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Kukendrarajah K, Farmaki AE, Lambiase PD, Schilling R, Finan C, Floriaan Schmidt A, Providencia R. Advancing drug development for atrial fibrillation by prioritising findings from human genetic association studies. EBioMedicine 2024; 105:105194. [PMID: 38941956 DOI: 10.1016/j.ebiom.2024.105194] [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: 09/22/2023] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Drug development for atrial fibrillation (AF) has failed to yield new approved compounds. We sought to identify and prioritise potential druggable targets with support from human genetics, by integrating the available evidence with bioinformatics sources relevant for AF drug development. METHODS Genetic hits for AF and related traits were identified through structured search of MEDLINE. Genes derived from each paper were cross-referenced with the OpenTargets platform for drug interactions. Confirmation/validation was demonstrated through structured searches and review of evidence on MEDLINE and ClinialTrials.gov for each drug and its association with AF. FINDINGS 613 unique drugs were identified, with 21 already included in AF Guidelines. Cardiovascular drugs from classes not currently used for AF (e.g. ranolazine and carperitide) and anti-inflammatory drugs (e.g. dexamethasone and mehylprednisolone) had evidence of potential benefit. Further targets were considered druggable but remain open for drug development. INTERPRETATION Our systematic approach, combining evidence from different bioinformatics platforms, identified drug repurposing opportunities and druggable targets for AF. FUNDING KK is supported by Barts Charity grant G-002089 and is mentored on the AFGen 2023-24 Fellowship funded by the AFGen NIH/NHLBI grant R01HL092577. RP is supported by the UCL BHF Research Accelerator AA/18/6/34223 and NIHR grant NIHR129463. AFS is supported by the BHF grants PG/18/5033837, PG/22/10989 and UCL BHF Accelerator AA/18/6/34223 as well as the UK Research and Innovation (UKRI) under the UK government's Horizon Europe funding guarantee EP/Z000211/1 and by the UKRI-NIHR grant MR/V033867/1 for the Multimorbidity Mechanism and Therapeutics Research Collaboration. AF is supported by UCL BHF Accelerator AA/18/6/34223. CF is supported by UCL BHF Accelerator AA/18/6/34223.
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Affiliation(s)
- Kishore Kukendrarajah
- Institute of Health Informatics, University College London, 222 Euston Road, NW1 2DA, United Kingdom; Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom.
| | - Aliki-Eleni Farmaki
- Institute of Health Informatics, University College London, 222 Euston Road, NW1 2DA, United Kingdom
| | - Pier D Lambiase
- Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom; Institute of Cardiovascular Science, University College London, Gower Street, WC1E 6HX, United Kingdom
| | - Richard Schilling
- Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom
| | - Chris Finan
- Institute of Cardiovascular Science, University College London, Gower Street, WC1E 6HX, United Kingdom; UCL British Heart Foundation Research Accelerator, United Kingdom; Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Amand Floriaan Schmidt
- Institute of Cardiovascular Science, University College London, Gower Street, WC1E 6HX, United Kingdom; UCL British Heart Foundation Research Accelerator, United Kingdom; Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, the Netherlands; Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centres, University of Amsterdam, the Netherlands
| | - Rui Providencia
- Institute of Health Informatics, University College London, 222 Euston Road, NW1 2DA, United Kingdom; Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom
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Vad OB, Monfort LM, Paludan-Müller C, Kahnert K, Diederichsen SZ, Andreasen L, Lotta LA, Nielsen JB, Lundby A, Svendsen JH, Olesen MS. Rare and Common Genetic Variation Underlying Atrial Fibrillation Risk. JAMA Cardiol 2024:2820520. [PMID: 38922602 PMCID: PMC11209175 DOI: 10.1001/jamacardio.2024.1528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 06/27/2024]
Abstract
