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Moreno-Manuel AI, Macías Á, Cruz FM, Gutiérrez LK, Martínez F, González-Guerra A, Martínez Carrascoso I, Bermúdez-Jimenez FJ, Sánchez-Pérez P, Vera-Pedrosa ML, Ruiz-Robles JM, Bernal JA, Jalife J. The Kir2.1E299V mutation increases atrial fibrillation vulnerability while protecting the ventricles against arrhythmias in a mouse model of short QT syndrome type 3. Cardiovasc Res 2024; 120:490-505. [PMID: 38261726 PMCID: PMC11060485 DOI: 10.1093/cvr/cvae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
AIMS Short QT syndrome type 3 (SQTS3) is a rare arrhythmogenic disease caused by gain-of-function mutations in KCNJ2, the gene coding the inward rectifier potassium channel Kir2.1. We used a multidisciplinary approach and investigated arrhythmogenic mechanisms in an in-vivo model of de-novo mutation Kir2.1E299V identified in a patient presenting an extremely abbreviated QT interval and paroxysmal atrial fibrillation. METHODS AND RESULTS We used intravenous adeno-associated virus-mediated gene transfer to generate mouse models, and confirmed cardiac-specific expression of Kir2.1WT or Kir2.1E299V. On ECG, the Kir2.1E299V mouse recapitulated the QT interval shortening and the atrial-specific arrhythmia of the patient. The PR interval was also significantly shorter in Kir2.1E299V mice. Patch-clamping showed extremely abbreviated action potentials in both atrial and ventricular Kir2.1E299V cardiomyocytes due to a lack of inward-going rectification and increased IK1 at voltages positive to -80 mV. Relative to Kir2.1WT, atrial Kir2.1E299V cardiomyocytes had a significantly reduced slope conductance at voltages negative to -80 mV. After confirming a higher proportion of heterotetrameric Kir2.x channels containing Kir2.2 subunits in the atria, in-silico 3D simulations predicted an atrial-specific impairment of polyamine block and reduced pore diameter in the Kir2.1E299V-Kir2.2WT channel. In ventricular cardiomyocytes, the mutation increased excitability by shifting INa activation and inactivation in the hyperpolarizing direction, which protected the ventricle against arrhythmia. Moreover, Purkinje myocytes from Kir2.1E299V mice manifested substantially higher INa density than Kir2.1WT, explaining the abbreviation in the PR interval. CONCLUSION The first in-vivo mouse model of cardiac-specific SQTS3 recapitulates the electrophysiological phenotype of a patient with the Kir2.1E299V mutation. Kir2.1E299V eliminates rectification in both cardiac chambers but protects against ventricular arrhythmias by increasing excitability in both Purkinje-fiber network and ventricles. Consequently, the predominant arrhythmias are supraventricular likely due to the lack of inward rectification and atrial-specific reduced pore diameter of the Kir2.1E299V-Kir2.2WT heterotetramer.
