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de Gonzalo-Calvo D, Karaduzovic-Hadziabdic K, Dalgaard LT, Dieterich C, Perez-Pons M, Hatzigeorgiou A, Devaux Y, Kararigas G. Machine learning for catalysing the integration of noncoding RNA in research and clinical practice. EBioMedicine 2024; 106:105247. [PMID: 39029428 PMCID: PMC11314885 DOI: 10.1016/j.ebiom.2024.105247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/17/2024] [Accepted: 07/02/2024] [Indexed: 07/21/2024] Open
Abstract
The human transcriptome predominantly consists of noncoding RNAs (ncRNAs), transcripts that do not encode proteins. The noncoding transcriptome governs a multitude of pathophysiological processes, offering a rich source of next-generation biomarkers. Toward achieving a holistic view of disease, the integration of these transcripts with clinical records and additional data from omic technologies ("multiomic" strategies) has motivated the adoption of artificial intelligence (AI) approaches. Given their intricate biological complexity, machine learning (ML) techniques are becoming a key component of ncRNA-based research. This article presents an overview of the potential and challenges associated with employing AI/ML-driven approaches to identify clinically relevant ncRNA biomarkers and to decipher ncRNA-associated pathogenetic mechanisms. Methodological and conceptual constraints are discussed, along with an exploration of ethical considerations inherent to AI applications for healthcare and research. The ultimate goal is to provide a comprehensive examination of the multifaceted landscape of this innovative field and its clinical implications.
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Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
| | | | | | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Germany; German Center for Cardiovascular Research (DZHK) - Partner Site Heidelberg/Mannheim, Germany
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Artemis Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Georgios Kararigas
- Department of Physiology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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Zhang Z, Shao B, Liu H, Huang B, Gao X, Qiu J, Wang C. Construction and Validation of a Predictive Model for Coronary Artery Disease Using Extreme Gradient Boosting. J Inflamm Res 2024; 17:4163-4174. [PMID: 38973999 PMCID: PMC11226989 DOI: 10.2147/jir.s464489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Early recognition of coronary artery disease (CAD) could delay its progress and significantly reduce mortality. Sensitive, specific, cost-efficient and non-invasive indicators for assessing individual CAD risk in community population screening are urgently needed. Patients and Methods 3112 patients with CAD and 3182 controls were recruited from three clinical centers in China, and differences in baseline and clinical characteristics were compared. For the discovery cohort, the least absolute shrinkage and selection operator (LASSO) regression was used to identify significant features and four machine learning algorithms (logistic regression, support vector machine (SVM), random forest (RF) and extreme gradient boosting (XGBoost)) were applied to construct models for CAD risk assessment, the receiver operating characteristics (ROC) curve and precision-recall (PR) curve were conducted to evaluate their predictive accuracy. The optimal model was interpreted by Shapley additive explanations (SHAP) analysis and assessed by the ROC curve, calibration curve, and decision curve analysis (DCA) and validated by two external cohorts. Results Using LASSO filtration, all included variables were considered to be statistically significant. Four machine learning models were constructed based on these features and the results of ROC and PR curve implied that the XGBoost model exhibited the highest predictive performance, which yielded a high area of ROC curve (AUC) of 0.988 (95% CI: 0.986-0.991) to distinguish CAD patients from controls with a sensitivity of 94.6% and a specificity of 94.6%. The calibration curve showed that the predicted results were in good agreement with actual observations, and DCA exhibited a better net benefit across a wide range of threshold probabilities. External validation of the model also exhibited favorable discriminatory performance, with an AUC, sensitivity, and specificity of 0.953 (95% CI: 0.945-0.960), 89.9%, and 87.1% in the validation cohort, and 0.935 (95% CI: 0.915-0.955), 82.0%, and 90.3% in the replication cohort. Conclusion Our model is highly informative for clinical practice and will be conducive to primary prevention and tailoring the precise management for CAD patients.