Importance Atrial fibrillation (AF) has a substantial genetic component. The importance of polygenic risk is well established, while the contribution of rare variants to disease risk warrants characterization in large cohorts. Objective To identify rare predicted loss-of-function (pLOF) variants associated with AF and elucidate their role in risk of AF, cardiomyopathy (CM), and heart failure (HF) in combination with a polygenic risk score (PRS). Design, Setting, and Participants This was a genetic association and nested case-control study. The impact of rare pLOF variants was evaluated on the risk of incident AF. HF and CM were assessed in cause-specific Cox regressions. End of follow-up was July 1, 2022. Data were analyzed from January to October 2023. The UK Biobank enrolled 502 480 individuals aged 40 to 69 years at inclusion in the United Kingdom between March 13, 2006, and October 1, 2010. UK residents of European ancestry were included. Individuals with prior diagnosis of AF were excluded from analyses of incident AF. Exposures Rare pLOF variants and an AF PRS. Main Outcomes and Measures Risk of AF and incident HF or CM prior to and subsequent to AF diagnosis. Results A total of 403 990 individuals (218 489 [54.1%] female) with a median (IQR) age of 58 (51-63) years were included; 24 447 were diagnosed with incident AF over a median (IQR) follow-up period of 13.3 (12.4-14.0) years. Rare pLOF variants in 6 genes (TTN, RPL3L, PKP2, CTNNA3, KDM5B, and C10orf71) were associated with AF. Of these, TTN, RPL3L, PKP2, CTNNA3, and KDM5B replicated in an external cohort. Combined with high PRS, rare pLOF variants conferred an odds ratio of 7.08 (95% CI, 6.03-8.28) for AF. Carriers with high PRS also had a substantial 10-year risk of AF (16% in female individuals and 24% in male individuals older than 60 years). Rare pLOF variants were associated with increased risk of CM both prior to AF (hazard ratio [HR], 3.13; 95% CI, 2.24-4.36) and subsequent to AF (HR, 2.98; 95% CI, 1.89-4.69). Conclusions and Relevance Rare and common genetic variation were associated with an increased risk of AF. The findings provide insights into the genetic underpinnings of AF and may aid in future genetic risk stratification.
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Affiliation(s)
- Oliver B. Vad
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laia M. Monfort
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Paludan-Müller
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Konstantin Kahnert
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Z. Diederichsen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Laura Andreasen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Alicia Lundby
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper H. Svendsen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Morten S. Olesen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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Bajpai AK, Gu Q, Orgil BO, Alberson NR, Towbin JA, Martinez HR, Lu L, Purevjav E. Exploring the Regulation and Function of Rpl3l in the Development of Early-Onset Dilated Cardiomyopathy and Congestive Heart Failure Using Systems Genetics Approach. Genes (Basel) 2023; 15:53. [PMID: 38254943 PMCID: PMC10815855 DOI: 10.3390/genes15010053] [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: 12/05/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cardiomyopathies, diseases affecting the myocardium, are common causes of congestive heart failure (CHF) and sudden cardiac death. Recently, biallelic variants in ribosomal protein L3-like (RPL3L) have been reported to be associated with severe neonatal dilated cardiomyopathy (DCM) and CHF. This study employs a systems genetics approach to gain understanding of the regulatory mechanisms underlying the role of RPL3L in DCM. METHODS Genetic correlation, expression quantitative trait loci (eQTL) mapping, differential expression analysis and comparative functional analysis were performed using cardiac gene expression data from the patients and murine genetic reference populations (GRPs) of BXD mice (recombinant inbred strains from a cross of C57BL/6J and DBA/2J mice). Additionally, immune infiltration analysis was performed to understand the relationship between DCM, immune cells and RPL3L expression. RESULTS Systems genetics analysis identified high expression of Rpl3l mRNA, which ranged from 11.31 to 12.16 across murine GRPs of BXD mice, with an ~1.8-fold difference. Pathways such as "diabetic cardiomyopathy", "focal adhesion", "oxidative phosphorylation" and "DCM" were significantly associated with Rpl3l. eQTL mapping suggested Myl4 (Chr 11) and Sdha (Chr 13) as the upstream regulators of Rpl3l. The mRNA expression of Rpl3l, Myl4 and Sdha was significantly correlated with multiple echocardiography traits in BXD mice. Immune infiltration analysis revealed a significant association of RPL3L and SDHA with seven immune cells (CD4, CD8-naive T cell, CD8 T cell, macrophages, cytotoxic T cell, gamma delta T cell and exhausted T cell) that were also differentially infiltrated between heart samples obtained from DCM patients and normal individuals. CONCLUSIONS RPL3L is highly expressed in the heart tissue of humans and mice. Expression of Rpl3l and its upstream regulators, Myl4 and Sdha, correlate with multiple cardiac function traits in murine GRPs of BXD mice, while RPL3L and SDHA correlate with immune cell infiltration in DCM patient hearts, suggesting important roles for RPL3L in DCM and CHF pathogenesis via immune inflammation, necessitating experimental validations of Myl4 and Sdha in Rpl3l regulation.