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MESH Headings
- Animals
- Humans
- Mice
- Action Potentials
- Arrhythmias, Cardiac/genetics
- Arrhythmias, Cardiac/physiopathology
- Arrhythmias, Cardiac/metabolism
- Atrial Fibrillation/genetics
- Atrial Fibrillation/physiopathology
- Atrial Fibrillation/metabolism
- Disease Models, Animal
- Genetic Predisposition to Disease
- Heart Rate/genetics
- Heart Ventricles/metabolism
- Heart Ventricles/physiopathology
- Mice, Inbred C57BL
- Mice, Transgenic
- Mutation
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Phenotype
- Potassium Channels, Inwardly Rectifying/genetics
- Potassium Channels, Inwardly Rectifying/metabolism
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Affiliation(s)
- Ana I Moreno-Manuel
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Álvaro Macías
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Francisco M Cruz
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Lilian K Gutiérrez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Fernando Martínez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Andrés González-Guerra
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Isabel Martínez Carrascoso
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Francisco José Bermúdez-Jimenez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Department of Cardiology, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Patricia Sánchez-Pérez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | | | - Juan Manuel Ruiz-Robles
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Juan A Bernal
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - José Jalife
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Departments of Internal Medicine and Molecular and Integrative Physiology, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI 4810, USA
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2
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Iacobas DA, Allen H, Iacobas S. Low-Salt Diet Regulates the Metabolic and Signal Transduction Genomic Fabrics, and Remodels the Cardiac Normal and Chronic Pathological Pathways. Curr Issues Mol Biol 2024; 46:2355-2385. [PMID: 38534766 DOI: 10.3390/cimb46030150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Low-salt diet (LSD) is a constant recommendation to hypertensive patients, but the genomic mechanisms through which it improves cardiac pathophysiology are still not fully understood. Our publicly accessible transcriptomic dataset of the left ventricle myocardium of adult male mice subjected to prolonged LSD or normal diet was analyzed from the perspective of the Genomic Fabric Paradigm. We found that LSD shifted the metabolic priorities by increasing the transcription control for fatty acids biosynthesis while decreasing it for steroid hormone biosynthesis. Moreover, LSD remodeled pathways responsible for cardiac muscle contraction (CMC), chronic Chagas (CHA), diabetic (DIA), dilated (DIL), and hypertrophic (HCM) cardiomyopathies, and their interplays with the glycolysis/glucogenesis (GLY), oxidative phosphorylation (OXP), and adrenergic signaling in cardiomyocytes (ASC). For instance, the statistically (p < 0.05) significant coupling between GLY and ASC was reduced by LSD from 13.82% to 2.91% (i.e., -4.75×), and that of ASC with HCM from 10.50% to 2.83% (-3.71×). The substantial up-regulation of the CMC, ASC, and OXP genes, and the significant weakening of the synchronization of the expression of the HCM, CHA, DIA, and DIL genes within their respective fabrics justify the benefits of the LSD recommendation.
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Affiliation(s)
- Dumitru A Iacobas
- Undergraduate Medical Academy, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Haile Allen
- Undergraduate Medical Academy, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA
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3
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Harbuz I, Banciu DD, David R, Cercel C, Cotîrță O, Ciurea BM, Radu SM, Dinescu S, Jinga SI, Banciu A. Perspectives on Scaffold Designs with Roles in Liver Cell Asymmetry and Medical and Industrial Applications by Using a New Type of Specialized 3D Bioprinter. Int J Mol Sci 2023; 24:14722. [PMID: 37834167 PMCID: PMC10573170 DOI: 10.3390/ijms241914722] [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: 06/20/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Cellular asymmetry is an important element of efficiency in the compartmentalization of intracellular chemical reactions that ensure efficient tissue function. Improving the current 3D printing methods by using cellular asymmetry is essential in producing complex tissues and organs such as the liver. The use of cell spots containing at least two cells and basement membrane-like bio support materials allows cells to be tethered at two points on the basement membrane and with another cell in order to maintain cell asymmetry. Our model is a new type of 3D bioprinter that uses oriented multicellular complexes with cellular asymmetry. This novel approach is necessary to replace the sequential and slow processes of organogenesis with rapid methods of growth and 3D organ printing. The use of the extracellular matrix in the process of bioprinting with cells allows one to preserve the cellular asymmetry in the 3D printing process and thus preserve the compartmentalization of biological processes and metabolic efficiency.
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Affiliation(s)
- Iuliana Harbuz
- Department of Biomaterials and Medical Devices, Faculty of Medical Engineering, Politehnica University of Bucharest, 1-7 Gh. Polizu Street, 011061 Bucharest, Romania; (I.H.); (O.C.); (B.M.C.); (S.I.J.)
| | - Daniel Dumitru Banciu
- Department of Biomaterials and Medical Devices, Faculty of Medical Engineering, Politehnica University of Bucharest, 1-7 Gh. Polizu Street, 011061 Bucharest, Romania; (I.H.); (O.C.); (B.M.C.); (S.I.J.)