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Affiliation(s)
- Zheng Zhang
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, People’s Republic of China
- Center for Gene Diagnosis, Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, People’s Republic of China
| | - Binbin Shao
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Healthcare Hospital, Nanjing, Jiangsu Province, People’s Republic of China
| | - Hongzhou Liu
- Center for Gene Diagnosis, Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, People’s Republic of China
- School of Clinical Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuang Province, People’s Republic of China
| | - Ben Huang
- Center for Gene Diagnosis, Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, People’s Republic of China
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People’s Republic of China
| | - Xuechen Gao
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, People’s Republic of China
| | - Jun Qiu
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, People’s Republic of China
| | - Chen Wang
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, People’s Republic of China
- Center for Gene Diagnosis, Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, People’s Republic of China
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Namous H, Krueger C, Cheng Y, Melo PHC, Peppas A, Kaluza GL, Stoffregen WC, Reed J, Khatib H, Granada JF. Longitudinal dynamics of circulating miRNAs in a swine model of familial hypercholesterolemia during early atherosclerosis. Sci Rep 2023; 13:19355. [PMID: 37935844 PMCID: PMC10630391 DOI: 10.1038/s41598-023-46762-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023] Open
Abstract
Atherosclerosis is a complex progressive disease involving intertwined biological mechanisms. We aimed to identify miRNA expression dynamics at the early stages of atherosclerosis using a large swine model (Wisconsin Miniature Swine, WMS). A total of 18 female pigs; 9 familial hypercholesterolemic (WMS-FH) and 9 normal control swine (WMS-N) were studied. miRNA sequencing was performed on plasma cell-free RNA at 3, 6, and 9 months of age. RT-qPCR validated DE miRNAs in a new cohort of animals (n = 30) with both sexes. Gene ontology and mRNA targets for DE miRNAs were identified. In vivo multimodality imaging and histopathology were performed to document the presence of atherosclerosis at termination. 20, 19, and 9 miRNAs were significantly DE between the groups at months 3, 6, and 9, respectively. Most DE miRNAs and their target genes are involved in human atherosclerosis development. Coronary atherosclerosis was documented in 7/9 WMS-FH pigs. Control animals had no lesions. miR-138, miR-152, miR-190a, and miR-196a showed a significant diagnostic power at month 3, whereas miR-486, miR-126-3p, miR-335, and miR-423-5p were of significant diagnostic power at month 9. In conclusion, specific DE miRNAs with significant discriminatory power may be promising biomarkers for the early detection of coronary atherosclerosis.
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Affiliation(s)
- Hadjer Namous
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, 1675 Observatory Drive, Madison, WI, 53706, USA
| | - Christian Krueger
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, 1675 Observatory Drive, Madison, WI, 53706, USA
| | - Yanping Cheng
- Skirball Center for Innovation, Cardiovascular Research Foundation, 1700 Broadway, 9th Floor, New York, NY, 10019, USA
| | - Pedro H C Melo
- Skirball Center for Innovation, Cardiovascular Research Foundation, 1700 Broadway, 9th Floor, New York, NY, 10019, USA
| | - Athanasios Peppas
- Skirball Center for Innovation, Cardiovascular Research Foundation, 1700 Broadway, 9th Floor, New York, NY, 10019, USA
| | - Grzegorz L Kaluza
- Skirball Center for Innovation, Cardiovascular Research Foundation, 1700 Broadway, 9th Floor, New York, NY, 10019, USA
| | | | - Jess Reed
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, 1675 Observatory Drive, Madison, WI, 53706, USA
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin Madison, 1675 Observatory Drive, Madison, WI, 53706, USA.
| | - Juan F Granada
- Skirball Center for Innovation, Cardiovascular Research Foundation, 1700 Broadway, 9th Floor, New York, NY, 10019, USA.
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de Gonzalo-Calvo D, Martinez-Camblor P, Belmonte T, Barbé F, Duarte K, Cowie MR, Angermann CE, Korte A, Riedel I, Labus J, Koenig W, Zannad F, Thum T, Bär C. Circulating miR-133a-3p defines a low-risk subphenotype in patients with heart failure and central sleep apnea: a decision tree machine learning approach. J Transl Med 2023; 21:742. [PMID: 37864227 PMCID: PMC10588036 DOI: 10.1186/s12967-023-04558-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/22/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Patients with heart failure with reduced ejection fraction (HFrEF) and central sleep apnea (CSA) are at a very high risk of fatal outcomes. OBJECTIVE To test whether the circulating miRNome provides additional information for risk stratification on top of clinical predictors in patients with HFrEF and CSA. METHODS The study included patients with HFrEF and CSA from the SERVE-HF trial. A three-step protocol was applied: microRNA (miRNA) screening (n = 20), technical validation (n = 60), and biological validation (n = 587). The primary outcome was either death from any cause, lifesaving cardiovascular intervention, or unplanned hospitalization for worsening of heart failure, whatever occurred first. MiRNA quantification was performed in plasma samples using miRNA sequencing and RT-qPCR. RESULTS Circulating miR-133a-3p levels were inversely associated with the primary study outcome. Nonetheless, miR-133a-3p did not improve a previously established clinical prognostic model in terms of discrimination or reclassification. A customized regression tree model constructed using the Classification and Regression Tree (CART) algorithm identified eight patient subphenotypes with specific risk patterns based on clinical and molecular characteristics. MiR-133a-3p entered the regression tree defining the group at the lowest risk; patients with log(NT-proBNP) ≤ 6 pg/mL (miR-133a-3p levels above 1.5 arbitrary units). The overall predictive capacity of suffering the event was highly stable over the follow-up (from 0.735 to 0.767). CONCLUSIONS The combination of clinical information, circulating miRNAs, and decision tree learning allows the identification of specific risk subphenotypes in patients with HFrEF and CSA.
