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Avecilla V, Doke M, Das M, Alcazar O, Appunni S, Rech Tondin A, Watts B, Ramamoorthy V, Rubens M, Das JK. Integrative Bioinformatics-Gene Network Approach Reveals Linkage between Estrogenic Endocrine Disruptors and Vascular Remodeling in Peripheral Arterial Disease. Int J Mol Sci 2024; 25:4502. [PMID: 38674087 PMCID: PMC11049860 DOI: 10.3390/ijms25084502] [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: 03/20/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Vascular diseases, including peripheral arterial disease (PAD), pulmonary arterial hypertension, and atherosclerosis, significantly impact global health due to their intricate relationship with vascular remodeling. This process, characterized by structural alterations in resistance vessels, is a hallmark of heightened vascular resistance seen in these disorders. The influence of environmental estrogenic endocrine disruptors (EEDs) on the vasculature suggests a potential exacerbation of these alterations. Our study employs an integrative approach, combining data mining with bioinformatics, to unravel the interactions between EEDs and vascular remodeling genes in the context of PAD. We explore the molecular dynamics by which EED exposure may alter vascular function in PAD patients. The investigation highlights the profound effect of EEDs on pivotal genes such as ID3, LY6E, FOS, PTP4A1, NAMPT, GADD45A, PDGF-BB, and NFKB, all of which play significant roles in PAD pathophysiology. The insights gained from our study enhance the understanding of genomic alterations induced by EEDs in vascular remodeling processes. Such knowledge is invaluable for developing strategies to prevent and manage vascular diseases, potentially mitigating the impact of harmful environmental pollutants like EEDs on conditions such as PAD.
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Affiliation(s)
- Vincent Avecilla
- Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL 33199, USA;
| | - Mayur Doke
- Diabetes Research Institute, University of Miami, Miami, FL 33136, USA; (M.D.); (O.A.); (A.R.T.); (B.W.)
| | - Madhumita Das
- Department of Biology, Miami Dade College, Miami, FL 33132, USA;
| | - Oscar Alcazar
- Diabetes Research Institute, University of Miami, Miami, FL 33136, USA; (M.D.); (O.A.); (A.R.T.); (B.W.)
| | - Sandeep Appunni
- Department of Biochemistry, Government Medical College, Kozhikode 673008, Kerala, India;
| | - Arthur Rech Tondin
- Diabetes Research Institute, University of Miami, Miami, FL 33136, USA; (M.D.); (O.A.); (A.R.T.); (B.W.)
| | - Brandon Watts
- Diabetes Research Institute, University of Miami, Miami, FL 33136, USA; (M.D.); (O.A.); (A.R.T.); (B.W.)
| | | | - Muni Rubens
- Baptist Health South Florida, Miami Gardens, FL 33176, USA; (V.R.); (M.R.)
| | - Jayanta Kumar Das
- Department of Health and Natural Sciences, Florida Memorial University, Miami Gardens, FL 33054, USA
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2
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Zhao Z, Chen S, Wei H, Ma W, Shi W, Si Y, Wang J, Wang L, Li X. Online application for the diagnosis of atherosclerosis by six genes. PLoS One 2024; 19:e0301912. [PMID: 38598492 PMCID: PMC11006159 DOI: 10.1371/journal.pone.0301912] [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: 11/29/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Atherosclerosis (AS) is a primary contributor to cardiovascular disease, leading to significant global mortality rates. Developing effective diagnostic indicators and models for AS holds the potential to substantially reduce the fatalities and disabilities associated with cardiovascular disease. Blood sample analysis has emerged as a promising avenue for facilitating diagnosis and assessing disease prognosis. Nonetheless, it lacks an accurate model or tool for AS diagnosis. Hence, the principal objective of this study is to develop a convenient, simple, and accurate model for the early detection of AS. METHODS We downloaded the expression data of blood samples from GEO databases. By dividing the mean values of housekeeping genes (meanHGs) and applying the comBat function, we aimed to reduce the batch effect. After separating the datasets into training, evaluation, and testing sets, we applied differential expression analyses (DEA) between AS and control samples from the training dataset. Then, a gradient-boosting model was used to evaluate the importance of genes and identify the hub genes. Using different machine learning algorithms, we constructed a prediction model with the highest accuracy in the testing dataset. Finally, we make the machine learning models publicly accessible by shiny app construction. RESULTS Seven datasets (GSE9874, GSE12288, GSE20129, GSE23746, GSE27034, GSE90074, and GSE202625), including 403 samples with AS and 325 healthy subjects, were obtained by comprehensive searching and filtering by specific requirements. The batch effect was successfully removed by dividing the meanHGs and applying the comBat function. 331 genes were found to be related to atherosclerosis by the DEA analysis between AS and health samples. The top 6 genes with the highest importance values from the gradient boosting model were identified. Out of the seven machine learning algorithms tested, the random forest model exhibited the most impressive performance in the testing datasets, achieving an accuracy exceeding 0.8. While the batch effect reduction analysis in our study could have contributed to the increased accuracy values, our comparison results further highlight the superiority of our model over the genes provided in published studies. This underscores the effectiveness of our approach in delivering superior predictive performance. The machine-learning models were then uploaded to the Shiny app's server, making it easy for users to distinguish AS samples from normal samples. CONCLUSIONS A prognostic Shiny application, built upon six potential atherosclerosis-associated genes, has been developed, offering an accurate diagnosis of atherosclerosis.
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Affiliation(s)
- Zunlan Zhao
- Department of General Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shouhang Chen
- Department of Infectious Diseases, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Henan, China
| | - Hongzhao Wei
- Department of Oncology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Weile Ma
- Department of General Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Weili Shi
- Department of General Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yixin Si
- Department of General Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jun Wang
- Department of General Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liuyi Wang
- Department of General Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiqing Li
- Department of Oncology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Ukkat J, Rebelo A, Trojanowicz B. Angiogenetic transcriptional profiling reveals potential targets modulated in blood of patients with cardiovascular disorders. Vascular 2023; 31:152-162. [PMID: 34816786 DOI: 10.1177/17085381211052379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Based on the angiogenetic, transcriptional profile of non-diseased and arteriosclerotic vessels, we aim to identify the leucocytic markers as a potential, minimal invasive tool supporting diagnosis of vascular pathology. METHODS Transcriptional profiling was performed with Angiogenesis RT2 Profiler PCR (Polymerase Chain Reaction) array on three non-pathological and three arteriosclerotic vessels, followed by immunohistochemical staining. Based on these screening results, selected transcripts were employed for qPCR with specific primers and investigated on the blood RNA (RiboNucleic Acid) obtained from nine healthy controls and 29 patients with cardiovascular disorders. Thereafter, expression of these transcripts was investigated in vitro in human monocytes under calcification-mimicking conditions. RESULTS AND CONCLUSIONS Transcriptional profiling on the vessels revealed that out of 84 targets investigated two were up-regulated more than 100-fold, 18 more than 30 and 15 more than 10, while the most noticeable down-regulation was observed by ephrin-A3 and platelet-derived growth factor alpha (PDGFA) genes. Based on the vessel results, investigations of the selected blood transcripts revealed that thrombospondin 1 (THBS1), thrombospondin 3 (THBS3), transforming growth factor, beta receptor 1 (TGFBR1), platelet-derived growth factor alpha, plasminogen activator, urokinase (PLAU) and platelet/endothelial cell adhesion molecule 1 (PECAM-1) were significantly elevated in cardiovascular blood as compared to corresponding controls. Induction of calcification-related conditions in vitro to human THP-1 monocytes led to noticeable modulation of these transcripts. Taken together, these data demonstrate that leucocytic THBS1, THBS3, TGFBR1, platelet-derived growth factor alpha, PLAU and PECAM-1 have a correlation with cardiovascular disorders and could be used as a supportive tool predicting development of this pathological condition.
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Affiliation(s)
- Joerg Ukkat
- Department of Visceral, Vascular and Endocrine Surgery, 9176Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Artur Rebelo
- Department of Visceral, Vascular and Endocrine Surgery, 9176Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Bogusz Trojanowicz
- Department of Visceral, Vascular and Endocrine Surgery, 9176Martin Luther University Halle-Wittenberg, Halle, Germany
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Milenkovic D, Rodriguez‐Mateos A, Lucosz M, Istas G, Declerck K, Sansone R, Deenen R, Köhrer K, Corral‐Jara KF, Altschmied J, Haendeler J, Kelm M, Berghe WV, Heiss C. Flavanol Consumption in Healthy Men Preserves Integrity of Immunological-Endothelial Barrier Cell Functions: Nutri(epi)genomic Analysis. Mol Nutr Food Res 2022; 66:e2100991. [PMID: 35094491 PMCID: PMC9787825 DOI: 10.1002/mnfr.202100991] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/16/2022] [Indexed: 12/30/2022]
Abstract
SCOPE While cocoa flavanol (CF) consumption improves cardiovascular risk biomarkers, molecular mechanisms underlying their protective effects are not understood. OBJECTIVE To investigate nutri(epi)genomic effects of CF and identify regulatory networks potential mediating vascular health benefits. METHODS AND RESULTS Twenty healthy middle-aged men consume CF (bi-daily 450 mg) or control drinks for 1 month. Microarray analysis identifies 2235 differentially expressed genes (DEG) involved in processes regulating immune response, cell adhesion, or cytoskeleton organization. Distinct patterns of DEG correlate with CF-related changes in endothelial function, arterial stiffness, and blood pressure. DEG profile negatively correlates with expression profiles of cardiovascular disease patients. CF modulated DNA methylation profile of genes implicates in cell adhesion, actin cytoskeleton organization, or cell signaling. In silico docking analyses indicate that CF metabolites have the potential of binding to cell signaling proteins and transcription factors. Incubation of plasma obtained after CF consumption decrease monocyte to endothelial adhesion and dose-dependently increase nitric oxide-dependent chemotaxis of circulating angiogenic cells further validating the biological functions of CF metabolites. CONCLUSION In healthy humans, CF consumption may mediate vascular protective effects by modulating gene expression and DNA methylation towards a cardiovascular protective effect, in agreement with clinical results, by preserving integrity of immunological-endothelial barrier functions.