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Affiliation(s)
- Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Buyan-Ochir Orgil
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Neely R. Alberson
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Jeffrey A. Towbin
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
- Cardiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hugo R. Martinez
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Enkhsaikhan Purevjav
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
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Jonker T, Barnett P, Boink GJJ, Christoffels VM. Role of Genetic Variation in Transcriptional Regulatory Elements in Heart Rhythm. Cells 2023; 13:4. [PMID: 38201209 PMCID: PMC10777909 DOI: 10.3390/cells13010004] [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: 09/27/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
Genetic predisposition to cardiac arrhythmias has been a field of intense investigation. Research initially focused on rare hereditary arrhythmias, but over the last two decades, the role of genetic variation (single nucleotide polymorphisms) in heart rate, rhythm, and arrhythmias has been taken into consideration as well. In particular, genome-wide association studies have identified hundreds of genomic loci associated with quantitative electrocardiographic traits, atrial fibrillation, and less common arrhythmias such as Brugada syndrome. A significant number of associated variants have been found to systematically localize in non-coding regulatory elements that control the tissue-specific and temporal transcription of genes encoding transcription factors, ion channels, and other proteins. However, the identification of causal variants and the mechanism underlying their impact on phenotype has proven difficult due to the complex tissue-specific, time-resolved, condition-dependent, and combinatorial function of regulatory elements, as well as their modest conservation across different model species. In this review, we discuss research efforts aimed at identifying and characterizing-trait-associated variant regulatory elements and the molecular mechanisms underlying their impact on heart rate or rhythm.
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Affiliation(s)
- Timo Jonker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
| | - Phil Barnett
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
| | - Gerard J. J. Boink
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
- Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands
| | - Vincent M. Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (T.J.); (P.B.); (G.J.J.B.)
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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [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: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
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Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
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7
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Lipov A, Jurgens SJ, Mazzarotto F, Allouba M, Pirruccello JP, Aguib Y, Gennarelli M, Yacoub MH, Ellinor PT, Bezzina CR, Walsh R. Exploring the complex spectrum of dominance and recessiveness in genetic cardiomyopathies. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1078-1094. [PMID: 38666070 PMCID: PMC11041721 DOI: 10.1038/s44161-023-00346-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/07/2023] [Indexed: 04/28/2024]
Abstract
Discrete categorization of Mendelian disease genes into dominant and recessive models often oversimplifies their underlying genetic architecture. Cardiomyopathies (CMs) are genetic diseases with complex etiologies for which an increasing number of recessive associations have recently been proposed. Here, we comprehensively analyze all published evidence pertaining to biallelic variation associated with CM phenotypes to identify high-confidence recessive genes and explore the spectrum of monoallelic and biallelic variant effects in established recessive and dominant disease genes. We classify 18 genes with robust recessive association with CMs, largely characterized by dilated phenotypes, early disease onset and severe outcomes. Several of these genes have monoallelic association with disease outcomes and cardiac traits in the UK Biobank, including LMOD2 and ALPK3 with dilated and hypertrophic CM, respectively. Our data provide insights into the complex spectrum of dominance and recessiveness in genetic heart disease and demonstrate how such approaches enable the discovery of unexplored genetic associations.
