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Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [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: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
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Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
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Hallab JC, Nim HT, Stolper J, Chahal G, Waylen L, Bolk F, Elliott DA, Porrello E, Ramialison M. Towards spatio-temporally resolved developmental cardiac gene regulatory networks in zebrafish. Brief Funct Genomics 2021:elab030. [PMID: 34170300 DOI: 10.1093/bfgp/elab030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/13/2021] [Accepted: 05/26/2021] [Indexed: 12/25/2022] Open
Abstract
Heart formation in the zebrafish involves a rapid, complex series of morphogenetic events in three-dimensional space that spans cardiac lineage specification through to chamber formation and maturation. This process is tightly orchestrated by a cardiac gene regulatory network (GRN), which ensures the precise spatio-temporal deployment of genes critical for heart formation. Alterations of the timing or spatial localisation of gene expression can have a significant impact in cardiac ontogeny and may lead to heart malformations. Hence, a better understanding of the cellular and molecular basis of congenital heart disease relies on understanding the behaviour of cardiac GRNs with precise spatiotemporal resolution. Here, we review the recent technical advances that have expanded our capacity to interrogate the cardiac GRN in zebrafish. In particular, we focus on studies utilising high-throughput technologies to systematically dissect gene expression patterns, both temporally and spatially during heart development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC, Australia
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Parisi C, Vashisht S, Winata CL. Fish-Ing for Enhancers in the Heart. Int J Mol Sci 2021; 22:3914. [PMID: 33920121 PMCID: PMC8069060 DOI: 10.3390/ijms22083914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.
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Affiliation(s)
- Costantino Parisi
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Shikha Vashisht
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Bu H, Sun G, Zhu Y, Yang Y, Tan Z, Zhao T, Hu S. The M310T mutation in the GATA4 gene is a novel pathogenic target of the familial atrial septal defect. BMC Cardiovasc Disord 2021; 21:12. [PMID: 33413087 PMCID: PMC7788758 DOI: 10.1186/s12872-020-01822-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although most cases of atrial septal defect (ASD) are sporadic, familial cases have been reported, which may be caused by mutation of transcription factor GATA binding protein 4 (GATA4). Herein we combined whole-exome sequencing and bioinformatics strategies to identify a novel mutation in GATA4 accounting for the etiology in a Chinese family with ASD. METHODS We identified kindred spanning 3 generations in which 3 of 12 (25.0%) individuals had ASD. Punctilious records for the subjects included complete physical examination, transthoracic echocardiography, electrocardiograph and surgical confirming. Whole-exome capture and high-throughput sequencing were performed on the proband III.1. Sanger sequencing was used to validate the candidate variants, and segregation analyses were performed in the family members. RESULTS Direct sequencing of GATA4 from the genomic DNA of family members identified a T-to-C transition at nucleotide 929 in exon 5 that predicted a methionine to threonine substitution at codon 310 (M310T) in the nuclear localization signal (NLS) region. Two affected members (II.2 and III.3) and the proband (III.1) who was recognized as a carrier exhibited this mutation, whereas the other unaffected family members or control individuals did not. More importantly, the mutation GATA4 (c.T929C: p.M310T) has not been reported previously in either familial or sporadic cases of congenital heart defects (CHD). CONCLUSIONS We identified for the first time a novel M310T mutation in the GATA4 gene that is located in the NLS region and leads to family ASD with arrhythmias. However, the mechanism by which this pathogenic mutation contributes to the development of heart defect and tachyarrhythmias remains to be ascertained.
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Affiliation(s)
- Haisong Bu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Guowen Sun
- Department of Cardiothoracic Surgery, Chenzhou No. 1 People's Hospital, Chenzhou, 423000, Hunan, People's Republic of China
| | - Yun Zhu
- Department of Cardiothoracic Surgery, Chenzhou No. 1 People's Hospital, Chenzhou, 423000, Hunan, People's Republic of China
| | - Yifeng Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Zhiping Tan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Tianli Zhao
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China.,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Shijun Hu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, 139 Renmin Central Road, Changsha, 410011, Hunan, People's Republic of China. .,Central South University Center for Clinical Gene Diagnosis and Treatment, the Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China. .,Department of Cardiovascular Surgery, The German Heart Centre, 80636, Munich, Germany.