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Affiliation(s)
- Dragan Milenkovic
- Department of NutritionUniversity of California DavisDavisCA95616USA,INRAEUNHUniversité Clermont AuvergneClermont‐FerrandF‐63000France
| | - Ana Rodriguez‐Mateos
- Division of CardiologyPulmonology, and Vascular MedicineMedical FacultyUniversity Hospital DüsseldorfDüsseldorfGermany,Department of Nutritional SciencesSchool of Life Course and Population SciencesFaculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Margarete Lucosz
- Division of CardiologyPulmonology, and Vascular MedicineMedical FacultyUniversity Hospital DüsseldorfDüsseldorfGermany
| | - Geoffrey Istas
- Division of CardiologyPulmonology, and Vascular MedicineMedical FacultyUniversity Hospital DüsseldorfDüsseldorfGermany,Department of Nutritional SciencesSchool of Life Course and Population SciencesFaculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Ken Declerck
- PPESDepartment of Biomedical SciencesUniversity of Antwerp (UA)WilrijkBelgium
| | - Roberto Sansone
- Division of CardiologyPulmonology, and Vascular MedicineMedical FacultyUniversity Hospital DüsseldorfDüsseldorfGermany
| | - René Deenen
- Biological and Medical Research Center (BMFZ)Heinrich Heine UniversityDüsseldorfGermany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ)Heinrich Heine UniversityDüsseldorfGermany
| | | | - Joachim Altschmied
- Environmentally‐induced Cardiovascular DegenerationClinical Chemistry and Laboratory DiagnosticsMedical FacultyUniversity Hospital and Heinrich‐Heine UniversityDüsseldorfGermany,IUF‐Leibniz Research Institute for Environmental MedicineDüsseldorfGermany
| | - Judith Haendeler
- Environmentally‐induced Cardiovascular DegenerationClinical Chemistry and Laboratory DiagnosticsMedical FacultyUniversity Hospital and Heinrich‐Heine UniversityDüsseldorfGermany
| | - Malte Kelm
- Division of CardiologyPulmonology, and Vascular MedicineMedical FacultyUniversity Hospital DüsseldorfDüsseldorfGermany
| | - Wim Vanden Berghe
- PPESDepartment of Biomedical SciencesUniversity of Antwerp (UA)WilrijkBelgium
| | - Christian Heiss
- Division of CardiologyPulmonology, and Vascular MedicineMedical FacultyUniversity Hospital DüsseldorfDüsseldorfGermany,Clinical Medicine SectionDepartment of Clinical and Experimental MedicineFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK,Department of Vascular MedicineSurrey and Sussex NHS Healthcare TrustEast Surrey HospitalRedhillUK
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5
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The Genetic Architecture of the Etiology of Lower Extremity Peripheral Artery Disease: Current Knowledge and Future Challenges in the Era of Genomic Medicine. Int J Mol Sci 2022; 23:ijms231810481. [PMID: 36142394 PMCID: PMC9499674 DOI: 10.3390/ijms231810481] [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: 08/24/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022] Open
Abstract
Lower extremity artery disease (LEAD), caused by atherosclerotic obstruction of the arteries of the lower limb extremities, has exhibited an increase in mortality and morbidity worldwide. The phenotypic variability of LEAD is correlated with its complex, multifactorial etiology. In addition to traditional risk factors, it has been shown that the interaction between genetic factors (epistasis) or between genes and the environment potentially have an independent role in the development and progression of LEAD. In recent years, progress has been made in identifying genetic variants associated with LEAD, by Genome-Wide Association Studies (GWAS), Whole Exome Sequencing (WES) studies, and epigenetic profiling. The aim of this review is to present the current knowledge about the genetic factors involved in the etiopathogenic mechanisms of LEAD, as well as possible directions for future research. We analyzed data from the literature, starting with candidate gene-based association studies, and then continuing with extensive association studies, such as GWAS and WES. The results of these studies showed that the genetic architecture of LEAD is extremely heterogeneous. In the future, the identification of new genetic factors will allow for the development of targeted molecular therapies, and the use of polygenic risk scores (PRS) to identify individuals at an increased risk of LEAD will allow for early prophylactic measures and personalized therapy to improve their prognosis.
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6
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Normahani P, Boyle JJ, Cave L, Brookes P, Woollard KJ, Jaffer U. Peripheral blood mononuclear cell gene expression and cytokine profiling in patients with intermittent claudication who exhibit exercise induced acute renal injury. PLoS One 2022; 17:e0265393. [PMID: 35298547 PMCID: PMC8929566 DOI: 10.1371/journal.pone.0265393] [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: 04/05/2021] [Accepted: 03/02/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Intermittent claudication (IC) is a common manifestation of peripheral arterial disease. Some patients with IC experience a rise in Urinary N-acetyl-β-D-Glucosaminidase (NAG)/ Creatinine (Cr) ratio, a marker of renal injury, following exercise. In this study, we aim to investigate whether peripheral blood mononuclear cells (PBMC) from patients with IC who exhibit a rise in urinary NAG/ Cr ratio following exercise exhibit differential IL-10/ IL-12 ratio and gene expression compared to those who do not have a rise in NAG/ Cr ratio. METHODS We conducted a single center observational cohort study of patients diagnosed with IC. Blood and urine samples were collected at rest and following a standardised treadmill exercise protocol. For comparative analysis patients were separated into those with any rise in NAG/Cr ratio (Group 1) and those with no rise in NAG/Cr ratio (Group 2) post exercise. Isolated PBMC from pre- and post-exercise blood samples were analysed using flow cytometry. PBMC were also cultured for 20 hours to perform further analysis of IL-10 and IL-12 cytokine levels. RNA-sequencing analysis was performed to identify differentially expressed genes between the groups. RESULTS 20 patients were recruited (Group 1, n = 8; Group 2, n = 12). We observed a significantly higher IL-10/IL-12 ratio in cell supernatant from participants in Group 1, as compared to Group 2, on exercise at 20 hours incubation; 47.24 (IQR 9.70-65.83) vs 6.13 (4.88-12.24), p = 0.04. 328 genes were significantly differentially expressed between Group 1 and 2. The modulated genes had signatures encompassing hypoxia, metabolic adaptation to starvation, inflammatory activation, renal protection, and oxidative stress. DISCUSSION Our results suggest that some patients with IC have an altered immune status making them 'vulnerable' to systemic inflammation and renal injury following exercise. We have identified a panel of genes which are differentially expressed in this group of patients.
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Affiliation(s)
- Pasha Normahani
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom.,Department of Surgery and Cancer, Imperial college London, London, United Kingdom
| | - Joseph J Boyle
- National Heart and Ling Institute, Imperial College London, London, United Kingdom
| | - Luke Cave
- National Heart and Ling Institute, Imperial College London, London, United Kingdom
| | - Paul Brookes
- Department of Pathology, Royal Brompton and Harefield hospitals, London, United Kingdom
| | - Kevin J Woollard
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Usman Jaffer
- Imperial Vascular Unit, Imperial College Healthcare NHS Trust, London, United Kingdom.,Department of Surgery and Cancer, Imperial college London, London, United Kingdom
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7
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Qian Y, Zhang L, Sun Z, Zang G, Li Y, Wang Z, Li L. Biomarkers of Blood from Patients with Atherosclerosis Based on Bioinformatics Analysis. Evol Bioinform Online 2021; 17:11769343211046020. [PMID: 34594098 PMCID: PMC8477683 DOI: 10.1177/11769343211046020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
Atherosclerosis is a multifaceted disease characterized by the formation and accumulation of plaques that attach to arteries and cause cardiovascular disease and vascular embolism. A range of diagnostic techniques, including selective coronary angiography, stress tests, computerized tomography, and nuclear scans, assess cardiovascular disease risk and treatment targets. However, there is currently no simple blood biochemical index or biological target for the diagnosis of atherosclerosis. Therefore, it is of interest to find a biochemical blood marker for atherosclerosis. Three datasets from the Gene Expression Omnibus (GEO) database were analyzed to obtain differentially expressed genes (DEG) and the results were integrated using the Robustrankaggreg algorithm. The genes considered more critical by the Robustrankaggreg algorithm were put into their own data set and the data set system with cell classification information for verification. Twenty-one possible genes were screened out. Interestingly, we found a good correlation between RPS4Y1, EIF1AY, and XIST. In addition, we know the general expression of these genes in different cell types and whole blood cells. In this study, we identified BTNL8 and BLNK as having good clinical significance. These results will contribute to the analysis of the underlying genes involved in the progression of atherosclerosis and provide insights for the discovery of new diagnostic and evaluation methods.
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Affiliation(s)
- Yongjiang Qian
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lili Zhang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Zhen Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Guangyao Zang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yalan Li
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Zhongqun Wang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lihua Li
- Department of Pathology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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8
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Peripheral Vascular Disease and Kidney Transplant Outcomes: Rethinking an Important Ongoing Complication. Transplantation 2021; 105:1188-1202. [PMID: 33148978 DOI: 10.1097/tp.0000000000003518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Peripheral vascular disease (PVD) is highly prevalent in patients on the waiting list for kidney transplantation (KT) and after transplantation and is associated with impaired transplant outcomes. Multiple traditional and nontraditional risk factors, as well as uremia- and transplant-related factors, affect 2 processes that can coexist, atherosclerosis and arteriosclerosis, leading to PVD. Some pathogenic mechanisms, such as inflammation-related endothelial dysfunction, mineral metabolism disorders, lipid alterations, or diabetic status, may contribute to the development and progression of PVD. Early detection of PVD before and after KT, better understanding of the mechanisms of vascular damage, and application of suitable therapeutic approaches could all minimize the impact of PVD on transplant outcomes. This review focuses on the following issues: (1) definition, epidemiological data, diagnosis, risk factors, and pathogenic mechanisms in KT candidates and recipients; (2) adverse clinical consequences and outcomes; and (3) classical and new therapeutic approaches.