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Affiliation(s)
- Alex Lipov
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
| | - Sean J. Jurgens
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Francesco Mazzarotto
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - James P. Pirruccello
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Division of Cardiology, University of California, San Francisco, San Francisco, CA USA
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Magdi H. Yacoub
- National Heart and Lung Institute, Imperial College London, London, UK
- Aswan Heart Centre, Magdi Yacoub Heart Foundation, Aswan, Egypt
- Harefield Heart Science Centre, Uxbridge, UK
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA USA
| | - Connie R. Bezzina
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
- European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart, Amsterdam, the Netherlands
| | - Roddy Walsh
- Department of Experimental Cardiology, Heart Centre, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands
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Haerinck J, Goossens S, Berx G. The epithelial-mesenchymal plasticity landscape: principles of design and mechanisms of regulation. Nat Rev Genet 2023; 24:590-609. [PMID: 37169858 DOI: 10.1038/s41576-023-00601-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
Epithelial-mesenchymal plasticity (EMP) enables cells to interconvert between several states across the epithelial-mesenchymal landscape, thereby acquiring hybrid epithelial/mesenchymal phenotypic features. This plasticity is crucial for embryonic development and wound healing, but also underlies the acquisition of several malignant traits during cancer progression. Recent research using systems biology and single-cell profiling methods has provided novel insights into the main forces that shape EMP, which include the microenvironment, lineage specification and cell identity, and the genome. Additionally, key roles have emerged for hysteresis (cell memory) and cellular noise, which can drive stochastic transitions between cell states. Here, we review these forces and the distinct but interwoven layers of regulatory control that stabilize EMP states or facilitate epithelial-mesenchymal transitions (EMTs) and discuss the therapeutic potential of manipulating the EMP landscape.
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Affiliation(s)
- Jef Haerinck
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Unit for Translational Research in Oncology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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9
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Raben TG, Lello L, Widen E, Hsu SDH. Biobank-scale methods and projections for sparse polygenic prediction from machine learning. Sci Rep 2023; 13:11662. [PMID: 37468507 PMCID: PMC10356957 DOI: 10.1038/s41598-023-37580-5] [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: 03/24/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023] Open
Abstract
In this paper we characterize the performance of linear models trained via widely-used sparse machine learning algorithms. We build polygenic scores and examine performance as a function of training set size, genetic ancestral background, and training method. We show that predictor performance is most strongly dependent on size of training data, with smaller gains from algorithmic improvements. We find that LASSO generally performs as well as the best methods, judged by a variety of metrics. We also investigate performance characteristics of predictors trained on one genetic ancestry group when applied to another. Using LASSO, we develop a novel method for projecting AUC and correlation as a function of data size (i.e., for new biobanks) and characterize the asymptotic limit of performance. Additionally, for LASSO (compressed sensing) we show that performance metrics and predictor sparsity are in agreement with theoretical predictions from the Donoho-Tanner phase transition. Specifically, a future predictor trained in the Taiwan Precision Medicine Initiative for asthma can achieve an AUC of [Formula: see text] and for height a correlation of [Formula: see text] for a Taiwanese population. This is above the measured values of [Formula: see text] and [Formula: see text], respectively, for UK Biobank trained predictors applied to a European population.
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Affiliation(s)
- Timothy G Raben
- Department of Physics and Astronomy, Michigan State University, Michigan, USA.