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Affiliation(s)
- David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Pablo Martinez-Camblor
- Anesthesiology Department, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Faculty of Health Sciences, Universidad Autonoma de Chile, Providencia, Chile
| | - Thalia Belmonte
- Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, IRBLleida, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Kevin Duarte
- INSERM 1433, CHRU de Nancy, Centre d'Investigations Cliniques Plurithématique, Institut Lorrain du Cœur et des Vaisseaux, Université de Lorraine, Nancy, France
| | - Martin R Cowie
- Department of Cardiology, Royal Brompton Hospital (Guy's & St Thomas's NHS Foundation Trust), London, UK
| | - Christiane E Angermann
- Comprehensive Heart Failure Center, University and University Hospital Würzburg, Würzburg, Germany
- Department of Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Andrea Korte
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Isabelle Riedel
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Josephine Labus
- Cellular Neurophysiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Ulm, Germany
| | - Faiez Zannad
- Université de Lorraine, Inserm, Centre d'Investigations Cliniques-Plurithématique 1433, Inserm U1116, CHRU Nancy, F-CRIN INI-CRCT Network, Nancy, France
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany.
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany.
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Matute-Blanco L, Fernández-Rodríguez D, Casanova-Sandoval J, Belmonte T, Benítez ID, Rivera K, Garcia-Guimaraes M, Cortés Villar C, Peral Disdier V, Millán Segovia R, Barriuso I, de Gonzalo-Calvo D, Barbé F, Worner F. Study protocol for the epigenetic characterization of angor pectoris according to the affected coronary compartment: Global and comprehensive assessment of the relationship between invasive coronary physiology and microRNAs. PLoS One 2023; 18:e0283097. [PMID: 37167303 PMCID: PMC10174526 DOI: 10.1371/journal.pone.0283097] [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: 11/03/2022] [Accepted: 03/01/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are noncoding RNAs involved in post-transcriptional genetic regulation with a proposed role in intercellular communication. miRNAs are considered promising biomarkers in ischemic heart disease. Invasive physiological evaluation allows a precise assessment of each affected coronary compartment. Although some studies have associated the expression of circulating miRNAs with invasive physiological indexes, their global relationship with coronary compartments has not been assessed. Here, we will evaluate circulating miRNAs profiles according to the coronary pattern of the vascular compartment affectation. STUDY AND DESIGN This is an investigator-initiated, multicentre, descriptive study to be conducted at three centres in Spain (NCT05374694). The study will include one hundred consecutive patients older than 18 years with chest pain of presumed coronary cause undergoing invasive physiological evaluation, including fractional flow reserve (FFR) and index of microvascular resistance (IMR). Patients will be initially classified into four groups, according to FFR and IMR: macrovascular and microvascular affectation (FFR≤0.80 / IMR≥25), isolated macrovascular affectation (FFR≤0.80 / IMR<25), isolated microvascular affectation (FFR>0.80 / IMR ≥25) and normal coronary indexes (FFR>0.80 / IMR<25). Patients with isolated microvascular affectation or normal indexes will also undergo the acetylcholine test and may be reclassified as a fifth group in the presence of spasm. A panel of miRNAs previously associated with molecular mechanisms linked to chronic coronary syndrome will be analysed using RT-qPCR. CONCLUSIONS The results of this study will identify miRNA profiles associated with patterns of coronary affectation and will contribute to a better understanding of the mechanistic pathways of coronary pathology.
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Affiliation(s)
- Lucía Matute-Blanco
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
| | - Diego Fernández-Rodríguez
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
| | - Juan Casanova-Sandoval
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
| | - Thalía Belmonte
- Institut de Reçerca Biomèdica de Lleida (IRBLleida), Translational Research in Respiratory Medicine Group, Lleida, Spain
- Institute of Health Carlos III, CIBER of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Iván D. Benítez
- Institut de Reçerca Biomèdica de Lleida (IRBLleida), Translational Research in Respiratory Medicine Group, Lleida, Spain
- Institute of Health Carlos III, CIBER of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Kristian Rivera
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
| | - Marcos Garcia-Guimaraes
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
| | | | | | - Raúl Millán Segovia
- Department of Cardiology, University Hospital Son Espases, Palma de Mallorca, Spain
| | - Ignacio Barriuso
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
| | - David de Gonzalo-Calvo
- Institut de Reçerca Biomèdica de Lleida (IRBLleida), Translational Research in Respiratory Medicine Group, Lleida, Spain
- Institute of Health Carlos III, CIBER of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Ferran Barbé
- Institut de Reçerca Biomèdica de Lleida (IRBLleida), Translational Research in Respiratory Medicine Group, Lleida, Spain
- Institute of Health Carlos III, CIBER of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Fernando Worner
- Department of Cardiology, Institut de Reçerca Biomèdica de Lleida (IRBLleida), University Hospital Arnau de Vilanova, Lleida, Spain
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6
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Meng L, Yu X, Han H, Jia X, Hu B, Zhang L, Wang Z, Zhang W, Zhong M, Zhu H. Circulating miR-143 and miR-145 as promising biomarkers for evaluating severity of coronary artery stenosis in patients with acute coronary syndrome. Clin Biochem 2023; 111:32-40. [PMID: 36241060 DOI: 10.1016/j.clinbiochem.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/17/2022] [Accepted: 10/07/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Multiple studies have provided evidence that miR-143 and miR-145 play a crucial role in the pathogenesis and progression of atherosclerosis. In the present study, we aim to investigate the expression of plasma miR-143 and miR-145 in patients with acute coronary syndrome (ACS) and their association with the severity of coronary artery stenosis. METHODS The study enrolled 279 patients with ACS, including 201 patients with unstable angina (UA) and 78 patients with acute myocardial infarction (AMI), and 65 matched subjects as the control group. The plasma levels of miR-143 and miR-145 were detected by quantitative real-time PCR (qRT-PCR). Gensini score was applied to evaluate the severity of coronary artery stenosis. RESULTS Plasma levels of miR-143 and miR-145 in patients with ACS were both decreased compared with the control group (p < 0.001). Plasma levels of miR-143 and miR-145 were negatively correlated with Gensini score (miR-143: r = -0.246, p < 0.001; miR-145: r = -0.222, p < 0.001). Logistic regression analysis showed that miR-143 and miR-145 were protective factors for the onset of ACS, UA, or AMI separately. MiR-143 (AUC: 0.786, p < 0.001) and miR-145 (AUC: 0.793, p < 0.001) were able to predict the degree of coronary artery stenosis greater than 50 %. CONCLUSION The plasma levels of miR-143 and miR-145 were significantly decreased in ACS patients and were negatively correlated with coronary stenosis. In conclusion, plasma miR-143 and miR-145 levels can be used as noninvasive biomarkers for evaluating coronary artery stenosis.