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Zhang H, Viveiros A, Nikhanj A, Nguyen Q, Wang K, Wang W, Freed DH, Mullen JC, MacArthur R, Kim DH, Tymchak W, Sergi CM, Kassiri Z, Wang S, Oudit GY. The Human Explanted Heart Program: A translational bridge for cardiovascular medicine. Biochim Biophys Acta Mol Basis Dis 2021; 1867:165995. [PMID: 33141063 PMCID: PMC7581399 DOI: 10.1016/j.bbadis.2020.165995] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
The progression of cardiovascular research is often impeded by the lack of reliable disease models that fully recapitulate the pathogenesis in humans. These limitations apply to both in vitro models such as cell-based cultures and in vivo animal models which invariably are limited to simulate the complexity of cardiovascular disease in humans. Implementing human heart tissue in cardiovascular research complements our research strategy using preclinical models. We established the Human Explanted Heart Program (HELP) which integrates clinical, tissue and molecular phenotyping thereby providing a comprehensive evaluation into human heart disease. Our collection and storage of biospecimens allow them to retain key pathogenic findings while providing novel insights into human heart failure. The use of human non-failing control explanted hearts provides a valuable comparison group for the diseased explanted hearts. Using HELP we have been able to create a tissue repository which have been used for genetic, molecular, cellular, and histological studies. This review describes the process of collection and use of explanted human heart specimens encompassing a spectrum of pediatric and adult heart diseases, while highlighting the role of these invaluable specimens in translational research. Furthermore, we highlight the efficient procurement and bio-preservation approaches ensuring analytical quality of heart specimens acquired in the context of heart donation and transplantation.
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Affiliation(s)
- Hao Zhang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Anissa Viveiros
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Anish Nikhanj
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Quynh Nguyen
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Kaiming Wang
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Wei Wang
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Darren H Freed
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - John C Mullen
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Roderick MacArthur
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel H Kim
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Wayne Tymchak
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Consolato M Sergi
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Anatomical Pathology, Department of Laboratory Medicine & Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Zamaneh Kassiri
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Shaohua Wang
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada; Division of Cardiac Surgery, Department of Surgery, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Division of Cardiology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada.
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6
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Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury. PLoS One 2020; 15:e0232963. [PMID: 32730272 PMCID: PMC7392272 DOI: 10.1371/journal.pone.0232963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/24/2020] [Indexed: 12/25/2022] Open
Abstract
Mammalian cardiomyocytes exit the cell cycle shortly after birth. As a result, an occurrence of coronary occlusion-induced myocardial infarction often results in heart failure, postinfarction LV dilatation, or death, and represents one of the most significant public health morbidities worldwide. Interestingly however, the hearts of neonatal pigs have been shown to regenerate following an acute myocardial infarction (MI) occuring on postnatal day 1 (P1); a recovery period which is accompanied by an increased expression of markers for cell-cycle activity, and suggests that early postnatal myocardial regeneration may be driven in part by the MI-induced proliferation of pre-existing cardiomyocytes. In this study, we identified signaling pathways known to regulate the cell cycle, and determined of these, the pathways persistently upregulated in response to MI injury. We identified five pathways (mitogen associated protein kinase [MAPK], Hippo, cyclic [cAMP], Janus kinase/signal transducers and activators of transcription [JAK-STAT], and Ras) which were comprehensively upregulated in cardiac tissues collected on day 7 (P7) and/or P28 of the P1 injury hearts. Several of the initiating master regulators (e.g., CSF1/CSF1R, TGFB, and NPPA) and terminal effector molecules (e.g., ATF4, FOS, RELA/B, ITGB2, CCND1/2/3, PIM1, RAF1, MTOR, NKF1B) in these pathways were persistently upregulated at day 7 through day 28, suggesting there exists at least some degree of regenerative activity up to 4 weeks following MI at P1. Our observations provide a list of key regulators to be examined in future studies targeting cell-cycle activity as an avenue for myocardial regeneration.
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Locatelli P, Belaich MN, López AE, Olea FD, Uranga Vega M, Giménez CS, Simonin JA, Bauzá MDR, Castillo MG, Cuniberti LA, Crottogini A, Cerrudo CS, Ghiringhelli PD. Novel insights into cardiac regeneration based on differential fetal and adult ovine heart transcriptomic analysis. Am J Physiol Heart Circ Physiol 2020; 318:H994-H1007. [PMID: 32167779 DOI: 10.1152/ajpheart.00610.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The adult mammalian cardiomyocyte has a very limited capacity to reenter the cell cycle and advance into mitosis. Therefore, diseases characterized by lost contractile tissue usually evolve into myocardial remodeling and heart failure. Analyzing the cardiac transcriptome at different developmental stages in a large mammal closer to the human than laboratory rodents may serve to disclose positive and negative cardiomyocyte cell cycle regulators potentially targetable to induce cardiac regeneration in the clinical setting. Thus we aimed at characterizing the transcriptomic profiles of the early fetal, late fetal, and adult sheep heart by employing RNA-seq technique and bioinformatic analysis to detect protein-encoding genes that in some of the stages were turned off, turned on, or differentially expressed. Genes earlier proposed as positive cell cycle regulators such as cyclin A, cdk2, meis2, meis3, and PCNA showed higher expression in fetal hearts and lower in AH, as expected. In contrast, genes previously proposed as cell cycle inhibitors, such as meis1, p16, and sav1, tended to be higher in fetal than in adult hearts, suggesting that these genes are involved in cell processes other than cell cycle regulation. Additionally, we described Gene Ontology (GO) enrichment of different sets of genes. GO analysis revealed that differentially expressed gene sets were mainly associated with metabolic and cellular processes. The cell cycle-related genes fam64a, cdc20, and cdk1, and the metabolism-related genes pitx and adipoq showed strong differential expression between fetal and adult hearts, thus being potent candidates to be targeted in human cardiac regeneration strategies.NEW & NOTEWORTHY We characterized the transcriptomic profiles of the fetal and adult sheep hearts employing RNAseq technique and bioinformatic analyses to provide sets of transcripts whose variation in expression level may link them to a specific role in cell cycle regulation. It is important to remark that this study was performed in a large mammal closer to humans than laboratory rodents. In consequence, the results can be used for further translational studies in cardiac regeneration.