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Newman JD, Cornwell MG, Zhou H, Rockman C, Heguy A, Suarez Y, Cheng HS, Feinberg MW, Hochman JS, Ruggles KV, Berger JS. Gene Expression Signature in Patients With Symptomatic Peripheral Artery Disease. Arterioscler Thromb Vasc Biol 2021; 41:1521-1533. [PMID: 33657880 PMCID: PMC8048111 DOI: 10.1161/atvbaha.120.315857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Jonathan D. Newman
- Department of Medicine, Division of Cardiology and the Center for the Prevention of Cardiovascular Disease
| | - MacIntosh G. Cornwell
- Department of Medicine, Division of Translational Medicine
- Institute of Systems Genetics
| | - Hua Zhou
- Applied Bioinformatics Laboratories
| | - Caron Rockman
- Department of Surgery, Division of Vascular Surgery, New York University School of Medicine, New York, NY, 10016
| | - Adriana Heguy
- Department of Pathology, NYU School of Medicine
- Genome Technology Center, Division of Advanced Research Technologies, NYU School of Medicine
| | - Yajaira Suarez
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
| | - Henry S. Cheng
- Department of Surgery, Division of Vascular Surgery, New York University School of Medicine, New York, NY, 10016
| | - Mark W. Feinberg
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA 02115
| | - Judith S. Hochman
- Department of Medicine, Division of Cardiology and the Center for the Prevention of Cardiovascular Disease
| | - Kelly V. Ruggles
- Department of Medicine, Division of Translational Medicine
- Institute of Systems Genetics
| | - Jeffrey S. Berger
- Department of Medicine, Division of Cardiology and the Center for the Prevention of Cardiovascular Disease
- Department of Surgery, Division of Vascular Surgery, New York University School of Medicine, New York, NY, 10016
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10
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Seifert S, Gundlach S, Junge O, Szymczak S. Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. Bioinformatics 2021; 36:4301-4308. [PMID: 32399562 PMCID: PMC7520048 DOI: 10.1093/bioinformatics/btaa483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION High-throughput technologies allow comprehensive characterization of individuals on many molecular levels. However, training computational models to predict disease status based on omics data is challenging. A promising solution is the integration of external knowledge about structural and functional relationships into the modeling process. We compared four published random forest-based approaches using two simulation studies and nine experimental datasets. RESULTS The self-sufficient prediction error approach should be applied when large numbers of relevant pathways are expected. The competing methods hunting and learner of functional enrichment should be used when low numbers of relevant pathways are expected or the most strongly associated pathways are of interest. The hybrid approach synthetic features is not recommended because of its high false discovery rate. AVAILABILITY AND IMPLEMENTATION An R package providing functions for data analysis and simulation is available at GitHub (https://github.com/szymczak-lab/PathwayGuidedRF). An accompanying R data package (https://github.com/szymczak-lab/DataPathwayGuidedRF) stores the processed and quality controlled experimental datasets downloaded from Gene Expression Omnibus (GEO). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stephan Seifert
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Sven Gundlach
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel 24105, Germany
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11
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Kalinin RE, Suchkov IA, Shumskaia EI, Mzhavanadze ND, Uporov MM, Nekliudov MS. [Study of gene expression in patients with peripheral artery disease]. ANGIOLOGIIA I SOSUDISTAIA KHIRURGIIA = ANGIOLOGY AND VASCULAR SURGERY 2021; 27:11-16. [PMID: 35050244 DOI: 10.33529/angio2021410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Currently, there are no widely used available techniques for reliable prognosis of the onset and course of peripheral artery disease. Working out of optimal test systems including genetic ones for assessment of risks for the development of the disease, its progression or development of complications in patients with peripheral atherosclerosis is an important mission of modern medicine. This article deals with a promising technique of genetic studies in patients with peripheral artery disease, i. e., study of gene expression. Also provided herein is a literature review devoted to the main techniques used for the analysis of the profile of gene expression. This is followed by evaluating the possibility of using DNA chips, as well as describing the state of the art and unsolved problems of studying gene expression in patients with peripheral artery disease.
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Affiliation(s)
- R E Kalinin
- I.P. Pavlov Ryazan State Medical University of the RF Ministry of Public Health, Ryazan, Russia
| | - I A Suchkov
- I.P. Pavlov Ryazan State Medical University of the RF Ministry of Public Health, Ryazan, Russia
| | - E I Shumskaia
- I.P. Pavlov Ryazan State Medical University of the RF Ministry of Public Health, Ryazan, Russia
| | - N D Mzhavanadze
- I.P. Pavlov Ryazan State Medical University of the RF Ministry of Public Health, Ryazan, Russia
| | - M M Uporov
- I.P. Pavlov Ryazan State Medical University of the RF Ministry of Public Health, Ryazan, Russia
| | - M S Nekliudov
- I.P. Pavlov Ryazan State Medical University of the RF Ministry of Public Health, Ryazan, Russia
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12
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Zöller B, Svensson PJ, Huang W, Jianguang J. Reactome Pathway Analysis of Venous Thromboembolism, Peripheral Artery Disease, Stroke, and Coronary Artery Disease. Thromb Haemost 2020; 121:964-966. [PMID: 33212516 DOI: 10.1055/a-1315-2307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Bengt Zöller
- Department of Clinical Sciences, Center for Primary Health Care Research, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Peter J Svensson
- Department of Coagulation Disorders, Skåne University Hospital, Lund University, Lund, Sweden
| | - Wuqing Huang
- Department of Clinical Sciences, Center for Primary Health Care Research, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Ji Jianguang
- Department of Clinical Sciences, Center for Primary Health Care Research, Skåne University Hospital, Lund University, Malmö, Sweden
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13
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Juarez PD, Hood DB, Song MA, Ramesh A. Use of an Exposome Approach to Understand the Effects of Exposures From the Natural, Built, and Social Environments on Cardio-Vascular Disease Onset, Progression, and Outcomes. Front Public Health 2020; 8:379. [PMID: 32903514 PMCID: PMC7437454 DOI: 10.3389/fpubh.2020.00379] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
Obesity, diabetes, and hypertension have increased by epidemic proportions in recent years among African Americans in comparison to Whites resulting in significant adverse cardiovascular disease (CVD) disparities. Today, African Americans are 30% more likely to die of heart disease than Whites and twice as likely to have a stroke. The causes of these disparities are not yet well-understood. Improved methods for identifying underlying risk factors is a critical first step toward reducing Black:White CVD disparities. This article will focus on environmental exposures in the external environment and how they can lead to changes at the cellular, molecular, and organ level to increase the personal risk for CVD and lead to population level CVD racial disparities. The external environment is defined in three broad domains: natural (air, water, land), built (places you live, work, and play) and social (social, demographic, economic, and political). We will describe how environmental exposures in the natural, built, and social environments "get under the skin" to affect gene expression though epigenetic, pan-omics, and related mechanisms that lead to increased risk for adverse CVD health outcomes and population level disparities. We also will examine the important role of metabolomics, proteomics, transcriptomics, genomics, and epigenomics in understanding how exposures in the natural, built, and social environments lead to CVD disparities with implications for clinical, public health, and policy interventions. In this review, we apply an exposome approach to Black:White CVD racial disparities. The exposome is a measure of all the exposures of an individual across the life course and the relationship of those exposures to health effects. The exposome represents the totality of exogenous (external) and endogenous (internal) exposures from conception onwards, simultaneously distinguishing, characterizing, and quantifying etiologic, mediating, moderating, and co-occurring risk and protective factors and their relationship to disease. Specifically, it assesses the biological mechanisms and underlying pathways through which chemical and non-chemical environmental exposures are associated with CVD onset, progression and outcomes. The exposome is a promising approach for understanding the complex relationships among environment, behavior, biology, genetics, and disease phenotypes that underlie population level, Black: White CVD disparities.
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Affiliation(s)
- Paul D Juarez
- Meharry Medical College, Nashville, TN, United States
| | - Darryl B Hood
- College of Public Health, The Ohio State University, Columbus, OH, United States
| | - Min-Ae Song
- College of Public Health, The Ohio State University, Columbus, OH, United States
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14
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Hounkpe BW, Benatti RDO, Carvalho BDS, De Paula EV. Identification of common and divergent gene expression signatures in patients with venous and arterial thrombosis using data from public repositories. PLoS One 2020; 15:e0235501. [PMID: 32780732 PMCID: PMC7418995 DOI: 10.1371/journal.pone.0235501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/17/2020] [Indexed: 12/31/2022] Open
Abstract
STRENGTHS AND LIMITATIONS OF THIS STUDY Our results represent the first comparison of venous and arterial thrombosis at the transcriptomic level.Our main result was the demonstration that immunothrombosis pathways are important to the pathophysiology of these conditions, also at the transcriptomic level.A specific signature for venous and arterial thrombosis was described, and validated in independent cohorts.The limited number of public repositories with gene expression data from patients with venous thromboembolism limits the representation of these patients in our analyses.In order to gather a meaningful number of studies with gene expression data we had to include patients in different time-points since the index thrombotic event, which might have increased the heterogeneity of our population.
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Affiliation(s)
| | | | - Benilton de Sá Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas, Campinas, SP, Brazil
| | - Erich Vinicius De Paula
- School of Medical Sciences, University of Campinas, Campinas, SP, Brazil
- Hematology and Hemotherapy Center, University of Campinas, Campinas, SP, Brazil
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15
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Logan JG, Yun S, Bao Y, Farber E, Farber CR. RNA-sequencing analysis of differential gene expression associated with arterial stiffness. Vascular 2020; 28:655-663. [PMID: 32375599 DOI: 10.1177/1708538120922650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Arterial stiffness is recognized as an important predictor of cardiovascular disease morbidity and mortality, independent of traditional cardiovascular disease risk factors. Given that arterial tissue is not easily accessible, most gene expression studies on arterial stiffness have been conducted on animals or on patients who have undergone by-pass surgeries. In order to obtain a deeper understanding of early changes of arterial stiffness, this study compared transcriptome profiles between healthy adults with higher and lower arterial stiffness. METHODS The sample included 20 healthy female adults without cardiovascular disease. Arterial stiffness was measured by carotid-femoral pulse wave velocity, the "gold-standard" measure of central arterial stiffness. Peripheral blood samples collected to PAXgene™ RNA tubes were used for RNA sequencing (RNA-seq). The potential confounding effects of age, body mass index, and mean arterial pressure were controlled for in RNA-seq analysis. To validate RNA-seq results, quantitative real-time PCR (qRT-PCR) was performed for six selected genes. RESULTS The findings demonstrated that genes including CAPN9, IL32, ERAP2, RAB6B, MYBPH, and miRNA626 were down-regulated, and that MOCS1 gene was up-regulated among the people with higher arterial stiffness. Real-time PCR showed that the changes of CAPN9, IL32, ERAP2, and RAB6B were in concordance with RNA-seq data, and confirmed the validity of the gene expression profiles obtained by RNA-seq analysis. CONCLUSIONS Previous studies have suggested the potential roles of CAPN9, IL32, and ERAP2 in structural changes of the arterial wall through up-regulation of metalloproteinases. However, the current study showed that CAPN9, IL32, and ERAP2 were down-regulated in the individuals with higher arterial stiffness, compared with those with lower arterial stiffness. The unexpected directions of expression of these genes may indicate an effort to maintain vascular homeostasis during increased arterial stiffness among healthy individuals. Further studies are guaranteed to investigate the roles of CAPN9, IL32, and ERAP2 in regulating arterial stiffness in people with and without cardiovascular disease.
