human cohorts linked to biologic data remain significant challenges. Here, we discuss two specific types of complex data sources-gene regulatory networks and DNA-linked electronic medical record cohorts-that illustrate the promise, challenges, and current limitations of these approaches to understanding and managing pulmonary vascular disease.
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Affiliation(s)
- Evan L Brittain
- Division of Cardiovascular Medicine and Vanderbilt Translational and Clinical Cardiovascular Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephen Y Chan
- Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA; and Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Zhao M, Zhao Z. Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study. BMC Genomics 2016; 17 Suppl 7:532. [PMID: 27556634 PMCID: PMC5001246 DOI: 10.1186/s12864-016-2904-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background Tumor suppressor genes (TSGs) encode the guardian molecules to control cell growth. The genomic alteration of TSGs may cause tumorigenesis and promote cancer progression. So far, investigators have mainly studied the functional effects of somatic single nucleotide variants in TSGs. Copy number variation (CNV) is another important form of genetic variation, and is often involved in cancer biology and drug treatment, but studies of CNV in TSGs are less represented in literature. In addition, there is a lack of a combinatory analysis of gene expression and CNV in this important gene set. Such a study may provide more insights into the relationship between gene dosage and tumorigenesis. To meet this demand, we performed a systematic analysis of CNVs and gene expression in TSGs to provide a systematic view of CNV and gene expression change in TSGs in pan-cancer. Results We identified 1170 TSGs with copy number gain or loss in 5846 tumor samples. Among them, 207 TSGs tended to have copy number loss (CNL), from which fifteen CNL hotspot regions were identified. The functional enrichment analysis revealed that the 207 TSGs were enriched in cancer-related pathways such as P53 signaling pathway and the P53 interactome. We further performed integrative analyses of CNV with gene expression using the data from the matched tumor samples. We found 81 TSGs with concordant CNL events and decreased gene expression in the tumor samples we examined. Remarkably, seven TSGs displayed concordant CNL and gene down-regulation in at least 50 tumor samples: MTAP (212 samples), PTEN (139), MCPH1 (85), FBXO25 (67), SMAD4 (64), TRIM35 (57), and RB1 (54). Specifically to MTAP, this concordance was found in 14 cancer types, an observation that is not much reported in literature yet. Further network-based analysis revealed that these TSGs with concordant CNL and gene down-regulation were highly connected. Conclusions This study provides a draft landscape of CNV in pan-cancer. Our findings of systematic concordance between CNL and down-regulation of gene expression may help better understand the TSG biology in tumorigenesis and cancer progression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2904-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA. .,Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, 37212, USA. .,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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