| | - Rodica David
- Institute for Research on the Quality of Society and the Sciences of Education, University Constantin Brancusi of Targu Jiu, Republicii 1, 210185 Targu Jiu, Romania;
- Department of Mechanical Industrial and Transportation Engineering, University of Petrosani, 332006 Petrosani, Romania; (S.M.R.); (S.D.)
| | - Cristina Cercel
- University of Medicine and Pharmacy “Carol Davila” Bucharest, 37 Dionisie Lupu Street, 020021 Bucharest, Romania;
| | - Octavian Cotîrță
- Department of Biomaterials and Medical Devices, Faculty of Medical Engineering, Politehnica University of Bucharest, 1-7 Gh. Polizu Street, 011061 Bucharest, Romania; (I.H.); (O.C.); (B.M.C.); (S.I.J.)
| | - Bogdan Marius Ciurea
- Department of Biomaterials and Medical Devices, Faculty of Medical Engineering, Politehnica University of Bucharest, 1-7 Gh. Polizu Street, 011061 Bucharest, Romania; (I.H.); (O.C.); (B.M.C.); (S.I.J.)
| | - Sorin Mihai Radu
- Department of Mechanical Industrial and Transportation Engineering, University of Petrosani, 332006 Petrosani, Romania; (S.M.R.); (S.D.)
| | - Stela Dinescu
- Department of Mechanical Industrial and Transportation Engineering, University of Petrosani, 332006 Petrosani, Romania; (S.M.R.); (S.D.)
| | - Sorin Ion Jinga
- Department of Biomaterials and Medical Devices, Faculty of Medical Engineering, Politehnica University of Bucharest, 1-7 Gh. Polizu Street, 011061 Bucharest, Romania; (I.H.); (O.C.); (B.M.C.); (S.I.J.)
| | - Adela Banciu
- Department of Biomaterials and Medical Devices, Faculty of Medical Engineering, Politehnica University of Bucharest, 1-7 Gh. Polizu Street, 011061 Bucharest, Romania; (I.H.); (O.C.); (B.M.C.); (S.I.J.)
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4
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Ahmad FS, Jin Y, Grassam-Rowe A, Zhou Y, Yuan M, Fan X, Zhou R, Mu-u-min R, O'Shea C, Ibrahim AM, Hyder W, Aguib Y, Yacoub M, Pavlovic D, Zhang Y, Tan X, Lei M, Terrar DA. Generation of cardiomyocytes from human-induced pluripotent stem cells resembling atrial cells with ability to respond to adrenoceptor agonists. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220312. [PMID: 37122218 PMCID: PMC10150206 DOI: 10.1098/rstb.2022.0312] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/07/2022] [Indexed: 05/02/2023] Open
Abstract
Atrial fibrillation (AF) is the most common chronic arrhythmia presenting a heavy disease burden. We report a new approach for generating cardiomyocytes (CMs) resembling atrial cells from human-induced pluripotent stem cells (hiPSCs) using a combination of Gremlin 2 and retinoic acid treatment. More than 40% of myocytes showed rod-shaped morphology, expression of CM proteins (including ryanodine receptor 2, α-actinin-2 and F-actin) and striated appearance, all of which were broadly similar to the characteristics of adult atrial myocytes (AMs). Isolated myocytes were electrically quiescent until stimulated to fire action potentials with an AM profile and an amplitude of approximately 100 mV, arising from a resting potential of approximately -70 mV. Single-cell RNA sequence analysis showed a high level of expression of several atrial-specific transcripts including NPPA, MYL7, HOXA3, SLN, KCNJ4, KCNJ5 and KCNA5. Amplitudes of calcium transients recorded from spontaneously beating cultures were increased by the stimulation of α-adrenoceptors (activated by phenylephrine and blocked by prazosin) or β-adrenoceptors (activated by isoproterenol and blocked by CGP20712A). Our new approach provides human AMs with mature characteristics from hiPSCs which will facilitate drug discovery by enabling the study of human atrial cell signalling pathways and AF. This article is part of the theme issue 'The heartbeat: its molecular basis and physiological mechanisms'.