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Affiliation(s)
| | | | - Yongde Bao
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, USA
| | - Emily Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, USA
| | - Charles R Farber
- Department of Public Health Sciences and Biochemistry and Molecular Genetics, Center for Public Health Genomics, University of Virginia, Charlottesville, USA
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16
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van der Heijden CDCC, Smeets EMM, Aarntzen EHJG, Noz MP, Monajemi H, Kersten S, Kaffa C, Hoischen A, Deinum J, Joosten LAB, Netea MG, Riksen NP. Arterial Wall Inflammation and Increased Hematopoietic Activity in Patients With Primary Aldosteronism. J Clin Endocrinol Metab 2020; 105:5686861. [PMID: 31875423 PMCID: PMC7105350 DOI: 10.1210/clinem/dgz306] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022]
Abstract
CONTEXT Primary aldosteronism (PA) confers an increased risk of cardiovascular disease (CVD), independent of blood pressure. Animal models have shown that aldosterone accelerates atherosclerosis through proinflammatory changes in innate immune cells; human data are scarce. OBJECTIVE The objective of this article is to explore whether patients with PA have increased arterial wall inflammation, systemic inflammation, and reprogramming of monocytes. DESIGN A cross-sectional cohort study compared vascular inflammation on 2'-deoxy-2'-(18F)fluoro-D-glucose; (18F-FDG) positron emission tomography-computed tomography, systemic inflammation, and monocyte phenotypes and transcriptome between PA patients and controls. SETTING This study took place at Radboudumc and Rijnstate Hospital, the Netherlands. PATIENTS Fifteen patients with PA and 15 age-, sex-, and blood pressure-matched controls with essential hypertension (EHT) participated. MAIN OUTCOME MEASURES AND RESULTS PA patients displayed a higher arterial 18F-FDG uptake in the descending and abdominal aorta (P < .01, P < .05) and carotid and iliac arteries (both P < .01). In addition, bone marrow uptake was higher in PA patients (P < .05). Although PA patients had a higher monocyte-to-lymphocyte ratio (P < .05), systemic inflammatory markers, cytokine production capacity, and transcriptome of circulating monocytes did not differ. Monocyte-derived macrophages from PA patients expressed more TNFA; monocyte-derived macrophages of healthy donors cultured in PA serum displayed increased interleukin-6 and tumor necrosis factor-α production. CONCLUSIONS Because increased arterial wall inflammation is associated with accelerated atherogenesis and unstable plaques, this might importantly contribute to the increased CVD risk in PA patients. We did not observe inflammatory reprogramming of circulating monocytes. However, subtle inflammatory changes are present in the peripheral blood cell composition and monocyte transcriptome of PA patients, and in their monocyte-derived macrophages. Most likely, arterial inflammation in PA requires interaction between various cell types.
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Affiliation(s)
- Charlotte D C C van der Heijden
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Esther M M Smeets
- Department of Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erik H J G Aarntzen
- Department of Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marlies P Noz
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Houshang Monajemi
- Department of Internal Medicine, Rijnstate Hospital, Arnhem, the Netherlands
| | - Simone Kersten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Charlotte Kaffa
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medicine, University Hospital Dresden, Technische Universität, Dresden, Germany
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences 12 Institute, University of Bonn, Bonn, Germany
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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17
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Saenz-Pipaon G, San Martín P, Planell N, Maillo A, Ravassa S, Vilas-Zornoza A, Martinez-Aguilar E, Rodriguez JA, Alameda D, Lara-Astiaso D, Prosper F, Paramo JA, Orbe J, Gomez-Cabrero D, Roncal C. Functional and transcriptomic analysis of extracellular vesicles identifies calprotectin as a new prognostic marker in peripheral arterial disease (PAD). J Extracell Vesicles 2020; 9:1729646. [PMID: 32158521 PMCID: PMC7048174 DOI: 10.1080/20013078.2020.1729646] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023] Open
Abstract
Peripheral arterial disease (PAD) is associated with a high risk of cardiovascular events and death and is postulated to be a critical socioeconomic cost in the future. Extracellular vesicles (EVs) have emerged as potential candidates for new biomarker discovery related to their protein and nucleic acid cargo. In search of new prognostic and therapeutic targets in PAD, we determined the prothrombotic activity, the cellular origin and the transcriptomic profile of circulating EVs. This prospective study included control and PAD patients. Coagulation time (Procoag-PPL kit), EVs cellular origin and phosphatidylserine exposure were determined by flow cytometry in platelet-free plasma (n = 45 PAD). Transcriptomic profiles of medium/large EVs were generated using the MARS-Seq RNA-Seq protocol (n = 12/group). The serum concentration of the differentially expressed gene S100A9, in serum calprotectin (S100A8/A9), was validated by ELISA in control (n = 100) and PAD patients (n = 317). S100A9 was also determined in EVs and tissues of human atherosclerotic plaques (n = 3). Circulating EVs of PAD patients were mainly of platelet origin, predominantly Annexin V positive and were associated with the procoagulant activity of platelet-free plasma. Transcriptomic analysis of EVs identified 15 differentially expressed genes. Among them, serum calprotectin was elevated in PAD patients (p < 0.05) and associated with increased amputation risk before and after covariate adjustment (mean follow-up 3.6 years, p < 0.01). The combination of calprotectin with hs-CRP in the multivariate analysis further improved risk stratification (p < 0.01). Furthermore, S100A9 was also expressed in femoral plaque derived EVs and tissues. In summary, we found that PAD patients release EVs, mainly of platelet origin, highly positive for AnnexinV and rich in transcripts related to platelet biology and immune responses. Amputation risk prediction improved with calprotectin and was significantly higher when combined with hs-CRP. Our results suggest that EVs can be a promising component of liquid biopsy to identify the molecular signature of PAD patients.
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Affiliation(s)
- Goren Saenz-Pipaon
- Laboratory of Atherothrombosis, Program of Cardiovascular Diseases, Cima Universidad de Navarra, Pamplona, Spain.,IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Patxi San Martín
- Oncohematology Program, Cima Universidad de Navarra, Pamplona, Spain
| | - Núria Planell
- Translational Bioinformatics Unit, Navarrabiomed, Pamplona, Spain
| | - Alberto Maillo
- Translational Bioinformatics Unit, Navarrabiomed, Pamplona, Spain
| | - Susana Ravassa
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,Laboratory of Heart Failure, Program of Cardiovascular Diseases, Cima Universidad de Navarra, Pamplona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Amaia Vilas-Zornoza
- Oncohematology Program, Cima Universidad de Navarra, Pamplona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Esther Martinez-Aguilar
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,Departamento de Angiología y Cirugía Vascular, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - José Antonio Rodriguez
- Laboratory of Atherothrombosis, Program of Cardiovascular Diseases, Cima Universidad de Navarra, Pamplona, Spain.,IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Alameda
- Oncohematology Program, Cima Universidad de Navarra, Pamplona, Spain
| | | | - Felipe Prosper
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,Oncohematology Program, Cima Universidad de Navarra, Pamplona, Spain.,CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.,Hematology Service, Clínica Universidad de Navarra, Pamplona, Spain
| | - José Antonio Paramo
- Laboratory of Atherothrombosis, Program of Cardiovascular Diseases, Cima Universidad de Navarra, Pamplona, Spain.,IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Hematology Service, Clínica Universidad de Navarra, Pamplona, Spain
| | - Josune Orbe
- Laboratory of Atherothrombosis, Program of Cardiovascular Diseases, Cima Universidad de Navarra, Pamplona, Spain.,IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Carmen Roncal
- Laboratory of Atherothrombosis, Program of Cardiovascular Diseases, Cima Universidad de Navarra, Pamplona, Spain.,IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
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18
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Cooper DM, Radom-Aizik S. Exercise-associated prevention of adult cardiovascular disease in children and adolescents: monocytes, molecular mechanisms, and a call for discovery. Pediatr Res 2020; 87:309-318. [PMID: 31649340 PMCID: PMC11177628 DOI: 10.1038/s41390-019-0581-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 08/15/2019] [Indexed: 12/28/2022]
Abstract
Atherosclerosis originates in childhood and adolescence. The goal of this review is to highlight how exercise and physical activity during childhood and adolescence, critical periods of growth and development, can prevent adult cardiovascular disease (CVD), particularly through molecular mechanisms of monocytes, a key cell of the innate immune system. Monocytes are heterogeneous and pluripotential cells that can, paradoxically, play a role in both the instigation and prevention of atherosclerosis. Recent discoveries in young adults reveal that brief exercise affects monocyte gene pathways promoting a cell phenotype that patrols the vascular system and repairs injuries. Concurrently, exercise inhibits pro-inflammatory monocytes, cells that contribute to vascular damage and plaque formation. Because CVD is typically asymptomatic in youth, minimally invasive techniques must be honed to study the subtle anatomic and physiologic evidence of vascular dysfunction. Exercise gas exchange and heart rate measures can be combined with ultrasound assessments of vascular anatomy and reactivity, and near-infrared spectroscopy to quantify impaired O2 transport that is often hidden at rest. Combined with functional, transcriptomic, and epigenetic monocyte expression and measures of monocyte-endothelium interaction, molecular mechanisms of early CVD can be formulated, and then translated into effective physical activity-based strategies in youth to prevent adult-onset CVD.
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Affiliation(s)
- Dan M Cooper
- Pediatric Exercise and Genomics Research Center, University of California Irvine School of Medicine, Pediatrics, Irvine, CA, USA.
| | - Shlomit Radom-Aizik
- Pediatric Exercise and Genomics Research Center, University of California Irvine School of Medicine, Pediatrics, Irvine, CA, USA
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19
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Pizzimenti M, Riou M, Charles AL, Talha S, Meyer A, Andres E, Chakfé N, Lejay A, Geny B. The Rise of Mitochondria in Peripheral Arterial Disease Physiopathology: Experimental and Clinical Data. J Clin Med 2019; 8:jcm8122125. [PMID: 31810355 PMCID: PMC6947197 DOI: 10.3390/jcm8122125] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/21/2022] Open
Abstract
Peripheral arterial disease (PAD) is a frequent and serious condition, potentially life-threatening and leading to lower-limb amputation. Its pathophysiology is generally related to ischemia-reperfusion cycles, secondary to reduction or interruption of the arterial blood flow followed by reperfusion episodes that are necessary but also—per se—deleterious. Skeletal muscles alterations significantly participate in PAD injuries, and interestingly, muscle mitochondrial dysfunctions have been demonstrated to be key events and to have a prognosis value. Decreased oxidative capacity due to mitochondrial respiratory chain impairment is associated with increased release of reactive oxygen species and reduction of calcium retention capacity leading thus to enhanced apoptosis. Therefore, targeting mitochondria might be a promising therapeutic approach in PAD.
