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Ma Q, Zhang YH, Guo W, Feng K, Huang T, Cai YD. Machine Learning in Identifying Marker Genes for Congenital Heart Diseases of Different Cardiac Cell Types. Life (Basel) 2024; 14:1032. [PMID: 39202774 PMCID: PMC11355424 DOI: 10.3390/life14081032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Congenital heart disease (CHD) represents a spectrum of inborn heart defects influenced by genetic and environmental factors. This study advances the field by analyzing gene expression profiles in 21,034 cardiac fibroblasts, 73,296 cardiomyocytes, and 35,673 endothelial cells, utilizing single-cell level analysis and machine learning techniques. Six CHD conditions: dilated cardiomyopathy (DCM), donor hearts (used as healthy controls), hypertrophic cardiomyopathy (HCM), heart failure with hypoplastic left heart syndrome (HF_HLHS), Neonatal Hypoplastic Left Heart Syndrome (Neo_HLHS), and Tetralogy of Fallot (TOF), were investigated for each cardiac cell type. Each cell sample was represented by 29,266 gene features. These features were first analyzed by six feature-ranking algorithms, resulting in several feature lists. Then, these lists were fed into incremental feature selection, containing two classification algorithms, to extract essential gene features and classification rules and build efficient classifiers. The identified essential genes can be potential CHD markers in different cardiac cell types. For instance, the LASSO identified key genes specific to various heart cell types in CHD subtypes. FOXO3 was found to be up-regulated in cardiac fibroblasts for both Dilated and hypertrophic cardiomyopathy. In cardiomyocytes, distinct genes such as TMTC1, ART3, ARHGAP24, SHROOM3, and XIST were linked to dilated cardiomyopathy, Neo-Hypoplastic Left Heart Syndrome, hypertrophic cardiomyopathy, HF-Hypoplastic Left Heart Syndrome, and Tetralogy of Fallot, respectively. Endothelial cell analysis further revealed COL25A1, NFIB, and KLF7 as significant genes for dilated cardiomyopathy, hypertrophic cardiomyopathy, and Tetralogy of Fallot. LightGBM, Catboost, MCFS, RF, and XGBoost further delineated key genes for specific CHD subtypes, demonstrating the efficacy of machine learning in identifying CHD-specific genes. Additionally, this study developed quantitative rules for representing the gene expression patterns related to CHDs. This research underscores the potential of machine learning in unraveling the molecular complexities of CHD and establishes a foundation for future mechanism-based studies.
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Affiliation(s)
- Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
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Kennedy KG, Ghugre NR, Roifman I, Qi X, Saul K, McCrindle BW, Macgowan CK, MacIntosh BJ, Goldstein BI. Impaired coronary microvascular reactivity in youth with bipolar disorder. Psychol Med 2024; 54:1196-1206. [PMID: 37905407 DOI: 10.1017/s0033291723003021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
BACKGROUND Cardiovascular disease (CVD) is excessively prevalent and premature in bipolar disorder (BD), even after controlling for traditional cardiovascular risk factors. The increased risk of CVD in BD may be subserved by microvascular dysfunction. We examined coronary microvascular function in relation to youth BD. METHODS Participants were 86 youth, ages 13-20 years (n = 39 BD, n = 47 controls). Coronary microvascular reactivity (CMVR) was assessed using quantitative T2 magnetic resonance imaging during a validated breathing-paradigm. Quantitative T2 maps were acquired at baseline, following 60-s of hyperventilation, and every 10-s thereafter during a 40-s breath-hold. Left ventricular structure and function were evaluated based on 12-15 short- and long-axis cardiac-gated cine images. A linear mixed-effects model that controlled for age, sex, and body mass index assessed for between-group differences in CMVR (time-by-group interaction). RESULTS The breathing-paradigm induced a significant time-related increase in T2 relaxation time for all participants (i.e. CMVR; β = 0.36, p < 0.001). CMVR was significantly lower in BD v. controls (β = -0.11, p = 0.002). Post-hoc analyses found lower T2 relaxation time in BD youth after 20-, 30-, and 40 s of breath-holding (d = 0.48, d = 0.72, d = 0.91, respectively; all pFDR < 0.01). Gross left ventricular structure and function (e.g. mass, ejection fraction) were within normal ranges and did not differ between groups. CONCLUSION Youth with BD showed evidence of subclinically impaired coronary microvascular function, despite normal gross cardiac structure and function. These results converge with prior findings in adults with major depressive disorder and post-traumatic stress disorder. Future studies integrating larger samples, prospective follow-up, and blood-based biomarkers are warranted.