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Affiliation(s)
- Linlin Meng
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xin Yu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Cardiology, The People's Hospital of Pingyi County, Shandong, China
| | - Haitao Han
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xu Jia
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Boang Hu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lei Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Zhihao Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Geriatric Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Shandong key Laboratory of Cardiovascular Proteomics, Jinan, Shandong, 250012, China
| | - Wei Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Ming Zhong
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hui Zhu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
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7
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Rozhkov AN, Shchekochikhin DY, Ashikhmin YI, Mitina YO, Evgrafova VV, Zhelankin AV, Gognieva DG, Akselrod AS, Kopylov PY. The Profile of Circulating Blood microRNAs in Outpatients with Vulnerable and Stable Atherosclerotic Plaques: Associations with Cardiovascular Risks. Noncoding RNA 2022; 8:ncrna8040047. [PMID: 35893230 PMCID: PMC9326687 DOI: 10.3390/ncrna8040047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs reflect many biological processes in the human body, including athero-sclerosis. In a cardiology outpatient department cohort (N = 83), we aimed to compare the levels of circulating microRNAs in groups with vulnerable plaques (N = 22), stable plaques (N = 23) and plaque-free (N = 17) depending on coronary computed tomography angiography and to evaluate associations of microRNA levels with calculated cardiovascular risks (CVR), based on the SCORE2 (+OP), ACC/AHA, ATP-III and MESA scales. Coronary computed tomography was performed on a 640-slice computed tomography scanner. Relative plasma levels of microRNA were assessed via a real-time polymerase chain reaction. We found significant differences in miR-143-3p levels (p = 0.0046 in plaque-free vs. vulnerable plaque groups) and miR-181b-5p (p = 0.0179 in stable vs. vulnerable plaques groups). Analysis of microRNA associations with CVR did not show significant differences for SCORE2 (+OP) and ATPIII scales. MiR-126-5p and miR-150-5p levels were significantly higher (p < 0.05) in patients with ACC/AHA risk >10% and miR-145-5p had linear relationships with ACC/AHA score (adjusted p = 0.0164). The relative plasma level of miR-195 was higher (p < 0.05) in patients with MESA risk > 7.5% and higher (p < 0.05) in patients with zero coronary calcium index (p = 0.036). A linear relationship with coronary calcium was observed for miR-126-3p (adjusted p = 0.0484). A positive correlation with high coronary calcium levels (> 100 Agatson units) was found for miR-181-5p (p = 0.036). Analyzing the biological pathways of these microRNAs, we suggest that miR-143-3p and miR-181-5p can be potential markers of the atherosclerosis process. Other miRNAs (miR-126-3p, 126-5p, 145-5p, 150-5p, 195-5p) can be considered as potential cardiovascular risk modifiers, but it is necessary to validate our results in a large prospective trial.
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Affiliation(s)
- Andrey N. Rozhkov
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.G.G.); (P.Y.K.)
- Correspondence: ; Tel.: +7-915-085-32-95
| | - Dmitry Yu. Shchekochikhin
- Department of Cardiology, Functional and Ultrasound Diagnostics, N.V. Sklifosovsky Institute of Clinical Medicine, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.Y.S.); (V.V.E.); (A.S.A.)
| | - Yaroslav I. Ashikhmin
- International Medical Cluster, 40 Bolshoy Boulevard Skolkovo Innovation Center, 121205 Moscow, Russia;
| | - Yulia O. Mitina
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Veronika V. Evgrafova
- Department of Cardiology, Functional and Ultrasound Diagnostics, N.V. Sklifosovsky Institute of Clinical Medicine, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.Y.S.); (V.V.E.); (A.S.A.)
| | - Andrey V. Zhelankin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia;
| | - Daria G. Gognieva
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.G.G.); (P.Y.K.)