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Affiliation(s)
- Paola Locatelli
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Mariano N Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular; CONICET, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Ayelén E López
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Fernanda D Olea
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Martín Uranga Vega
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Carlos S Giménez
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Jorge Alejandro Simonin
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular; CONICET, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - María Del Rosario Bauzá
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Marta G Castillo
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Luis A Cuniberti
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Alberto Crottogini
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería (IMETTYB), Universidad Favaloro-CONICET, Buenos Aires, Argentina
| | - Carolina S Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular; CONICET, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Pablo D Ghiringhelli
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular; CONICET, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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8
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Costa MC, Gabriel AF, Enguita FJ. Bioinformatics Research Methodology of Non-coding RNAs in Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:49-64. [PMID: 32285404 DOI: 10.1007/978-981-15-1671-9_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The transcriptional complexity generated by the human genomic output is within the core of cell and organ physiology, but also could be in the origin of pathologies. In cardiovascular diseases, the role of specific families of RNA transcripts belonging to the group of the non-coding RNAs started to be unveiled in the last two decades. The knowledge of the functional rules and roles of non-coding RNAs in the context of cardiovascular diseases is an important factor to derive new diagnostic methods, but also to design targeted therapeutic strategies. The characterization and analysis of ncRNA function requires a deep knowledge of the regulatory mechanism of these RNA species that often relies on intricated interaction networks. The use of specific bioinformatic tools to interrogate biological data and to derive functional implications is particularly relevant and needs to be extended to the general practice of translational researchers. This chapter briefly summarizes the bioinformatic tools and strategies that could be used for the characterization and functional analysis of non-coding RNAs, with special emphasis in their applications to the cardiovascular field.
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Affiliation(s)
- Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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9
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Soucy JR, Askaryan J, Diaz D, Koppes AN, Annabi N, Koppes RA. Glial cells influence cardiac permittivity as evidenced through in vitro and in silico models. Biofabrication 2019; 12:015014. [PMID: 31593932 PMCID: PMC11062241 DOI: 10.1088/1758-5090/ab4c0a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Excitation-contraction (EC) coupling in the heart has, until recently, been solely accredited to cardiomyocytes. The inherent complexities of the heart make it difficult to examine non-muscle contributions to contraction in vivo, and conventional in vitro models fail to capture multiple features and cellular heterogeneity of the myocardium. Here, we report on the development of a 3D cardiac μTissue to investigate changes in the cellular composition of native myocardium in vitro. Cells are encapsulated within micropatterned gelatin-based hydrogels formed via visible light photocrosslinking. This system enables spatial control of the microarchitecture, perturbation of the cellular composition, and functional measures of EC coupling via video microscopy and a custom algorithm to quantify beat frequency and degree of coordination. To demonstrate the robustness of these tools and evaluate the impact of altered cell population densities on cardiac μTissues, contractility and cell morphology were assessed with the inclusion of exogenous non-myelinating Schwann cells (SCs). Results demonstrate that the addition of exogenous SCs alter cardiomyocyte EC, profoundly inhibiting the response to electrical pacing. Computational modeling of connexin-mediated coupling suggests that SCs impact cardiomyocyte resting potential and rectification following depolarization. Cardiac μTissues hold potential for examining the role of cellular heterogeneity in heart health, pathologies, and cellular therapies.
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Affiliation(s)
- Jonathan R Soucy
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, United States of America
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10
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Grabherr MG, Kaminska B, Komorowski J. Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal. Genes (Basel) 2018; 9:genes9100505. [PMID: 30340386 PMCID: PMC6210603 DOI: 10.3390/genes9100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Affiliation(s)
- Manfred G Grabherr
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden.
- National Bioinformatics Infrastructure Sweden, Uppsala University, 752 36 Uppsala, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Bozena Kaminska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02-093 Warsaw, Poland.
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China.
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden.
- Institute of Computer Science of the Polish Academy of Sciences, 02-093 Warsaw, Poland.
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