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Affiliation(s)
- Faizzan S. Ahmad
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
- Cure8bio, Inc, 395 Fulton Street, Westbury, NY 11590, USA
| | - Yongcheng Jin
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | | | - Yafei Zhou
- Key Laboratory of Medical Electrophysiology of the Ministry of Education and Institute of Cardiovascular Research, Southwest Medical University, Luzhou 6400, People's Republic of China
- Shaanxi Institute for Pediatric Diseases, Department of Cardiology, Xi'an Children's Hospital, Xi'an 710003, People's Republic of China
| | - Meng Yuan
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Xuehui Fan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education and Institute of Cardiovascular Research, Southwest Medical University, Luzhou 6400, People's Republic of China
| | - Rui Zhou
- Key Laboratory of Medical Electrophysiology of the Ministry of Education and Institute of Cardiovascular Research, Southwest Medical University, Luzhou 6400, People's Republic of China
| | - Razik Mu-u-min
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Christopher O'Shea
- Institute of Cardiovascular Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ayman M. Ibrahim
- Aswan Heart Centre, Aswan 1242770, Egypt
- Department of Zoology, Faculty of Science, Cairo University, Cairo 12613, Egypt
| | - Wajiha Hyder
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Yasmine Aguib
- Aswan Heart Centre, Aswan 1242770, Egypt
- National Heart and Lung Institute, Heart Science Centre, Imperial College London, Middlesex SW3 6LY, UK
| | - Magdi Yacoub
- Aswan Heart Centre, Aswan 1242770, Egypt
- National Heart and Lung Institute, Heart Science Centre, Imperial College London, Middlesex SW3 6LY, UK
| | - Davor Pavlovic
- Institute of Cardiovascular Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yanmin Zhang
- Shaanxi Institute for Pediatric Diseases, Department of Cardiology, Xi'an Children's Hospital, Xi'an 710003, People's Republic of China
| | - Xiaoqiu Tan
- Key Laboratory of Medical Electrophysiology of the Ministry of Education and Institute of Cardiovascular Research, Southwest Medical University, Luzhou 6400, People's Republic of China
| | - Ming Lei
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Derek A. Terrar
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
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5
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Mathew R, Iacobas S, Huang J, Iacobas DA. Metabolic Deregulation in Pulmonary Hypertension. Curr Issues Mol Biol 2023; 45:4850-4874. [PMID: 37367058 DOI: 10.3390/cimb45060309] [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: 04/27/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The high morbidity and mortality rate of pulmonary arterial hypertension (PAH) is partially explained by metabolic deregulation. The present study complements our previous publication in "Genes" by identifying significant increases of the glucose transporter solute carrier family 2 (Slc2a1), beta nerve growth factor (Ngf), and nuclear factor erythroid-derived 2-like 2 (Nfe2l2) in three standard PAH rat models. PAH was induced by subjecting the animals to hypoxia (HO), or by injecting with monocrotaline in either normal (CM) or hypoxic (HM) atmospheric conditions. The Western blot and double immunofluorescent experiments were complemented with novel analyses of previously published transcriptomic datasets of the animal lungs from the perspective of the Genomic Fabric Paradigm. We found substantial remodeling of the citrate cycle, pyruvate metabolism, glycolysis/gluconeogenesis, and fructose and mannose pathways. According to the transcriptomic distance, glycolysis/gluconeogenesis was the most affected functional pathway in all three PAH models. PAH decoupled the coordinated expression of many metabolic genes, and replaced phosphomannomutase 2 (Pmm2) with phosphomannomutase 1 (Pmm1) in the center of the fructose and mannose metabolism. We also found significant regulation of key genes involved in PAH channelopathies. In conclusion, our data show that metabolic dysregulation is a major PAH pathogenic factor.