- Department of Cardiology, Functional and Ultrasound Diagnostics, N.V. Sklifosovsky Institute of Clinical Medicine, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.Y.S.); (V.V.E.); (A.S.A.)
| | - Anna S. Akselrod
- Department of Cardiology, Functional and Ultrasound Diagnostics, N.V. Sklifosovsky Institute of Clinical Medicine, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.Y.S.); (V.V.E.); (A.S.A.)
| | - Philippe Yu. Kopylov
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.G.G.); (P.Y.K.)
- Department of Cardiology, Functional and Ultrasound Diagnostics, N.V. Sklifosovsky Institute of Clinical Medicine, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (D.Y.S.); (V.V.E.); (A.S.A.)
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de Gonzalo‐Calvo D, Pérez‐Boza J, Curado J, Devaux Y. Challenges of microRNA-based biomarkers in clinical application for cardiovascular diseases. Clin Transl Med 2022; 12:e585. [PMID: 35167732 PMCID: PMC8846372 DOI: 10.1002/ctm2.585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 12/23/2022] Open
Affiliation(s)
- David de Gonzalo‐Calvo
- Translational Research in Respiratory MedicineUniversity Hospital Arnau de Vilanova and Santa MariaLleidaSpain
- CIBER of Respiratory Diseases (CIBERES)Institute of Health Carlos IIIMadridSpain
| | | | | | - Yvan Devaux
- Cardiovascular Research UnitLuxembourg Institute of HealthLuxembourgLuxembourg
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9
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Monocyte-to-albumin ratio as a novel predictor of long-term adverse outcomes in patients after percutaneous coronary intervention. Biosci Rep 2021; 41:229050. [PMID: 34137842 PMCID: PMC8243340 DOI: 10.1042/bsr20210154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Monocyte count and serum albumin (Alb) have been proven to be involved in the process of systemic inflammation. Therefore, we investigated the prognostic value of monocyte-to-albumin ratio (MAR) in patients who underwent percutaneous coronary intervention (PCI). Methods: We enrolled a total of 3561 patients in the present study from January 2013 to December 2017. They were divided into two groups according to MAR cut-off value (MAR < 0.014, n=2220; MAR ≥ 0.014, n=1119) as evaluated by receiver operating characteristic (ROC) curve. The average follow-up time was 37.59 ± 22.24 months. Results: The two groups differed significantly in the incidences of all-cause mortality (ACM; P<0.001), cardiac mortality (CM; P<0.001), major adverse cardiovascular events (MACEs; P=0.038), and major adverse cardiovascular and cerebrovascular events (MACCEs; P=0.037). Multivariate Cox regression analyses revealed MAR as an independent prognostic factor for ACM and CM. The incidence of ACM increased by 56.5% (hazard ratio [HR] = 1.565; 95% confidence interval [CI], 1.086–2.256; P=0.016) and that of CM increased by 76.3% (HR = 1.763; 95% CI, 1.106–2.810; P=0.017) in patients in the higher-MAR group. Kaplan–Meier survival analysis suggested that patients with higher MAR tended to have an increased accumulated risk of ACM (Log-rank P<0.001) and CM (Log-rank P<0.001). Conclusion: The findings of the present study suggested that MAR was a novel independent predictor of long-term mortality in patients who underwent PCI.
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10
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Pinilla L, Benitez ID, González J, Torres G, Barbé F, de Gonzalo-Calvo D. Peripheral blood microRNAs and the COVID-19 patient: methodological considerations, technical challenges and practice points. RNA Biol 2021; 18:688-695. [PMID: 33530819 PMCID: PMC8078525 DOI: 10.1080/15476286.2021.1885188] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/30/2021] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 emergency pandemic resulting from infection with SARS-CoV-2 represents a major threat to public health worldwide. There is an urgent clinical demand for easily accessible tools to address weaknesses and gaps in the management of COVID-19 patients. In this context, transcriptomic profiling of liquid biopsies, especially microRNAs (miRNAs), has recently emerged as a robust source of potential clinical indicators for medical decision-making. Nevertheless, the analysis of the circulating miRNA signature and its translation to clinical practice requires strict control of a wide array of methodological details. In this review, we indicate the main methodological aspects that should be addressed when evaluating the circulating miRNA profiles in COVID-19 patients, from preanalytical and analytical variables to the experimental design, impact of confounding, analysis of the data and interpretation of the findings, among others. Additionally, we provide practice points to ensure the rigour and reproducibility of miRNA-based biomarker investigations of this condition.Abbreviations: ACE: angiotensin-converting enzyme; ARDS: acute respiratory distress syndrome; COVID-19: coronavirus disease 2019; ERDN: early Detection Research Network; LMWH: low molecular weight heparin; miRNA: microRNA; ncRNA: noncoding RNA; SARS-CoV-2: severe acute respiratory syndrome coronavirus-2; SOP: standard operating procedure.