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Affiliation(s)
- Mégane Pizzimenti
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Physiology and Functional Exploration Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
| | - Marianne Riou
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Physiology and Functional Exploration Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
| | - Anne-Laure Charles
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
| | - Samy Talha
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Physiology and Functional Exploration Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
| | - Alain Meyer
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Physiology and Functional Exploration Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
| | - Emmanuel Andres
- Internal Medicine, Diabete and Metabolic Diseases Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France;
| | - Nabil Chakfé
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Vascular Surgery and Kidney Transplantation Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
| | - Anne Lejay
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Vascular Surgery and Kidney Transplantation Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
| | - Bernard Geny
- Unistra, Translational Medicine Federation of Strasbourg (FMTS), Faculty of Medicine, Team 3072 «Mitochondria, Oxidative Stress and Muscle Protection», 11 Rue Humann, 67000 Strasbourg, France; (M.P.); (M.R.); (A.-L.C.); (S.T.); (A.M.); (A.L.)
- Physiology and Functional Exploration Service, University Hospital of Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg CEDEX, France
- Correspondence:
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20
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Sun Y, Gao Y, Song T, Yu C, Nie Z, Wang X. MicroRNA-15b participates in the development of peripheral arterial disease by modulating the growth of vascular smooth muscle cells. Exp Ther Med 2019; 18:77-84. [PMID: 31258640 PMCID: PMC6566083 DOI: 10.3892/etm.2019.7552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 02/06/2019] [Indexed: 12/21/2022] Open
Abstract
As an atherosclerotic disease, the process of peripheral arterial disease (PAD) is complicated and includes the abnormal proliferation of vascular smooth muscle. The current study aimed to determine the role of microRNA-15b (miR-15b) in the development of PAD and its associated mechanisms. Human vascular smooth muscle cells (hVSMCs) were used in the current study. To assess the effects of miR-15b on hVSMCs, miR-15b was up- or downregulated in hVSMCs using miR-15b mimics or miR-15b inhibitors respectively. Cell viability, migration and apoptosis were then determined via MTT, transwell and flow cytometry assays, respectively. TargetScan bioinformatics software was utilized to predict the targets of miR-15b, and the binding sites between insulin growth factor 1 receptor (IGF1R) and miR-15b were confirmed by dual-luciferase reporter assay. The results reveled that the miR-15b mimic significantly reduced hVSMC cell viability and migration, and promoted cell apoptosis. However, the opposite effect was observed following miR-15b inhibitor transfection. It was also determined that miR-15b directly targeted IGF1R and negatively regulated its expression in hVSMCs. Additionally, the results demonstrated that the miR-15b mimic inhibited the PI3K/AKT signaling pathway in hVSMCs, whereas the miR-15b inhibitor promoted it. Furthermore, the results indicated that the effect of the miR-15b mimic on hVSMCs was reversed by IGF1R overexpression. In conclusion, the data indicated that miR-15b participated in the occurrence and development of PAD by modulating hVSMC proliferation, apoptosis and migration via the regulation of IGF1R expression.
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Affiliation(s)
- Yong Sun
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yong Gao
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Tao Song
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Chaowen Yu
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Zhonglin Nie
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Xiaogao Wang
- Department of Vascular Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
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21
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Schiffman C, McHale CM, Hubbard AE, Zhang L, Thomas R, Vermeulen R, Li G, Shen M, Rappaport SM, Yin S, Lan Q, Smith MT, Rothman N. Identification of gene expression predictors of occupational benzene exposure. PLoS One 2018; 13:e0205427. [PMID: 30300410 PMCID: PMC6177191 DOI: 10.1371/journal.pone.0205427] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Previously, using microarrays and mRNA-Sequencing (mRNA-Seq) we found that occupational exposure to a range of benzene levels perturbed gene expression in peripheral blood mononuclear cells. OBJECTIVES In the current study, we sought to identify gene expression biomarkers predictive of benzene exposure below 1 part per million (ppm), the occupational standard in the U.S. METHODS First, we used the nCounter platform to validate altered expression of 30 genes in 33 unexposed controls and 57 subjects exposed to benzene (<1 to ≥5 ppm). Second, we used SuperLearner (SL) to identify a minimal number of genes for which altered expression could predict <1 ppm benzene exposure, in 44 subjects with a mean air benzene level of 0.55±0.248 ppm (minimum 0.203ppm). RESULTS nCounter and microarray expression levels were highly correlated (coefficients >0.7, p<0.05) for 26 microarray-selected genes. nCounter and mRNA-Seq levels were poorly correlated for 4 mRNA-Seq-selected genes. Using negative binomial regression with adjustment for covariates and multiple testing, we confirmed differential expression of 23 microarray-selected genes in the entire benzene-exposed group, and 27 genes in the <1 ppm-exposed subgroup, compared with the control group. Using SL, we identified 3 pairs of genes that could predict <1 ppm benzene exposure with cross-validated AUC estimates >0.9 (p<0.0001) and were not predictive of other exposures (nickel, arsenic, smoking, stress). The predictive gene pairs are PRG2/CLEC5A, NFKBI/CLEC5A, and ACSL1/CLEC5A. They play roles in innate immunity and inflammatory responses. CONCLUSIONS Using nCounter and SL, we validated the altered expression of multiple mRNAs by benzene and identified gene pairs predictive of exposure to benzene at levels below the US occupational standard of 1ppm.
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Affiliation(s)
- Courtney Schiffman
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Cliona M. McHale
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Alan E. Hubbard
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Luoping Zhang
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Reuben Thomas
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Roel Vermeulen
- Institute of Risk assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Guilan Li
- Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Min Shen
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, United States of America
| | - Stephen M. Rappaport
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Songnian Yin
- Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing Lan
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, United States of America
| | - Martyn T. Smith
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, United States of America
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22
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A Network-Biology Informed Computational Drug Repositioning Strategy to Target Disease Risk Trajectories and Comorbidities of Peripheral Artery Disease. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2018; 2017:108-117. [PMID: 29888052 PMCID: PMC5961807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, drug discovery approaches focus on the design of therapies that alleviate an index symptom by reengineering the underlying biological mechanism in agonistic or antagonistic fashion. For example, medicines are routinely developed to target an essential gene that drives the disease mechanism. Therapeutic overloading where patients get multiple medications to reduce the primary and secondary side effect burden is standard practice. This single-symptom based approach may not be scalable, as we understand that diseases are more connected than random and molecular interactions drive disease comorbidities. In this work, we present a proof-of-concept drug discovery strategy by combining network biology, disease comorbidity estimates, and computational drug repositioning, by targeting the risk factors and comorbidities of peripheral artery disease, a vascular disease associated with high morbidity and mortality. Individualized risk estimation and recommending disease sequelae based therapies may help to lower the mortality and morbidity of peripheral artery disease.
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23
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Wan M, Bennett BD, Pittman GS, Campbell MR, Reynolds LM, Porter DK, Crowl CL, Wang X, Su D, Englert NA, Thompson IJ, Liu Y, Bell DA. Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:047015. [PMID: 29706059 PMCID: PMC6071796 DOI: 10.1289/ehp2395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Cigarette smoke is a causal factor in cancers and cardiovascular disease. Smoking-associated differentially methylated regions (SM-DMRs) have been observed in disease studies, but the causal link between altered DNA methylation and transcriptional change is obscure. OBJECTIVE Our objectives were to finely resolve SM-DMRs and to interrogate the mechanistic link between SM-DMRs and altered transcription of enhancer noncoding RNA (eRNA) and mRNA in human circulating monocytes. METHOD We integrated SM-DMRs identified by reduced representation bisulfite sequencing (RRBS) of circulating CD14+ monocyte DNA collected from two independent human studies [n=38 from Clinical Research Unit (CRU) and n=55 from the Multi-Ethnic Study of Atherosclerosis (MESA), about half of whom were active smokers] with gene expression for protein-coding genes and noncoding RNAs measured by RT-PCR or RNA sequencing. Candidate SM-DMRs were compared with RRBS of purified CD4+ T cells, CD8+ T cells, CD15+ granulocytes, CD19+ B cells, and CD56+ NK cells (n=19 females, CRU). DMRs were validated using pyrosequencing or bisulfite amplicon sequencing in up to 85 CRU volunteers, who also provided saliva DNA. RESULTS RRBS identified monocyte SM-DMRs frequently located in putative gene regulatory regions. The most significant monocyte DMR occurred at a poised enhancer in the aryl-hydrocarbon receptor repressor gene (AHRR) and it was also detected in both granulocytes and saliva DNA. To our knowledge, we identify for the first time that SM-DMRs in or near AHRR, C5orf55-EXOC-AS, and SASH1 were associated with increased noncoding eRNA as well as mRNA in monocytes. Functionally, the AHRR SM-DMR appeared to up-regulate AHRR mRNA through activating the AHRR enhancer, as suggested by increased eRNA in the monocytes, but not granulocytes, from smokers compared with nonsmokers. CONCLUSIONS Our findings suggest that AHRR SM-DMR up-regulates AHRR mRNA in a monocyte-specific manner by activating the AHRR enhancer. Cell type-specific activation of enhancers at SM-DMRs may represent a mechanism driving smoking-related disease. https://doi.org/10.1289/EHP2395.
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Affiliation(s)
- Ma Wan
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - Gary S Pittman
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Michelle R Campbell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Devin K Porter
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Christopher L Crowl
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Dan Su
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Neal A Englert
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Isabel J Thompson
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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24
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Vogiatzi G, Oikonomou E, Deftereos S, Siasos G, Tousoulis D. Peripheral artery disease: a micro-RNA-related condition? Curr Opin Pharmacol 2018; 39:105-112. [PMID: 29679926 DOI: 10.1016/j.coph.2018.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/06/2017] [Accepted: 04/02/2018] [Indexed: 01/20/2023]
Abstract
Peripheral artery disease (PAD) is a vascular problem of diffuse atherosclerosis and is a major cause of cardiovascular morbidity and mortality. Many studies have tried to gain insight into the molecular mechanisms involved in PAD. Lately, highly stable circulating small noncoding RNAs, microRNAs (miRNAs), seem to have disease-specific expression. Thus, miRNAs are emerging as new measurable diagnostic biomarkers and a start point for individualized treatment. To date, the association of miRNA regulation in angiogenesis and maintenance of vascular integrity in PAD has attracted little interest. In this review, we will provide an overview of studies regarding the roles of specific miRNAs in PAD and their potential to act as a minimally invasive tool for diagnosis and risk stratification.