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Erik Widen
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
| | - Stephen D H Hsu
- Department of Physics and Astronomy, Michigan State University, Michigan, USA
- Genomic Prediction, Inc., North Brunswick, NJ, USA
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10
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Milenkovic I, Santos Vieira HG, Lucas MC, Ruiz-Orera J, Patone G, Kesteven S, Wu J, Feneley M, Espadas G, Sabidó E, Hübner N, van Heesch S, Völkers M, Novoa EM. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res 2023; 51:5301-5324. [PMID: 36882085 PMCID: PMC10287911 DOI: 10.1093/nar/gkad121] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. We identify a rescue mechanism in which, upon RPL3L depletion, RPL3 becomes up-regulated, yielding RPL3-containing ribosomes instead of RPL3L-containing ribosomes that are typically found in cardiomyocytes. Using both ribosome profiling (Ribo-seq) and a novel orthogonal approach consisting of ribosome pulldown coupled to nanopore sequencing (Nano-TRAP), we find that RPL3L modulates neither translational efficiency nor ribosome affinity towards a specific subset of transcripts. In contrast, we show that depletion of RPL3L leads to increased ribosome-mitochondria interactions in cardiomyocytes, which is accompanied by a significant increase in ATP levels, potentially as a result of fine-tuning of mitochondrial activity. Our results demonstrate that the existence of tissue-specific RP paralogues does not necessarily lead to enhanced translation of specific transcripts or modulation of translational output. Instead, we reveal a complex cellular scenario in which RPL3L modulates the expression of RPL3, which in turn affects ribosomal subcellular localization and, ultimately, mitochondrial activity.
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Affiliation(s)
- Ivan Milenkovic
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Morghan C Lucas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
| | - Scott Kesteven
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Jianxin Wu
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Michael Feneley
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Guadalupe Espadas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), D-13125 Berlin, Germany
- Charité -Universitätsmedizin, D-10117 Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, D-13347 Berlin, Germany
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | | | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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11
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Bocher O, Willer CJ, Zeggini E. Unravelling the genetic architecture of human complex traits through whole genome sequencing. Nat Commun 2023; 14:3520. [PMID: 37316478 DOI: 10.1038/s41467-023-39259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
- Ozvan Bocher
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Ismaninger Str. 22, 81675, Munich, Germany.
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12
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Yang Q, Zhang Q, Qin Z, Zhang S, Yi S, Yi S, Zhang Q, Luo J. Novel compound heterozygous variants in the RPL3L gene causing dilated cardiomyopathy type-2D: a case report and literature review. BMC Med Genomics 2023; 16:127. [PMID: 37308880 DOI: 10.1186/s12920-023-01567-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/04/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy type-2D (CMD2D) is a rare heart disease causing a severe cardiomyopathy with neonatal onset and rapid progression to cardiac decompensation and death in untreated patients. CMD2D is an autosomal recessive disease resulting from variants in the RPL3L gene, which encodes the 60 S ribosomal protein exclusively expressed in skeletal and cardiac muscle and plays an essential role in myoblast growth and fusion. Previous reports have only associated CMD2D with a small duplication and seven nucleotide substitution in the RPL3L gene. CASE PRESENTATION In this study, we report the case of a 31 days old Chinese infant patient with severe dilated cardiomyopathy (DCM) and rapid decompensation along with other cardiac malformations. In addition to previously reported clinical features, the patient showed the previously unreported complication of occasional premature atrial contractions and a first-degree atrioventricular block. Whole-exome sequencing (WES) revealed compound heterozygous variants (c.80G > A (p.Gly27Asp) and c.1074dupA (p.Ala359fs*6)) in RPL3L (NM_005061.3). The latter novel variant may result in the absence of protein production with a significant decrease in mRNA level, suggesting it is a loss-of-function mutation. CONCLUSIONS This is the first case report of RPL3L-associated neonatal dilated cardiomyopathy in China. The molecular confirmation of the patient expands the genetic spectrum of CMD2D, and the clinical manifestation of CMD2D in the patient provides additional clinical information regarding this disease.
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Affiliation(s)
- Qi Yang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shujie Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sheng Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qinle Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, No. 59, Xiangzhu Road, Nanning, China.