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Affiliation(s)
- Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ivan D. Benitez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Respiratory Department, University Hospital Arnau de Vilanova-Santa María, Translational Research in Respiratory Medicine, IRBLleida, University of Lleida, Lleida, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- Respiratory Department, University Hospital Arnau de Vilanova-Santa María, Translational Research in Respiratory Medicine, IRBLleida, University of Lleida, Lleida, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Respiratory Department, University Hospital Arnau de Vilanova-Santa María, Translational Research in Respiratory Medicine, IRBLleida, University of Lleida, Lleida, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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11
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Wang C, Zhao Y, Jin B, Gan X, Liang B, Xiang Y, Zhang X, Lu Z, Zheng F. Development and Validation of a Predictive Model for Coronary Artery Disease Using Machine Learning. Front Cardiovasc Med 2021; 8:614204. [PMID: 33634169 PMCID: PMC7902072 DOI: 10.3389/fcvm.2021.614204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/15/2021] [Indexed: 01/06/2023] Open
Abstract
Early identification of coronary artery disease (CAD) can prevent the progress of CAD and effectually lower the mortality rate, so we intended to construct and validate a machine learning model to predict the risk of CAD based on conventional risk factors and lab test data. There were 3,112 CAD patients and 3,182 controls enrolled from three centers in China. We compared the baseline and clinical characteristics between two groups. Then, Random Forest algorithm was used to construct a model to predict CAD and the model was assessed by receiver operating characteristic (ROC) curve. In the development cohort, the Random Forest model showed a good AUC 0.948 (95%CI: 0.941–0.954) to identify CAD patients from controls, with a sensitivity of 90%, a specificity of 85.4%, a positive predictive value of 0.863 and a negative predictive value of 0.894. Validation of the model also yielded a favorable discriminatory ability with the AUC, sensitivity, specificity, positive predictive value, and negative predictive value of 0.944 (95%CI: 0.934–0.955), 89.5%, 85.8%, 0.868, and 0.886 in the validation cohort 1, respectively, and 0.940 (95%CI: 0.922–0.960), 79.5%, 94.3%, 0.932, and 0.823 in the validation cohort 2, respectively. An easy-to-use tool that combined 15 indexes to assess the CAD risk was constructed and validated using Random Forest algorithm, which showed favorable predictive capability (http://45.32.120.149:3000/randomforest). Our model is extremely valuable for clinical practice, which will be helpful for the management and primary prevention of CAD patients.
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Affiliation(s)
- Chen Wang
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yue Zhao
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bingyu Jin
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xuedong Gan
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bin Liang
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yang Xiang
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaokang Zhang
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhibing Lu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fang Zheng
- Department of Laboratory Medicine, Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
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12
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Pinilla L, Barbé F, de Gonzalo-Calvo D. MicroRNAs to guide medical decision-making in obstructive sleep apnea: A review. Sleep Med Rev 2021; 59:101458. [PMID: 33582532 DOI: 10.1016/j.smrv.2021.101458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
Obstructive sleep apnea (OSA) is a common and frequently underdiagnosed sleep disorder tightly associated with a wide range of morbidities and an elevated risk of the main causes of mortality. This condition represents a major public health concern due to its increasing worldwide prevalence and its serious pathological consequences. Current clinical guidelines support the importance of effective diagnosis and treatment of OSA and emphasize the unmet need for biomarkers to guide medical decision-making. In recent years, the noncoding transcriptome has emerged as a new opportunity for biomarker discovery. In this review, we provide a brief overview of the current understanding of noncoding RNAs, specifically microRNAs (miRNAs). Then, we carefully address the potential role of miRNAs as novel indicators for the management of both pediatric and adult OSA, highlighting their translational applicability, particularly for diagnosis and therapy allocation. Finally, we identify the gaps in the research state-of-art, discuss current methodological and conceptual limitations and propose future key steps and perspectives for the incorporation of miRNAs into routine clinical practice.
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Affiliation(s)
- Lucía Pinilla
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.
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13
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Optimal classification scores based on multivariate marker transformations. ASTA-ADVANCES IN STATISTICAL ANALYSIS 2021. [DOI: 10.1007/s10182-020-00388-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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de Gonzalo-Calvo D, Martínez-Camblor P, Bär C, Duarte K, Girerd N, Fellström B, Schmieder RE, Jardine AG, Massy ZA, Holdaas H, Rossignol P, Zannad F, Thum T. Improved cardiovascular risk prediction in patients with end-stage renal disease on hemodialysis using machine learning modeling and circulating microribonucleic acids. Theranostics 2020; 10:8665-8676. [PMID: 32754270 PMCID: PMC7392028 DOI: 10.7150/thno.46123] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/18/2020] [Indexed: 12/29/2022] Open
Abstract
Rationale: To test whether novel biomarkers, such as microribonucleic acids (miRNAs), and nonstandard predictive models, such as decision tree learning, provide useful information for medical decision-making in patients on hemodialysis (HD). Methods: Samples from patients with end-stage renal disease receiving HD included in the AURORA trial were investigated (n=810). The study included two independent phases: phase I (matched cases and controls, n=410) and phase II (unmatched cases and controls, n=400). The composite endpoint was cardiovascular death, nonfatal myocardial infarction or nonfatal stroke. miRNA quantification was performed using miRNA sequencing and RT-qPCR. The CART algorithm was used to construct regression tree models. A bagging-based procedure was used for validation. Results: In phase I, miRNA sequencing in a subset of samples (n=20) revealed miR-632 as a candidate (fold change=2.9). miR-632 was associated with the endpoint, even after adjusting for confounding factors (HR from 1.43 to 1.53). These findings were not reproduced in phase II. Regression tree models identified eight patient subgroups with specific risk patterns. miR-186-5p and miR-632 entered the tree by redefining two risk groups: patients older than 64 years and with hsCRP<0.827 mg/L and diabetic patients younger than 64 years. miRNAs improved the discrimination accuracy at the beginning of the follow-up (24 months) compared to the models without miRNAs (integrated AUC [iAUC]=0.71). Conclusions: The circulating miRNA profile complements conventional risk factors to identify specific cardiovascular risk patterns among patients receiving maintenance HD.