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Affiliation(s)
- Georgia Vogiatzi
- 1st Department of Cardiology, 'Hippokration' Hospital, University of Athens, Medical School, Athens, Greece
| | - Evangelos Oikonomou
- 1st Department of Cardiology, 'Hippokration' Hospital, University of Athens, Medical School, Athens, Greece
| | - Spyridon Deftereos
- 1st Department of Cardiology, 'Hippokration' Hospital, University of Athens, Medical School, Athens, Greece
| | - Gerasimos Siasos
- 1st Department of Cardiology, 'Hippokration' Hospital, University of Athens, Medical School, Athens, Greece
| | - Dimitris Tousoulis
- 1st Department of Cardiology, 'Hippokration' Hospital, University of Athens, Medical School, Athens, Greece.
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25
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Lucatelli P, Fagnani C, Tarnoki AD, Tarnoki DL, Sacconi B, Fejer B, Stazi MA, Salemi M, Cirelli C, d'Adamo A, Fanelli F, Catalano C, Maurovich-Horvat P, Jermendy AL, Jermendy G, Merkely B, Molnar AA, Pucci G, Schillaci G, Farina F, Meneghetti G, Baracchini C, Medda E. Genetic influence on femoral plaque and its relationship with carotid plaque: an international twin study. Int J Cardiovasc Imaging 2017; 34:531-541. [PMID: 29022127 DOI: 10.1007/s10554-017-1256-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/06/2017] [Indexed: 01/26/2023]
Abstract
To disentangle genetic and environmental influences on the development of femoral plaques using a population of adult twins. To evaluate the potential role of shared genetic and environmental factors in the co-occurrence of femoral and carotid plaques. The sample included 566 twins belonging to 164 monozygotic (MZ) and 119 dizygotic (DZ) twin pairs, who underwent peripheral arterial assessment by B-mode ultrasound in different centers. The variance in femoral plaques onset was due to genetic factors and the remaining 50% was explained by common (15%) and unique (35%) environmental factors. Findings on sidedness and number of femoral plaques indicated that also these traits were mainly under genetic control. No effect of common environment was found on plaques composition, and variability of this trait was explained by genetics (64%) and unique environment (36%). Covariation between the liabilities to carotid and femoral plaques was mainly attributed to shared genes (77%), with the remaining 23% explained by individual-specific environmental factors shared by the two districts. Inter-individual differences in plaque onset as well as in their number, sidedness and composition are mainly genetic in origin. The results on the cooccurrence of carotid and femoral plaque underline the genetic role in atherogenesis.
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Affiliation(s)
- Pierleone Lucatelli
- Vascular and Interventional Radiology Unit, Department of Radiology, Oncology and Anatomic Pathology, Policlinico Umberto I, "Sapienza" University of Rome, Rome, Italy.
| | - Corrado Fagnani
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Adam Domonkos Tarnoki
- Department of Radiology, Semmelweis University, Budapest, Hungary.,Hungarian Twin Registry, Budapest, Hungary
| | - David Laszlo Tarnoki
- Department of Radiology, Semmelweis University, Budapest, Hungary.,Hungarian Twin Registry, Budapest, Hungary
| | - Beatrice Sacconi
- Vascular and Interventional Radiology Unit, Department of Radiology, Oncology and Anatomic Pathology, Policlinico Umberto I, "Sapienza" University of Rome, Rome, Italy
| | - Bence Fejer
- Department of Radiology, Semmelweis University, Budapest, Hungary
| | - Maria Antonietta Stazi
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Miriam Salemi
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Carlo Cirelli
- Vascular and Interventional Radiology Unit, Department of Radiology, Oncology and Anatomic Pathology, Policlinico Umberto I, "Sapienza" University of Rome, Rome, Italy
| | - Alessandro d'Adamo
- Vascular and Endovascular Surgery Division, Department of Surgery "Paride Stefanini", Policlinico Umberto I, "Sapienza" University of Rome, Rome, Italy
| | - Fabrizio Fanelli
- Vascular and Interventional Radiology Unit, Department of Radiology, Oncology and Anatomic Pathology, Policlinico Umberto I, "Sapienza" University of Rome, Rome, Italy
| | - Carlo Catalano
- Vascular and Interventional Radiology Unit, Department of Radiology, Oncology and Anatomic Pathology, Policlinico Umberto I, "Sapienza" University of Rome, Rome, Italy
| | - Pal Maurovich-Horvat
- MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Adam L Jermendy
- MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Gyorgy Jermendy
- 3rd Department of Internal Medicine, Bajcsy Zsilinszky Hospital, Budapest, Hungary
| | - Bela Merkely
- MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Andrea A Molnar
- MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Giacomo Pucci
- Unità di Medicina Interna, Ospedale 'S. Maria', Università di Perugia, Terni, Italy
| | - Giuseppe Schillaci
- Unità di Medicina Interna, Ospedale 'S. Maria', Università di Perugia, Terni, Italy
| | - Filippo Farina
- Department of Neurosciences, University of Padua School of Medicine, Padua, Italy
| | - Giorgio Meneghetti
- Department of Neurosciences, University of Padua School of Medicine, Padua, Italy
| | - Claudio Baracchini
- Department of Neurosciences, University of Padua School of Medicine, Padua, Italy
| | - Emanuela Medda
- Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
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26
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Park BR, Ma JK, Park KB, Hong KW. Recapitulation of Genome-wide Association Study on Chronic Periodontitis in a Korean Population. ACTA ACUST UNITED AC 2017. [DOI: 10.15616/bsl.2017.23.2.133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bo-Ruem Park
- TheragenEtex Bio Institute, Suwon, Gyeonggi-do 16229, Korea
| | | | | | - Kyung-Won Hong
- TheragenEtex Bio Institute, Suwon, Gyeonggi-do 16229, Korea
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27
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Ward-Caviness CK, Neas LM, Blach C, Haynes CS, LaRocque-Abramson K, Grass E, Dowdy ZE, Devlin RB, Diaz-Sanchez D, Cascio WE, Miranda ML, Gregory SG, Shah SH, Kraus WE, Hauser ER. A genome-wide trans-ethnic interaction study links the PIGR-FCAMR locus to coronary atherosclerosis via interactions between genetic variants and residential exposure to traffic. PLoS One 2017; 12:e0173880. [PMID: 28355232 PMCID: PMC5371323 DOI: 10.1371/journal.pone.0173880] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 02/28/2017] [Indexed: 12/31/2022] Open
Abstract
Air pollution is a worldwide contributor to cardiovascular disease mortality and morbidity. Traffic-related air pollution is a widespread environmental exposure and is associated with multiple cardiovascular outcomes such as coronary atherosclerosis, peripheral arterial disease, and myocardial infarction. Despite the recognition of the importance of both genetic and environmental exposures to the pathogenesis of cardiovascular disease, studies of how these two contributors operate jointly are rare. We performed a genome-wide interaction study (GWIS) to examine gene-traffic exposure interactions associated with coronary atherosclerosis. Using race-stratified cohorts of 538 African-Americans (AA) and 1562 European-Americans (EA) from a cardiac catheterization cohort (CATHGEN), we identify gene-by-traffic exposure interactions associated with the number of significantly diseased coronary vessels as a measure of chronic atherosclerosis. We found five suggestive (P<1x10-5) interactions in the AA GWIS, of which two (rs1856746 and rs2791713) replicated in the EA cohort (P < 0.05). Both SNPs are in the PIGR-FCAMR locus and are eQTLs in lymphocytes. The protein products of both PIGR and FCAMR are implicated in inflammatory processes. In the EA GWIS, there were three suggestive interactions; none of these replicated in the AA GWIS. All three were intergenic; the most significant interaction was in a regulatory region associated with SAMSN1, a gene previously associated with atherosclerosis and B cell activation. In conclusion, we have uncovered several novel genes associated with coronary atherosclerosis in individuals chronically exposed to increased ambient concentrations of traffic air pollution. These genes point towards inflammatory pathways that may modify the effects of air pollution on cardiovascular disease risk.
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Affiliation(s)
- Cavin K. Ward-Caviness
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Lucas M. Neas
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Colette Blach
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Carol S. Haynes
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Karen LaRocque-Abramson
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Elizabeth Grass
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Z. Elaine Dowdy
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Robert B. Devlin
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - David Diaz-Sanchez
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Wayne E. Cascio
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Marie Lynn Miranda
- National Center for Geospatial Medicine, Rice University, Houston, TX, United States of America
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
| | - Svati H. Shah
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Division of Cardiology, Duke University School of Medicine, Durham, NC, United States of America
| | - William E. Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Division of Cardiology, Duke University School of Medicine, Durham, NC, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, United States of America
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States of America
- Cooperative Studies Program Epidemiology Center-Durham, Veterans Affairs Medical Center, Durham, NC, United States of America
- * E-mail:
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28
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Blood-based omic profiling supports female susceptibility to tobacco smoke-induced cardiovascular diseases. Sci Rep 2017; 7:42870. [PMID: 28225026 PMCID: PMC5320491 DOI: 10.1038/srep42870] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 01/16/2017] [Indexed: 12/11/2022] Open
Abstract
We recently reported that differential gene expression and DNA methylation profiles in blood leukocytes of apparently healthy smokers predicts with remarkable efficiency diseases and conditions known to be causally associated with smoking, suggesting that blood-based omic profiling of human populations may be useful for linking environmental exposures to potential health effects. Here we report on the sex-specific effects of tobacco smoking on transcriptomic and epigenetic features derived from genome-wide profiling in white blood cells, identifying 26 expression probes and 92 CpG sites, almost all of which are affected only in female smokers. Strikingly, these features relate to numerous genes with a key role in the pathogenesis of cardiovascular disease, especially thrombin signaling, including the thrombin receptors on platelets F2R (coagulation factor II (thrombin) receptor; PAR1) and GP5 (glycoprotein 5), as well as HMOX1 (haem oxygenase 1) and BCL2L1 (BCL2-like 1) which are involved in protection against oxidative stress and apoptosis, respectively. These results are in concordance with epidemiological evidence of higher female susceptibility to tobacco-induced cardiovascular disease and underline the potential of blood-based omic profiling in hazard and risk assessment.