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Affiliation(s)
- Rajamma Mathew
- Department of Pediatrics, New York Medical College, Valhalla, NY 10595, USA
- Department of Physiology, New York Medical College, Valhalla, NY 10595, USA
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA
| | - Jing Huang
- Department of Pathology and Laboratory Medicine, Rutgers University Biomedical and Health Sciences, New Brunswick, NJ 08901, USA
| | - Dumitru Andrei Iacobas
- Personalized Genomics Laboratory, Texas Undergraduate Medical Academy, Prairie View A&M University, Prairie View, TX 77446, USA
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Souza DS, Chignalia AZ, Carvalho-de-Souza JL. Modulation of cardiac voltage-activated K + currents by glypican 1 heparan sulfate proteoglycan. Life Sci 2022; 308:120916. [PMID: 36049528 PMCID: PMC11105158 DOI: 10.1016/j.lfs.2022.120916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/15/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Glypican 1 (Gpc1) is a heparan sulfate proteoglycan attached to the cell membrane via a glycosylphosphatidylinositol anchor, where it holds glycosaminoglycans nearby. We have recently shown that Gpc1 knockout (Gpc1-/-) mice feature decreased systemic blood pressure. To date, none has been reported regarding the role of Gpc1 on the electrical properties of the heart and specifically, in regard to a functional interaction between Gpc1 and voltage-gated K+ channels. METHODS We used echocardiography and in vivo (electrocardiographic recordings) and in vitro (patch clamping) electrophysiology to study mechanical and electric properties of mice hearts. We used RT-PCR to probe K+ channels' gene transcription in heart tissue. RESULTS Gpc1-/- hearts featured increased cardiac stroke volume and preserved ejection fraction. Gpc1-/- electrocardiograms showed longer QT intervals, abnormalities in the ST segment, and delayed T waves, corroborated by longer action potentials in isolated ventricular cardiomyocytes. In voltage-clamp, these cells showed decreased Ito and IK voltage-activated K+ current densities. Moreover, IK showed activation at less negative voltages, but a higher level of inactivation at a given membrane potential. Kcnh2 and Kcnq1 voltage-gated K+ channels subunits' transcripts were remarkably more abundant in heart tissues from Gpc1-/- mice, suggesting that Gpc1 may interfere in the steps between transcription and translation in these cases. CONCLUSION Our data reveals an unprecedented connection between Gpc1 and voltage-gated K+ channels expressed in the heart and this knowledge contributes to the understanding of the role of this HSPG in cardiac function which may play a role in the development of cardiovascular disease.
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Affiliation(s)
- Diego Santos Souza
- Department of Anesthesiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Andreia Zago Chignalia
- Department of Anesthesiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA; Department of Physiology, College of Medicine University of Arizona, Tucson, AZ 85724, USA; Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85724, USA
| | - Joao Luis Carvalho-de-Souza
- Department of Anesthesiology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA; Department of Physiology, College of Medicine University of Arizona, Tucson, AZ 85724, USA; Department of Ophthalmology and Visual Sciences, College of Medicine, University of Arizona, Tucson, AZ 85724, USA; BIO5 Institute, University of Arizona, Tucson, AZ 85724, USA.
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Theory and Applications of the (Cardio) Genomic Fabric Approach to Post-Ischemic and Hypoxia-Induced Heart Failure. J Pers Med 2022; 12:jpm12081246. [PMID: 36013195 PMCID: PMC9410512 DOI: 10.3390/jpm12081246] [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: 06/14/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
The genomic fabric paradigm (GFP) characterizes the transcriptome topology by the transcripts’ abundances, the variability of the expression profile, and the inter-coordination of gene expressions in each pathophysiological condition. The expression variability analysis provides an indirect estimate of the cell capability to limit the stochastic fluctuations of the expression levels of key genes, while the expression coordination analysis determines the gene networks in functional pathways. This report illustrates the theoretical bases and the mathematical framework of the GFP with applications to our microarray data from mouse models of post ischemic, and constant and intermittent hypoxia-induced heart failures. GFP analyses revealed the myocardium priorities in keeping the expression of key genes within narrow intervals, determined the statistically significant gene interlinkages, and identified the gene master regulators in the mouse heart left ventricle under normal and ischemic conditions. We quantified the expression regulation, alteration of the expression control, and remodeling of the gene networks caused by the oxygen deprivation and determined the efficacy of the bone marrow mono-nuclear stem cell injections to restore the normal transcriptome. Through the comprehensive assessment of the transcriptome, GFP would pave the way towards the development of personalized gene therapy of cardiac diseases.