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15
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Association of Circulating microRNAs with Coronary Artery Disease and Usefulness for Reclassification of Healthy Individuals: The REGICOR Study. J Clin Med 2020; 9:jcm9051402. [PMID: 32397522 PMCID: PMC7290581 DOI: 10.3390/jcm9051402] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
Risk prediction tools cannot identify most individuals at high coronary artery disease (CAD) risk. Oxidized low-density lipoproteins (oxLDLs) and microRNAs are actively involved in atherosclerosis. Our aim was to examine the association of CAD and oxLDLs-induced microRNAs, and to assess the microRNAs predictive capacity of future CAD events. Human endothelial and vascular smooth muscle cells were treated with oxidized/native low-density lipoproteins, and microRNA expression was analyzed. Differentially expressed and CAD-related miRNAs were examined in serum samples from (1) a case-control study with 476 myocardial infarction (MI) patients and 487 controls, and (2) a case-cohort study with 105 incident CAD cases and 455 randomly-selected cohort participants. MicroRNA expression was analyzed with custom OpenArray plates, log rank tests and Cox regression models. Twenty-one microRNAs, two previously undescribed (hsa-miR-193b-5p and hsa-miR-1229-5p), were up- or down-regulated upon cell treatment with oxLDLs. One of the 21, hsa-miR-122-5p, was also upregulated in MI cases (fold change = 4.85). Of the 28 CAD-related microRNAs tested, 11 were upregulated in MI cases-1 previously undescribed (hsa-miR-16-5p)-, and 1/11 was also associated with CAD incidence (adjusted hazard ratio = 0.55 (0.35–0.88)) and improved CAD risk reclassification, hsa-miR-143-3p. We identified 2 novel microRNAs modulated by oxLDLs in endothelial cells, 1 novel microRNA upregulated in AMI cases compared to controls, and one circulating microRNA that improved CAD risk classification.
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16
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Vilades D, Martínez‐Camblor P, Ferrero‐Gregori A, Bär C, Lu D, Xiao K, Vea À, Nasarre L, Sanchez Vega J, Leta R, Carreras F, Thum T, Llorente‐Cortés V, de Gonzalo‐Calvo D. Plasma circular RNA hsa_circ_0001445 and coronary artery disease: Performance as a biomarker. FASEB J 2020; 34:4403-4414. [DOI: 10.1096/fj.201902507r] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022]
Affiliation(s)
- David Vilades
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
| | | | - Andreu Ferrero‐Gregori
- Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
- REBIRTH Center for Translational Regenerative Medicine Hannover Medical School Hannover Germany
| | - Dongchao Lu
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
| | - Àngela Vea
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
| | - Laura Nasarre
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
| | - Jesus Sanchez Vega
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
| | - Rubén Leta
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
| | - Francesc Carreras
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
- REBIRTH Center for Translational Regenerative Medicine Hannover Medical School Hannover Germany
| | - Vicenta Llorente‐Cortés
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC) Barcelona Spain
| | - David de Gonzalo‐Calvo
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC) Barcelona Spain
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Calderon-Dominguez M, Belmonte T, Quezada-Feijoo M, Ramos-Sánchez M, Fernández-Armenta J, Pérez-Navarro A, Cesar S, Peña-Peña L, Vea À, Llorente-Cortés V, Mangas A, de Gonzalo-Calvo D, Toro R. Emerging role of microRNAs in dilated cardiomyopathy: evidence regarding etiology. Transl Res 2020; 215:86-101. [PMID: 31505160 DOI: 10.1016/j.trsl.2019.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 02/08/2023]
Abstract
Dilated cardiomyopathy (DCM) is a heart muscle disease characterized by ventricular dilation and systolic dysfunction in the absence of abnormal loading conditions or coronary artery disease. This cardiac disorder is a major health problem due to its high prevalence, morbidity, and mortality. DCM is a complex disease with a common phenotype but heterogeneous pathological mechanisms. Early etiological diagnosis and prognosis stratification is crucial for the clinical management of the patient. Advances in imaging technology and genetic tests have provided useful tools for clinical practice. Nevertheless, the assessment of the disease remains challenging. Novel noninvasive indicators are still needed to assist in decision-making. microRNAs (miRNAs), a group of small noncoding RNAs, have been identified as key mediators of cell biology. They are found in a stable form in body fluids and their concentration is altered in response to stress. Previous research has suggested that the miRNA signature constitutes a novel source of noninvasive biomarkers for a wide array of cardiovascular diseases. Specifically, several studies have reported the potential role of miRNAs as clinical indicators among the etiologies of DCM. However, this field has not been reviewed in detail. Here, we summarize the evidence of intracellular and circulating miRNAs in DCM and their usefulness in the development of novel diagnostic, prognostic and therapeutic approaches, with a focus on DCM etiology. Although the findings are still preliminary, due to methodological and technical limitations and the lack of robust population-based studies, miRNAs constitute a promising tool to assist in the clinical management of DCM.