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29
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Kini AS, Vengrenyuk Y, Shameer K, Maehara A, Purushothaman M, Yoshimura T, Matsumura M, Aquino M, Haider N, Johnson KW, Readhead B, Kidd BA, Feig JE, Krishnan P, Sweeny J, Milind M, Moreno P, Mehran R, Kovacic JC, Baber U, Dudley JT, Narula J, Sharma S. Intracoronary Imaging, Cholesterol Efflux, and Transcriptomes After Intensive Statin Treatment. J Am Coll Cardiol 2017; 69:628-640. [DOI: 10.1016/j.jacc.2016.10.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022]
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30
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Yin DX, Zhao HM, Sun DJ, Yao J, Ding DY. Identification of candidate target genes for human peripheral arterial disease using weighted gene co‑expression network analysis. Mol Med Rep 2015; 12:8107-12. [PMID: 26498853 DOI: 10.3892/mmr.2015.4450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 09/16/2015] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to identify the potential treatment targets of peripheral arterial disease (PAD) and provide further insights into the underlying mechanism of PAD, based on a weighted gene co‑expression network analysis (WGCNA) method. The mRNA expression profiles (accession. no. GSE27034), which included 19 samples from patients with PAD and 18 samples from normal control individuals were extracted from the Gene Expression Omnibus database. Subsequently, the differentially expressed genes (DEGs) were obtained using the Limma package and the co‑expression network modules were screened using the WGCNA approach. In addition, the protein‑protein interaction network for the DEGs in the most significant module was constructed using Cytoscape software. Functional enrichment analyses of the DEGs in the most significant module were also performed using the Database for Annotation, Visualization and Integrated Discovery and Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology‑Based Annotation System, respectively. A total of 148 DEGs were identified in PAD, which were used to construct the WGCN, in which two modules (gray module and turquoise module) were identified, with the gray module exhibiting a higher gene significance (GS) value than the turquoise module. In addition, a co‑expression network was constructed for 60 DEGs in the gray module. The functional enrichment results showed that the DEGs in the gray module were enriched in five Gene Ontology terms and four KEGG pathways. For example, cyclin‑dependent kinase inhibitor 1A (CDKN1A), FBJ murine osteosarcoma viral oncogene homolog (FOS) and prostaglandin‑endoperoxide synthase 2 (PTGS2) were enriched in response to glucocorticoid stimulus. The results of the present study suggested that DEGs in the gray module, including CDKN1A, FOS and PTGS2, may be associated with the pathogenesis of PAD, by modulating the cell cycle, and may offer potential for use as candidate treatment targets for PAD.
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Affiliation(s)
- De-Xin Yin
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Hao-Min Zhao
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Da-Jun Sun
- Department of Vascular Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Jian Yao
- Department of Thoracic Surgery, Jilin Hospital of Jilin Province People's Hospital, Changchun, Jilin 130031, P.R. China
| | - Da-Yong Ding
- Department of Gastroenterology Surgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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31
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Hong KW, Shin MS, Ahn YB, Lee HJ, Kim HD. Genomewide association study on chronic periodontitis in Korean population: results from the Yangpyeong health cohort. J Clin Periodontol 2015. [DOI: 10.1111/jcpe.12437] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Kyung-Won Hong
- Theragen Etex Bio Institute; Suwonsi Gyeonggi-do Korea
- Division of Biomedical Informatics; Center for Genome Science; National Institute of Health; KCDC; Cheongju-si Chungbuk Korea
| | - Myung-Seop Shin
- Department of Preventive and Social Dentistry; School of Dentistry; Seoul National University; Daehak-ro Seoul Korea
| | - Yoo-Been Ahn
- Department of Preventive and Social Dentistry; School of Dentistry; Seoul National University; Daehak-ro Seoul Korea
| | - Hyun-Jin Lee
- Department of Preventive and Social Dentistry; School of Dentistry; Seoul National University; Daehak-ro Seoul Korea
| | - Hyun-Duck Kim
- Department of Preventive and Social Dentistry; School of Dentistry; Seoul National University; Daehak-ro Seoul Korea
- Dental Research Institute; School of Dentistry; Seoul National University; Daehak-ro Seoul Korea
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Corkum CP, Ings DP, Burgess C, Karwowska S, Kroll W, Michalak TI. Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient. BMC Immunol 2015; 16:48. [PMID: 26307036 PMCID: PMC4549105 DOI: 10.1186/s12865-015-0113-0] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/17/2015] [Indexed: 01/25/2023] Open
Abstract
Background High quality genetic material is an essential pre-requisite when analyzing gene expression using microarray technology. Peripheral blood mononuclear cells (PBMC) are frequently used for genomic analyses, but several factors can affect the integrity of nucleic acids prior to their extraction, including the methods of PBMC collection and isolation. Due to the lack of the relevant data published, we compared the Ficoll-Paque density gradient centrifugation and BD Vacutainer cell preparation tube (CPT) protocols to determine if either method offered a distinct advantage in preparation of PBMC-derived immune cell subsets for their use in gene expression analysis. We evaluated the yield and purity of immune cell subpopulations isolated from PBMC derived by both methods, the quantity and quality of extracted nucleic acids, and compared gene expression in PBMC and individual immune cell types from Ficoll and CPT isolation protocols using Affymetrix microarrays. Results The mean yield and viability of fresh PBMC acquired by the CPT method (1.16 × 106 cells/ml, 93.3 %) were compatible to those obtained with Ficoll (1.34 × 106 cells/ml, 97.2 %). No differences in the mean purity, recovery, and viability of CD19+ (B cells), CD8+ (cytotoxic T cells), CD4+ (helper T cell) and CD14+ (monocytes) positively selected from CPT- or Ficoll-isolated PBMC were found. Similar quantities of high quality RNA and DNA were extracted from PBMC and immune cells obtained by both methods. Finally, the PBMC isolation methods tested did not impact subsequent recovery and purity of individual immune cell subsets and, importantly, their gene expression profiles. Conclusions Our findings demonstrate that the CPT and Ficoll PBMC isolation protocols do not differ in their ability to purify high quality immune cell subpopulations. Since there was no difference in the gene expression profiles between immune cells obtained by these two methods, the Ficoll isolation can be substituted by the CPT protocol without conceding phenotypic changes of immune cells and compromising the gene expression studies. Given that the CPT protocol is less elaborate, minimizes cells’ handling and processing time, this method offers a significant operating advantage, especially in large-scale clinical studies aiming at dissecting gene expression in PBMC and PBMC-derived immune cell subpopulations. Electronic supplementary material The online version of this article (doi:10.1186/s12865-015-0113-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher P Corkum
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, NL, A1B3V6, Canada.
| | - Danielle P Ings
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, NL, A1B3V6, Canada.
| | | | - Sylwia Karwowska
- Novartis Oncology Companion Diagnostics, Cambridge, MA, 02139, USA.
| | - Werner Kroll
- Novartis Oncology Companion Diagnostics, Cambridge, MA, 02139, USA. .,Present address: Quidel Corporation, San Diego, CA, 92130, USA.
| | - Tomasz I Michalak
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, NL, A1B3V6, Canada.
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Chu LH, Annex BH, Popel AS. Computational drug repositioning for peripheral arterial disease: prediction of anti-inflammatory and pro-angiogenic therapeutics. Front Pharmacol 2015; 6:179. [PMID: 26379552 PMCID: PMC4548203 DOI: 10.3389/fphar.2015.00179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/10/2015] [Indexed: 12/17/2022] Open
Abstract
Peripheral arterial disease (PAD) results from atherosclerosis that leads to blocked arteries and reduced blood flow, most commonly in the arteries of the legs. PAD clinical trials to induce angiogenesis to improve blood flow conducted in the last decade have not succeeded. We have recently constructed PADPIN, protein-protein interaction network (PIN) of PAD, and here we combine it with the drug-target relations to identify potential drug targets for PAD. Specifically, the proteins in the PADPIN were classified as belonging to the angiome, immunome, and arteriome, characterizing the processes of angiogenesis, immune response/inflammation, and arteriogenesis, respectively. Using the network-based approach we predict the candidate drugs for repositioning that have potential applications to PAD. By compiling the drug information in two drug databases DrugBank and PharmGKB, we predict FDA-approved drugs whose targets are the proteins annotated as anti-angiogenic and pro-inflammatory, respectively. Examples of pro-angiogenic drugs are carvedilol and urokinase. Examples of anti-inflammatory drugs are ACE inhibitors and maraviroc. This is the first computational drug repositioning study for PAD.
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Affiliation(s)
- Liang-Hui Chu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Brian H Annex
- Division of Cardiovascular Medicine, Department of Medicine and Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine Charlottesville, VA, USA
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University Baltimore, MD, USA
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Kullo IJ, Leeper NJ. The genetic basis of peripheral arterial disease: current knowledge, challenges, and future directions. Circ Res 2015; 116:1551-60. [PMID: 25908728 DOI: 10.1161/circresaha.116.303518] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several risk factors for atherosclerotic peripheral arterial disease (PAD), such as dyslipidemia, diabetes mellitus, and hypertension, are heritable. However, predisposition to PAD may be influenced by genetic variants acting independently of these risk factors. Identification of such genetic variants will provide insights into underlying pathophysiologic mechanisms and facilitate the development of novel diagnostic and therapeutic approaches. In contrast to coronary heart disease, relatively few genetic variants that influence susceptibility to PAD have been discovered. This may be, in part, because of greater clinical and genetic heterogeneity in PAD. In this review, we (1) provide an update on the current state of knowledge about the genetic basis of PAD, including results of family studies and candidate gene, linkage as well as genome-wide association studies; (2) highlight the challenges in investigating the genetic basis of PAD and possible strategies to overcome these challenges; and (3) discuss the potential of genome sequencing, RNA sequencing, differential gene expression, epigenetic profiling, and systems biology in increasing our understanding of the molecular genetics of PAD.
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Affiliation(s)
- Iftikhar J Kullo
- From the Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN (I.J.K.); and Department of Vascular Surgery, Stanford, Stanford, CA (N.J.L.).
| | - Nicholas J Leeper
- From the Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN (I.J.K.); and Department of Vascular Surgery, Stanford, Stanford, CA (N.J.L.)
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Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS. PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. Physiol Genomics 2015; 47:331-43. [PMID: 26058837 DOI: 10.1152/physiolgenomics.00125.2014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 06/04/2015] [Indexed: 11/22/2022] Open
Abstract
Peripheral arterial disease (PAD) results from an obstruction of blood flow in the arteries other than the heart, most commonly the arteries that supply the legs. The complexity of the known signaling pathways involved in PAD, including various growth factor pathways and their cross talks, suggests that analyses of high-throughput experimental data could lead to a new level of understanding of the disease as well as novel and heretofore unanticipated potential targets. Such bioinformatic analyses have not been systematically performed for PAD. We constructed global protein-protein interaction networks of angiogenesis (Angiome), immune response (Immunome), and arteriogenesis (Arteriome) using our previously developed algorithm GeneHits. The term "PADPIN" refers to the angiome, immunome, and arteriome in PAD. Here we analyze four microarray gene expression datasets from ischemic and nonischemic gastrocnemius muscles at day 3 posthindlimb ischemia (HLI) in two genetically different C57BL/6 and BALB/c mouse strains that display differential susceptibility to HLI to identify potential targets and signaling pathways in angiogenesis, immune, and arteriogenesis networks. We hypothesize that identification of the differentially expressed genes in ischemic and nonischemic muscles between the strains that recovers better (C57BL/6) vs. the strain that recovers more poorly (BALB/c) will help for the prediction of target genes in PAD. Our bioinformatics analysis identified several genes that are differentially expressed between the two mouse strains with known functions in PAD including TLR4, THBS1, and PRKAA2 and several genes with unknown functions in PAD including EphA4, TSPAN7, SLC22A4, and EIF2a.