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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13
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Shiraishi C, Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 2023; 14:2131. [PMID: 37080962 PMCID: PMC10119107 DOI: 10.1038/s41467-023-37838-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.
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Affiliation(s)
- Chisa Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Taishi Yamamoto
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Shouji Matsushima
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiroyuki Tsutsui
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
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14
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Grimes KM, Prasad V, Huo J, Kuwabara Y, Vanhoutte D, Baldwin TA, Bowers SLK, Johansen AKZ, Sargent MA, Lin SCJ, Molkentin JD. Rpl3l gene deletion in mice reduces heart weight over time. Front Physiol 2023; 14:1054169. [PMID: 36733907 PMCID: PMC9886673 DOI: 10.3389/fphys.2023.1054169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Introduction: The ribosomal protein L3-like (RPL3L) is a heart and skeletal muscle-specific ribosomal protein and paralogue of the more ubiquitously expressed RPL3 protein. Mutations in the human RPL3L gene are linked to childhood cardiomyopathy and age-related atrial fibrillation, yet the function of RPL3L in the mammalian heart remains unknown. Methods and Results: Here, we observed that mouse cardiac ventricles express RPL3 at birth, where it is gradually replaced by RPL3L in adulthood but re-expressed with induction of hypertrophy in adults. Rpl3l gene-deleted mice were generated to examine the role of this gene in the heart, although Rpl3l -/- mice showed no overt changes in cardiac structure or function at baseline or after pressure overload hypertrophy, likely because RPL3 expression was upregulated and maintained in adulthood. mRNA expression analysis and ribosome profiling failed to show differences between the hearts of Rpl3l null and wild type mice in adulthood. Moreover, ribosomes lacking RPL3L showed no differences in localization within cardiomyocytes compared to wild type controls, nor was there an alteration in cardiac tissue ultrastructure or mitochondrial function in adult Rpl3l -/- mice. Similarly, overexpression of either RPL3 or RPL3L with adeno-associated virus -9 in the hearts of mice did not cause discernable pathology. However, by 18 months of age Rpl3l -/- null mice had significantly smaller hearts compared to wild type littermates. Conclusion: Thus, deletion of Rpl3l forces maintenance of RPL3 expression within the heart that appears to fully compensate for the loss of RPL3L, although older Rpl3l -/- mice showed a mild but significant reduction in heart weight.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jeffery D. Molkentin
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
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15
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Das BB, Gajula V, Arya S, Taylor MB. Compound Heterozygous Missense Variants in RPL3L Genes Associated with Severe Forms of Dilated Cardiomyopathy: A Case Report and Literature Review. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9101495. [PMID: 36291431 PMCID: PMC9600237 DOI: 10.3390/children9101495] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 06/14/2023]
Abstract
Whole exome sequencing has identified an infant girl with fulminant dilated cardiomyopathy (DCM), leading to severe acute heart failure associated with ribosomal protein large 3-like (RPL3L) gene pathologic variants. Other genetic tests for mitochondrial disorders by sequence analysis and deletion testing of the mitochondrial genome were negative. Secondary causes for DCM due to metabolic and infectious etiologies were ruled out. She required a Berlin-Excor left ventricular assist device due to worsening of her heart failure as a bridge to orthotopic heart transplantation. At three months follow-up after heart transplantation, she has been doing well. We reviewed the literature on published RPL3L-related DCM cases and their outcomes. Bi-allelic variants in RPL3L have been reported in only seven patients from four unrelated families in the literature. RPL3L is a newer and likely pathogenic gene associated with a severe form of early-onset dilated cardiomyopathy with poor prognosis necessitating heart transplantation.