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Pressler MP, Horvath A, Entcheva E. Sex-dependent transcription of cardiac electrophysiology and links to acetylation modifiers based on the GTEx database. Front Cardiovasc Med 2022; 9:941890. [PMID: 35935618 PMCID: PMC9354462 DOI: 10.3389/fcvm.2022.941890] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Development of safer drugs based on epigenetic modifiers, e.g., histone deacetylase inhibitors (HDACi), requires better understanding of their effects on cardiac electrophysiology. Using RNAseq data from the genotype-tissue-expression database (GTEx), we created models that link the abundance of acetylation enzymes (HDAC/SIRT/HATs), and the gene expression of ion channels (IC) via select cardiac transcription factors (TFs) in male and female adult human hearts (left ventricle, LV). Gene expression data (transcripts per million, TPM) from GTEx donors (21–70 y.o.) were filtered, normalized and transformed to Euclidian space to allow quantitative comparisons in 84 female and 158 male LVs. Sex-specific partial least-square (PLS) regression models, linking gene expression data for HDAC/SIRT/HATs to TFs and to ICs gene expression, revealed tight co-regulation of cardiac ion channels by HDAC/SIRT/HATs, with stronger clustering in the male LV. Co-regulation of genes encoding excitatory and inhibitory processes in cardiac tissue by the acetylation modifiers may help explain their predominantly net-neutral effects on cardiac electrophysiology. ATP1A1, encoding for the Na/K pump, represented an outlier—with orthogonal regulation by the acetylation modifiers to most of the ICs. The HDAC/SIRT/HAT effects were mediated by strong (+) TF regulators of ICs, e.g., MEF2A and TBX5, in both sexes. Furthermore, for male hearts, PLS models revealed a stronger (+/-) mediatory role on ICs for NKX25 and TGF1B/KLF4, respectively, while RUNX1 exhibited larger (-) TF effects on ICs in females. Male-trained PLS models of HDAC/SIRT/HAT effects on ICs underestimated the effects on some ICs in females. Insights from the GTEx dataset about the co-expression and transcriptional co-regulation of acetylation-modifying enzymes, transcription factors and key cardiac ion channels in a sex-specific manner can help inform safer drug design.
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Affiliation(s)
- Michael P. Pressler
- Department of Biomedical Engineering, George Washington University, Washington, DC, United States
| | - Anelia Horvath
- Department of Biochemistry and Molecular Medicine, McCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC, United States
- *Correspondence: Emilia Entcheva,
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9
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Personalized 3-Gene Panel for Prostate Cancer Target Therapy. Curr Issues Mol Biol 2022; 44:360-382. [PMID: 35723406 PMCID: PMC8929157 DOI: 10.3390/cimb44010027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
Many years and billions spent for research did not yet produce an effective answer to prostate cancer (PCa). Not only each human, but even each cancer nodule in the same tumor, has unique transcriptome topology. The differences go beyond the expression level to the expression control and networking of individual genes. The unrepeatable heterogeneous transcriptomic organization among men makes the quest for universal biomarkers and “fit-for-all” treatments unrealistic. We present a bioinformatics procedure to identify each patient’s unique triplet of PCa Gene Master Regulators (GMRs) and predict consequences of their experimental manipulation. The procedure is based on the Genomic Fabric Paradigm (GFP), which characterizes each individual gene by the independent expression level, expression variability and expression coordination with each other gene. GFP can identify the GMRs whose controlled alteration would selectively kill the cancer cells with little consequence on the normal tissue. The method was applied to microarray data on surgically removed prostates from two men with metastatic PCas (each with three distinct cancer nodules), and DU145 and LNCaP PCa cell lines. The applications verified that each PCa case is unique and predicted the consequences of the GMRs’ manipulation. The predictions are theoretical and need further experimental validation.