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Affiliation(s)
- Liang-Hui Chu
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland;
| | - Chaitanya G Vijay
- Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Brian H Annex
- Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and
| | - Joel S Bader
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland; High-Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland
| | - Aleksander S Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland
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Sitras V, Fenton C, Acharya G. Gene expression profile in cardiovascular disease and preeclampsia: a meta-analysis of the transcriptome based on raw data from human studies deposited in Gene Expression Omnibus. Placenta 2014; 36:170-8. [PMID: 25555499 DOI: 10.1016/j.placenta.2014.11.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Cardiovascular disease (CVD) and preeclampsia (PE) share common clinical features. We aimed to identify common transcriptomic signatures involved in CVD and PE in humans. METHODS Meta-analysis of individual raw microarray data deposited in GEO, obtained from blood samples of patients with CVD versus controls and placental samples from women with PE versus healthy women with uncomplicated pregnancies. Annotation of cases versus control samples was taken directly from the microarray documentation. Genes that showed a significant differential expression in the majority of experiments were selected for subsequent analysis. Hypergeometric gene list analysis was performed using Bioconductor GOstats package. Bioinformatic analysis was performed in PANTHER. RESULTS Seven studies in CVD and 5 studies in PE were eligible for meta-analysis. A total of 181 genes were found to be differentially expressed in microarray studies investigating gene expression in blood samples obtained from patients with CVD compared to controls and 925 genes were differentially expressed between preeclamptic and healthy placentas. Among these differentially expressed genes, 22 were common between CVD and PE. DISCUSSION Bioinformatic analysis of these genes revealed oxidative stress, p-53 pathway feedback, inflammation mediated by chemokines and cytokines, interleukin signaling, B-cell activation, PDGF signaling, Wnt signaling, integrin signaling and Alzheimer disease pathways to be involved in the pathophysiology of both CVD and PE. Metabolism, development, response to stimulus, immune response and cell communication were the associated biologic processes in both conditions. Gene set enrichment analysis showed the following overlapping pathways between CVD and PE: TGF-β-signaling, apoptosis, graft-versus-host disease, allograft rejection, chemokine signaling, steroid hormone synthesis, type I and II diabetes mellitus, VEGF signaling, pathways in cancer, GNRH signaling, Huntingtons disease and Notch signaling. CONCLUSION CVD and PE share same common traits in their gene expression profile indicating common pathways in their pathophysiology.
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Affiliation(s)
- V Sitras
- Department of Obstetrics and Fetal Medicine, Oslo University Hospital, Rikshospitalet, Norway.
| | - C Fenton
- Microarray Resource Center, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - G Acharya
- Women's Health and Perinatology Research Group, Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway; Department of Obstetrics and Gynecology, University Hospital of Northern Norway, Tromsø, Norway; Department of Clinical Sciences, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
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Llorente-Cortés V, de Gonzalo-Calvo D, Orbe J, Páramo JA, Badimon L. Signature of subclinical femoral artery atherosclerosis in peripheral blood mononuclear cells. Eur J Clin Invest 2014; 44:539-48. [PMID: 24716741 DOI: 10.1111/eci.12267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/07/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Peripheral arterial disease is a relevant public health problem associated with increased risk of morbimortality. Most of the patients with this condition are asymptomatic. Therefore, the development of accessible biochemical markers seems to be necessary to anticipate diagnosis. Our hypothesis is that asymptomatic subjects with objectively confirmed femoral artery atherosclerosis could be distinguished from control subjects by gene expression analysis in peripheral blood mononuclear cells (PBMC). MATERIALS AND METHODS A total of 37 asymptomatic males over 50 years old were recruited at the University Clinic of Navarra (Spain). Nineteen participants were free from atherosclerotic vascular disease and 18 participants presented subclinical femoral artery atherosclerosis defined by means of Doppler ultrasound. PBMC were isolated from blood and the RNA extracted. A panel of atherosclerotic-related genes were evaluated by Taqman low-density array. RESULTS In univariate logistic regression models, we found a direct relationship between IL4, ITGAM and TLR2 expression levels in PBMC and femoral atherosclerosis, even when the models were adjusted for age and hypertension prevalence. Multivariate logistic regression models showed that elevated IL4 expression levels were intimately associated with subclinical femoral atherosclerosis after adjusting for the same potential confounders. CONCLUSIONS Current data suggest that gene expression in PBMC, in particular IL4 expression, could be a useful tool in the diagnosis of femoral artery atherosclerosis in asymptomatic patients. Furthermore, in patients with no differences in cardiovascular risk factors except for hypertension, the results point to the immune and inflammatory deregulation as a feature of subclinical peripheral atherosclerosis.
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Stather PW, Sylvius N, Wild JB, Choke E, Sayers RD, Bown MJ. Differential microRNA expression profiles in peripheral arterial disease. ACTA ACUST UNITED AC 2014; 6:490-7. [PMID: 24129592 DOI: 10.1161/circgenetics.111.000053] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Peripheral arterial disease (PAD) is a clinical condition caused by an atherosclerotic process affecting the arteries of the limbs. Despite major improvements in surgical endovascular techniques, PAD is still associated with high mortality and morbidity. Recently, microRNAs (miRNAs), a class of short noncoding RNA controlling gene expression, have emerged as major regulators of multiple biological processes. METHODS AND RESULTS A whole-miRNA transcriptome profiling was performed in peripheral blood from an initial sample set of patients and controls. A 12-miRNA PAD-specific signature, which includes let 7e, miR-15b, -16, -20b, -25, -26b, -27b, -28-5p, -126, -195, -335, and -363, was further investigated and validated in 2 additional sample sets. Each of these 12 miRNAs exhibited good diagnostic value as evidenced by receiver operating characteristic curve analyses. Pathway enrichment analysis using predicted and validated targets identified several signaling pathways relevant to vascular disorders. Several of these pathways, including cell adhesion molecules, were confirmed by quantifying the expression level of several candidate genes regulating the initial stages of the inflammatory atherosclerotic process. The expression level of 7 of these candidate genes exhibits striking inverse correlation with that of several, if not all, of the miRNAs of the PAD-specific miRNA signature. CONCLUSIONS These results demonstrate the potential of miRNAs for the diagnosis of PAD and provide further insight into the molecular mechanisms leading to the development of PAD, with the potential for future therapeutic targets.
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Affiliation(s)
- Philip W Stather
- Department of Cardiovascular Sciences and Department of Genetics and the NIHR Leicester Cardiovascular Biomedical Research Unit, University of Leicester, Leicester, United Kingdom
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Sharma P, Garg G, Kumar A, Mohammad F, Kumar SR, Tanwar VS, Sati S, Sharma A, Karthikeyan G, Brahmachari V, Sengupta S. Genome wide DNA methylation profiling for epigenetic alteration in coronary artery disease patients. Gene 2014; 541:31-40. [PMID: 24582973 DOI: 10.1016/j.gene.2014.02.034] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/29/2013] [Accepted: 02/17/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND The alteration in the epigenome forms an interface between the genotype and the environment. Epigenetic alteration is expected to make a significant contribution to the development of cardiovascular disease where environmental interactions play a key role in disease progression. We had previously shown that global DNA hypermethylation per se is associated with coronary artery disease (CAD) and is further accentuated by high levels of homocysteine, a thiol amino acid which is an independent risk factor for cardiovascular disease and is also a key modulator of macromolecular methylation. RESULTS We have identified 72 differentially methylated regions (DMRs) that were hypermethylated in CAD patients in the background of varying homocysteine levels. Following deep bisulfite sequencing of a few of the selected DMRs, we found significantly higher methylation in CAD cases. We get six CpG sites in three DMRs that included the intronic region of C1QL4 gene and upstream region of CCDC47 and TGFBR3 genes. CONCLUSION To the best of our knowledge, this is the first study to identify hypermethylated regions across the genome in patients with coronary artery disease. Further validation in different populations is necessary for this information to be used for disease risk assessment and management.
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Affiliation(s)
- Priyanka Sharma
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Gaurav Garg
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Arun Kumar
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Farhan Mohammad
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Sudha Ramesh Kumar
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Vinay Singh Tanwar
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Satish Sati
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Abhay Sharma
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
| | - Ganesan Karthikeyan
- All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi 110007, India.
| | - Shantanu Sengupta
- CSIR - Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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Readhead B, Dudley J. Translational Bioinformatics Approaches to Drug Development. Adv Wound Care (New Rochelle) 2013; 2:470-489. [PMID: 24527359 DOI: 10.1089/wound.2012.0422] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 04/07/2013] [Indexed: 12/16/2022] Open
Abstract
SIGNIFICANCE A majority of therapeutic interventions occur late in the pathological process, when treatment outcome can be less predictable and effective, highlighting the need for new precise and preventive therapeutic development strategies that consider genomic and environmental context. Translational bioinformatics is well positioned to contribute to the many challenges inherent in bridging this gap between our current reactive methods of healthcare delivery and the intent of precision medicine, particularly in the areas of drug development, which forms the focus of this review. RECENT ADVANCES A variety of powerful informatics methods for organizing and leveraging the vast wealth of available molecular measurements available for a broad range of disease contexts have recently emerged. These include methods for data driven disease classification, drug repositioning, identification of disease biomarkers, and the creation of disease network models, each with significant impacts on drug development approaches. CRITICAL ISSUES An important bottleneck in the application of bioinformatics methods in translational research is the lack of investigators who are versed in both biomedical domains and informatics. Efforts to nurture both sets of competencies within individuals and to increase interfield visibility will help to accelerate the adoption and increased application of bioinformatics in translational research. FUTURE DIRECTIONS It is possible to construct predictive, multiscale network models of disease by integrating genotype, gene expression, clinical traits, and other multiscale measures using causal network inference methods. This can enable the identification of the "key drivers" of pathology, which may represent novel therapeutic targets or biomarker candidates that play a more direct role in the etiology of disease.
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Affiliation(s)
- Ben Readhead
- Center for Biomedical Informatics, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joel Dudley
- Center for Biomedical Informatics, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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