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Affiliation(s)
- Bibhuti B. Das
- Department of Pediatrics, Division of Cardiology, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Viswanath Gajula
- Department of Pediatrics, Division of Critical Care, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Sandeep Arya
- Department of Pediatrics, Division of Critical Care, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Mary B. Taylor
- Department of Pediatrics, Division of Critical Care, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, MS 39216, USA
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16
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Maver A, Zigman T, Rangrez AY, Coric M, Homolak J, Saric D, Skific I, Udovicic M, Zekusic M, Saleem U, Laufer SD, Hansen A, Frey N, Baric I, Peterlin B. A biallelic loss-of-function variant in MYZAP is associated with a recessive form of severe dilated cardiomyopathy. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006221. [PMID: 35840178 PMCID: PMC9528970 DOI: 10.1101/mcs.a006221] [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: 05/25/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Dilated cardiomyopathy (DCM) is a primary disorder of the cardiac muscle, characterised by dilatation of the left ventricle and contractile dysfunction. About 50% of DCM cases can be attributed to monogenic causes, whereas the aetiology in the remaining patients remains unexplained. METHODS We report a family with two brothers affected by severe DCM with onset in the adolescent period. Using exome sequencing, we identified a homozygous premature termination variant in the MYZAP gene in both affected sibs. MYZAP encodes for myocardial zonula adherens protein - a conserved cardiac protein in the intercalated disc structure of cardiomyocytes. RESULTS The effect of the variant was demonstrated by light and electron microscopy of the heart muscle and immunohistochemical and Western blot analysis of MYZAP protein in the heart tissue of the proband. Functional characterization using patient-derived induced pluripotent stem cell cardiomyocytes revealed significantly lower force and longer time to peak contraction and relaxation consistent with severe contractile dysfunction. CONCLUSION We provide independent support for the role of biallelic loss-of-function MYZAP variants in dilated cardiomyopathy. This report extends the spectrum of cardiac disease associated with dysfunction of cardiac intercalated disc junction and sheds light on the mechanisms leading to DCM.
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Affiliation(s)
- Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Tamara Zigman
- Department of Pediatrics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ashraf Yusuf Rangrez
- Department of Internal Medicine III, Cardiology and Angiology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Marijana Coric
- Clinical Department of Pathology and Cytology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Jan Homolak
- Department of Pharmacology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Dalibor Saric
- Department of Pediatrics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Iva Skific
- Department of Pathology, University Hospital Dubrava, Zagreb, Croatia
| | - Mario Udovicic
- Division of Cardiology, Department of Internal Medicine, University Hospital Dubrava, Zagreb
| | - Marija Zekusic
- Department of Transfusion and Regenerative Medicine, University Hospital Center Sestre milosrdnice, Zagreb, Croatia
| | - Umber Saleem
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra D Laufer
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arne Hansen
- Department of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Norbert Frey
- Department of Internal Medicine III (Cardiology, Angiology & Pulmology), University of Heidelberg, Germany
| | - Ivo Baric
- Department of Pediatrics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
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17
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Morin C, Moyret-Lalle C, Mertani HC, Diaz JJ, Marcel V. Heterogeneity and dynamic of EMT through the plasticity of ribosome and mRNA translation. Biochim Biophys Acta Rev Cancer 2022; 1877:188718. [PMID: 35304296 DOI: 10.1016/j.bbcan.2022.188718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence exposes translation and its translational machinery as key players in establishing and maintaining physiological and pathological biological processes. Examining translation may not only provide new biological insight but also identify novel innovative therapeutic targets in several fields of biology, including that of epithelial-to-mesenchymal transition (EMT). EMT is currently considered as a dynamic and reversible transdifferentiation process sustaining the transition from an epithelial to mesenchymal phenotype, known to be mainly driven by transcriptional reprogramming. However, it seems that the characterization of EMT plasticity is challenging, relying exclusively on transcriptomic and epigenetic approaches. Indeed, heterogeneity in EMT programs was reported to depend on the biological context. Here, by reviewing the involvement of translational control, translational machinery and ribosome biogenesis characterizing the different types of EMT, from embryonic and adult physiological to pathological contexts, we discuss the added value of integrating translational control and its machinery to depict the heterogeneity and dynamics of EMT programs.
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Affiliation(s)
- Chloé Morin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Caroline Moyret-Lalle
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France.