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Affiliation(s)
- Kody G Kennedy
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Pharmacology, University of Toronto, Toronto, ON, Canada
| | - Nilesh R Ghugre
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Idan Roifman
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Xiuling Qi
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Kayla Saul
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Brian W McCrindle
- Division of Pediatric Cardiology, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Christopher K Macgowan
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Division of Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bradley J MacIntosh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Hurvitz Brain Sciences, Sunnybrook Research Institute, Toronto, ON, Canada
- Computational Radiology & Artificial Intelligence (CRAI) unit, Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Benjamin I Goldstein
- Centre for Youth Bipolar Disorder, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Pharmacology, University of Toronto, Toronto, ON, Canada
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Pesonen E, Liuba P, Aburawi EH. Review findings included diminished coronary flow reserve after surgery in children with congenital heart disease and inflammation. Acta Paediatr 2019; 108:218-223. [PMID: 30312493 DOI: 10.1111/apa.14613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/08/2018] [Accepted: 10/08/2018] [Indexed: 11/29/2022]
Abstract
AIM The aim of this review was to develop a deeper knowledge of the physiology of coronary blood flow and coronary flow reserve in young patients with congenital heart disease and inflammatory diseases. METHODS We searched for papers published in English on coronary blood flow and coronary flow reserve using the PubMed and Google search databases. This identified 42 papers extending back to 1976 and a book from 2008 (Davis et al. Microcirculation. Boston, MA: Elsevier, 2008: 161-284). RESULTS Our review showed that the implications of coronary blood flow and coronary flow reserve in paediatric patients with congenital heart disease and inflammatory diseases are still not fully understood. However, a key finding was that coronary flow reserve was diminished in patients with congenital heart disease and inflammation after surgery, with or without a cardiopulmonary bypass. Other findings discussed by this review relate to volume and pressure overload in acyanotic congenital heart disease, reduced myocardial perfusion and cyanotic congenital heart disease. CONCLUSION We still have much to discover about paediatric patients with congenital heart disease and inflammatory diseases. Understanding the pathophysiology of coronary blood flow could help the postoperative treatment of such patients.
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Affiliation(s)
- Erkki Pesonen
- Children's Heart Center; Skåne University Hospital Lund; Lund University; Lund Sweden
| | - Petru Liuba
- Children's Heart Center; Skåne University Hospital Lund; Lund University; Lund Sweden
| | - Elhadi H. Aburawi
- Children's Heart Center; Skåne University Hospital Lund; Lund University; Lund Sweden
- Department of Paediatrics; College of Medicine and Health Sciences; United Arab Emirates University; Al-Ain United Arab Emirates
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Cai QZ, Liang Y, Zhu ZH, Lu XZ. Influence of percutaneous atrial septal defect closure on inter- and intra-ventricular mechanical dyssynchrony in adults: evaluation of strain pattern. Int J Cardiovasc Imaging 2014; 30:721-7. [PMID: 24504492 DOI: 10.1007/s10554-014-0385-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/31/2014] [Indexed: 11/30/2022]
Abstract
Previous studies using speckle-tracking echocardiography (STE) for quantifying the functions of the right and left ventricles (RV and LV, respectively) in the presence of percutaneous atrial septal defect (ASD) closure have focused on the peak systolic strain (PSS). This study investigated changes in the mechanical dyssynchrony of ventricular contraction before and after ASD closure, issues that have been little addressed in the literature. Thirty-one adults with ASD were studied using two-dimensional STE before and 24 h after ASD closure. Thirty-one healthy age- and sex-matched subjects were recruited as controls. Global and segmental PSS values from the longitudinal, circumferential, and radial directions were analyzed. The time to peak systolic strain (PSST) and the standard deviation of the time to peak strain (SDT) among segments in each direction were calculated, to investigate the inter- and intra-ventricular mechanical dyssynchrony in these patients and improvements after closure. Compared to the control group, patients with ASD had higher RV free-wall longitudinal systolic strain, with increased PSST and SDT. The SDT values of the LV longitudinal and circumferential strains were also increased. By 24 h after ASD closure, the RV free-wall longitudinal strain and its PSST and SDT had reverted to normal levels. The LV circumferential strain was increased, and its SDT was decreased. The contraction period of the RV and myocardial contraction dyssynchrony in the RV and LV were increased in ASD patients. The inter- and intra-ventricular mechanical utilities were improved after percutaneous closure of the ASD.
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MESH Headings
- Adult
- Aged
- Cardiac Catheterization
- Case-Control Studies
- Echocardiography, Doppler
- Female
- Heart Septal Defects, Atrial/complications
- Heart Septal Defects, Atrial/diagnostic imaging
- Heart Septal Defects, Atrial/physiopathology
- Heart Septal Defects, Atrial/therapy
- Humans
- Male
- Middle Aged
- Myocardial Contraction
- Recovery of Function
- Time Factors
- Treatment Outcome
- Ventricular Dysfunction, Left/diagnostic imaging
- Ventricular Dysfunction, Left/etiology
- Ventricular Dysfunction, Left/physiopathology
- Ventricular Dysfunction, Right/diagnostic imaging
- Ventricular Dysfunction, Right/etiology
- Ventricular Dysfunction, Right/physiopathology
- Ventricular Function, Left
- Ventricular Function, Right
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Affiliation(s)
- Qi-Zhe Cai
- Department of Echocardiography, Cardiovascular Institute, Fu Wai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100037, China
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A welcome to the new journal, International Journal of Cardiology - Heart and Vessels (IJC-H + V). INTERNATIONAL JOURNAL OF CARDIOLOGY. HEART & VESSELS 2013; 1:1-10. [PMID: 29450152 PMCID: PMC5801079 DOI: 10.1016/j.ijchv.2013.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 11/03/2013] [Indexed: 11/20/2022]
Abstract
A new journal has been launched: IJC - Heart and Vessels [1]. It builds upon the success of the main journal International Journal of Cardiology. As an introduction to the new journal we will be publishing a series of summaries of the topics to be covered, highlighting the most important papers in the field that have been published recently in the main journal, International Journal of Cardiology. This article describes a topic review of congenital heart disease. IJC has become one of the most important sources of quality papers in this field and many excellent publications have been published in the main journal. The expansion of space occasioned by the launch of IJC - Heart and Vessels will allow us to publish more high quality papers in the expanding field of congenital heart disease.