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Affiliation(s)
- Maria Calderon-Dominguez
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, University of Cádiz, Cádiz, Spain
| | - Thalía Belmonte
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, University of Cádiz, Cádiz, Spain
| | - Maribel Quezada-Feijoo
- Department of Cardiology, Cruz Roja Central Hospital, Madrid, Spain; Alfonso X University (UAX), Madrid, Spain
| | - Monica Ramos-Sánchez
- Department of Cardiology, Cruz Roja Central Hospital, Madrid, Spain; Alfonso X University (UAX), Madrid, Spain
| | - Juan Fernández-Armenta
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, University of Cádiz, Cádiz, Spain; Department of Cardiology, Puerta del Mar Universitary Hospital, Cádiz, Spain
| | - Amparo Pérez-Navarro
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, University of Cádiz, Cádiz, Spain
| | - Sergi Cesar
- Department of Pediatric Cardiology, Sant Joan de Déu Hospital, Barcelona, Spain
| | - Luisa Peña-Peña
- Department of Cardiology, Virgen del Rocio Universitary Hospital, Sevilla, Spain
| | - Àngela Vea
- Institute of Biomedical Research of Barcelona (IIBB) - Spanish National Research Council (CSIC), Barcelona, Spain
| | - Vicenta Llorente-Cortés
- Institute of Biomedical Research of Barcelona (IIBB) - Spanish National Research Council (CSIC), Barcelona, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain; CIBERCV, Institute of Health Carlos III, Madrid, Spain
| | - Alipio Mangas
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, University of Cádiz, Cádiz, Spain; Department of Internal Medicine, Puerta del Mar Universitary Hospital, Cádiz, Spain; Department of Medicine, School of Medicine, University of Cádiz, Cádiz, Spain
| | - David de Gonzalo-Calvo
- Institute of Biomedical Research of Barcelona (IIBB) - Spanish National Research Council (CSIC), Barcelona, Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain; CIBERCV, Institute of Health Carlos III, Madrid, Spain.
| | - Rocio Toro
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, University of Cádiz, Cádiz, Spain; Department of Internal Medicine, Puerta del Mar Universitary Hospital, Cádiz, Spain; Department of Medicine, School of Medicine, University of Cádiz, Cádiz, Spain.
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18
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Wang XB, Cui NH, Liu X, Ming L. Identification of a blood-based 12-gene signature that predicts the severity of coronary artery stenosis: An integrative approach based on gene network construction, Support Vector Machine algorithm, and multi-cohort validation. Atherosclerosis 2019; 291:34-43. [PMID: 31689620 DOI: 10.1016/j.atherosclerosis.2019.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/25/2019] [Accepted: 10/08/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND AIMS We aimed to identify a blood-based gene expression score (GES) to predict the severity of coronary artery stenosis in patients with known or suspected coronary artery disease (CAD) by integrative use of gene network construction, Support Vector Machine (SVM) algorithm, and multi-cohort validation. METHODS In the discovery phase, a public blood-based microarray dataset of 110 patients with known CAD was analyzed by weighted gene coexpression network analysis and protein-protein interaction network analysis to identify candidate hub genes. In the training set with 151 CAD patients, bioinformatically identified hub genes were experimentally verified by real-time polymerase chain reaction, and statistically filtered with the SVM algorithm to develop a GES. Internal and external validation of GES was performed in patients with suspected CAD from two validation cohorts (n = 209 and 206). RESULTS The discovery phase screened 15 network-centric hub genes significantly correlated with the Duke CAD Severity Index. In the training cohort, 12 of 15 hub genes were filtered to construct a blood-based GES12, which showed good discrimination for higher modified Gensini scores (AUC: 0.798 and 0.812), higher Sullivan Extent scores (AUC: 0.776 and 0.778), and the presence of obstructive CAD (AUC: 0.834 and 0.792) in two validation cohorts. A nomogram comprising GES12, smoking status, hypertension status, low density lipoprotein cholesterol level, and body mass index further improved performance, with respect to discrimination, risk classification, and clinical utility, for prediction of coronary stenosis severity. CONCLUSIONS GES12 is useful in predicting the severity of coronary artery stenosis in patients with known or suspected CAD.
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Affiliation(s)
- Xue-Bin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ning-Hua Cui
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Xia'nan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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