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10
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Andriulė I, Pangonytė D, Almanaitytė M, Patamsytė V, Kuprytė M, Karčiauskas D, Mubagwa K, Mačianskienė R. Evidence for the expression of TRPM6 and TRPM7 in cardiomyocytes from all four chamber walls of the human heart. Sci Rep 2021; 11:15445. [PMID: 34326388 PMCID: PMC8322396 DOI: 10.1038/s41598-021-94856-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
The expression of the channels-enzymes TRPM6 and TRPM7 in the human heart remains poorly defined, and TRPM6 is generally considered not to be expressed in cardiomyocytes. We examined their expression at protein and mRNA levels using right atrial samples resected from patients (n = 72) with or without ischemic heart disease (IHD) and samples from all chamber walls of explanted human hearts (n = 9). TRPM6 and TRPM7 proteins were detected using immunofluorescence on isolated cardiomyocytes, ELISA on tissue homogenates, and immunostaining of cardiac tissue, whereas their mRNAs were detected by RT-qPCR. Both TRPM6 and TRPM7 were present in all chamber walls, with TRPM7 being more abundant. TRPM6 was co-expressed with TRPM7. The expression levels were dependent on cell incubation conditions (presence or absence of divalent cations, pH of the extracellular milieu, presence of TRP channel inhibitors 2-aminoethoxydiphenyl-borate and carvacrol). These drugs reduced TRPM7 immunofluorescence but increased that of TRPM6. TRPM6 and TRPM7 expression was increased in tissues from IHD patients. This is the first demonstration of the presence and co-expression of TRPM6 and TRPM7 in cardiomyocytes from all chamber walls of the human heart. The increased TRPM6 and TRPM7 expression in IHD suggests that the chanzymes are involved in the pathophysiology of the disease.
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Affiliation(s)
- Inga Andriulė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Dalia Pangonytė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mantė Almanaitytė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Patamsytė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Milda Kuprytė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Dainius Karčiauskas
- Department of Cardiac, Thoracic and Vascular Surgery, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kanigula Mubagwa
- Department of Cardiovascular Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Department of Basic Sciences, Faculty of Medicine, Université Catholique de Bukavu, Bukavu, DR, Congo
| | - Regina Mačianskienė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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Iacobas S, Iacobas DA. A Personalized Genomics Approach of the Prostate Cancer. Cells 2021; 10:cells10071644. [PMID: 34209090 PMCID: PMC8305988 DOI: 10.3390/cells10071644] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022] Open
Abstract
Decades of research identified genomic similarities among prostate cancer patients and proposed general solutions for diagnostic and treatments. However, each human is a dynamic unique with never repeatable transcriptomic topology and no gene therapy is good for everybody. Therefore, we propose the Genomic Fabric Paradigm (GFP) as a personalized alternative to the biomarkers approach. Here, GFP is applied to three (one primary—“A”, and two secondary—“B” & “C”) cancer nodules and the surrounding normal tissue (“N”) from a surgically removed prostate tumor. GFP proved for the first time that, in addition to the expression levels, cancer alters also the cellular control of the gene expression fluctuations and remodels their networking. Substantial differences among the profiled regions were found in the pathways of P53-signaling, apoptosis, prostate cancer, block of differentiation, evading apoptosis, immortality, insensitivity to anti-growth signals, proliferation, resistance to chemotherapy, and sustained angiogenesis. ENTPD2, AP5M1 BAIAP2L1, and TOR1A were identified as the master regulators of the “A”, “B”, “C”, and “N” regions, and potential consequences of ENTPD2 manipulation were analyzed. The study shows that GFP can fully characterize the transcriptomic complexity of a heterogeneous prostate tumor and identify the most influential genes in each cancer nodule.
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Affiliation(s)
- Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA;
| | - Dumitru A. Iacobas
- Personalized Genomics Laboratory, Center for Computational Systems Biology, Roy G Perry College of Engineering, Prairie View A&M University, Prairie View, TX 77446, USA
- Correspondence: ; Tel.: +1-936-261-9926
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