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Aburawi EH, Souid AK, Liuba P, Zoubeidi T, Pesonen E. Early changes in myocardial repolarization and coronary perfusion after cardiopulmonary bypass surgery for ASD repair in children. BMC Cardiovasc Disord 2013; 13:67. [PMID: 24015980 PMCID: PMC3846500 DOI: 10.1186/1471-2261-13-67] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 09/03/2013] [Indexed: 11/25/2022] Open
Abstract
Background In adults, impaired myocardial repolarization and increased risk of arrhythmia are known consequences of open heart surgery. Little is known, however, about post-operative consequences of cardiopulmonary bypass surgery in children. The aim of this study was to assess ventricular repolarization and coronary perfusion after bypass surgery for atrial septal defect (ASD) repair in children. Methods Twelve patients with ASD were assessed one day before and 5–6 days after ASD repair. Myocardial repolarization (corrected QT interval, QTc, QT dispersion, QTd, and PQ interval) was determined on 12-lead electrocardiograms. Coronary flow in proximal left anterior descending artery (peak flow velocity in diastole, PFVd) was assessed by transthoracic Doppler echocardiography. Results Ten of the 12 (83%) children had normal myocardial repolarization before and after surgery. After surgery, QTc increased 1-9% in 5 (42%) patients, decreased 2-11% in 5 (42%) patients and did not change in 2 (16%) patients. Post-op QTc positively correlated with bypass time (R=0.686, p=0.014) and changes in PFVd (R=0.741, p=0.006). After surgery, QTd increased 33-67% in 4 (33%) patients, decreased 25-50% in 6 patients (50%) and did not change in 2 (16%) patients. After surgery, PQ interval increased 5-30% in 4 (33%) patients, decreased 4-29% in 6 (50%) patients and did not change in 1 (8%) patient. Post-op PQ positively correlated with bypass time (R=0.636, p=0.027). As previously reported, PFVd significantly increased after surgery (p<0.001). Conclusions Changes in QTc, PQ and PFVd are common in young children undergoing surgery for ASD repair. Post-op QTc significantly correlates with bypass time, suggesting prolonged cardiopulmonary bypass may impair ventricular repolarization. Post-op QTc significantly correlates with PFVd changes, suggesting increased coronary flow may also impair ventricular repolarization. The clinical significance and reversibility of these alternations require further investigations.
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Affiliation(s)
- Elhadi H Aburawi
- Pediatric Department, Section of Pediatric Cardiology, Skane University Hospital, Lund University, Lund, Sweden.
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Cuypers J, Leirgul E, Larsen TH, Berg A, Omdal TR, Greve G. Assessment of vascular reactivity in the peripheral and coronary arteries by Cine 3T-magnetic resonance imaging in young normotensive adults after surgery for coarctation of the aorta. Pediatr Cardiol 2013; 34:661-9. [PMID: 23064837 DOI: 10.1007/s00246-012-0522-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 09/11/2012] [Indexed: 01/22/2023]
Abstract
This study aimed to investigate whether coarctation of the aorta in infancy indicates an altered vascular reactivity in the peripheral and coronary arteries apart from the secondary effect of hypertension or other complications of the disease. Patients with repaired coarctation of the aorta have a high prevalence of premature cardiovascular complications. The etiology still is not fully understood, and the cause is most likely multifactorial. Endothelial function was assessed by peripheral flow mediated dilation (FMD) and coronary flow reserve (CFR) in a study of 10 control subjects and 10 patients with a successfully repaired coarctation of the aorta (mean age, 20.9 years; 20.5 years after repair). No one had re- or rest-coarctation of the aorta, hypertension, pathologic blood pressure response during exercise, or associated cardiac malformations such as bicuspid aortic valve. CFR was achieved by phase-contrast velocity encoding cine magnetic resonance imaging in the coronary sinus before and during infusion with adenosine (0.14 mg/kg/min). FMD was measured in the brachial artery before and after 5 min of arterial occlusion. A normal CFR and FMD was found in both groups. Most studies have been conducted with large, unselected groups. The current study group represented the best outcome of the coarctation spectrum (i.e., patients with no evidence of a residual gradient across the coarctation site or systemic hypertension). The findings reassuringly suggest that significant endothelial dysfunction and atherosclerotic changes were not present in this selected cohort.
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Affiliation(s)
- Jochem Cuypers
- Department of Clinical Medicine, University of Bergen, 5021, Bergen, Norway.
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