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18
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Nannapaneni H, Ghaleb S, Arya S, Gajula V, Taylor MB, Das BB. Further Evidence of Autosomal Recessive Inheritance of RPL3L Pathogenic Variants with Rapidly Progressive Neonatal Dilated Cardiomyopathy. J Cardiovasc Dev Dis 2022; 9:jcdd9030065. [PMID: 35323613 PMCID: PMC8955827 DOI: 10.3390/jcdd9030065] [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: 12/19/2021] [Revised: 01/31/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
Neonatal dilated cardiomyopathy (DCM) is rare with high etiologic heterogeneity. Recently, biallelic, autosomal recessive, pathogenic variants in RPL3L (ribosomal protein L3-like) have been reported in the literature with severe early-onset DCM. In the present brief report, we identified two pathogenic RPL3L variants, each harbored in unaffected heterozygous parents: mother (RPL3L c.1076_1080delCCGTG (p.Ala359Glyfs*4)) and father (RPL3L c.80G > A (p.Gly27Asp)). Pathogenic variants were segregated as autosomal recessive to two offspring born with compound heterozygous RPL3L variants and affected by neonatal DCM. This is the second report in the literature to the best of our knowledge and our findings support the pathogenicity of biallelic RPL3L pathologic variants associated with rapidly progressive neonatal DCM and heart failure with a poor prognosis.
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Affiliation(s)
| | - Stephanie Ghaleb
- Department of Pediatrics, Division of Pediatric Cardiology, Children’s of Mississippi Heart Center, University of Mississippi Medical Center, Jackson, MS 39216, USA;
| | - Sandeep Arya
- Department of Pediatrics, Division of Critical Care, Children’s of Mississippi Heart Center, University of Mississippi Medical Center, Jackson, MS 39216, USA; (S.A.); (V.G.); (M.B.T.)
| | - Viswanath Gajula
- Department of Pediatrics, Division of Critical Care, Children’s of Mississippi Heart Center, University of Mississippi Medical Center, Jackson, MS 39216, USA; (S.A.); (V.G.); (M.B.T.)
| | - Mary B. Taylor
- Department of Pediatrics, Division of Critical Care, Children’s of Mississippi Heart Center, University of Mississippi Medical Center, Jackson, MS 39216, USA; (S.A.); (V.G.); (M.B.T.)
| | - Bibhuti B. Das
- Department of Pediatrics, Division of Pediatric Cardiology, Children’s of Mississippi Heart Center, University of Mississippi Medical Center, Jackson, MS 39216, USA;
- Correspondence: ; Tel.: +1-601-984-5250; Fax: +1-601-984-5283
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19
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Jaouadi H, Chabrak S, Lahbib S, Abdelhak S, Zaffran S. Identification of two variants in
AGRN
and
RPL3L
genes in a patient with catecholaminergic polymorphic ventricular tachycardia suggesting new candidate disease genes and digenic inheritance. Clin Case Rep 2022; 10:e05339. [PMID: 35341025 PMCID: PMC8858789 DOI: 10.1002/ccr3.5339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 11/30/2022] Open
Abstract
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an arrhythmogenic syndrome characterized by life‐threatening arrhythmias, a normal resting electrocardiogram and the absence of overt structural heart abnormalities. Mutations in RyR2 gene account for the large part of CPVT cases. Less frequently, mutations in CASQ2 gene have been linked to the recessive form of the disease. Overall, approximately 35% of CPVT patients remain without a genetic etiology implying that other genes might be found causative of the disease. Here, we present a 6‐year‐old boy born to first‐degree related parents, with a typical phenotype of CPVT and a family history of sudden cardiac death of his brother at 7 years. A trio‐based whole exome sequencing was performed, and we identified a homozygous variant in AGRN gene and a heterozygous variant in RPL3L gene. We hypothesized that the presence of the homozygous variant in AGRN accounts for the CPVT phenotype in this family and the heterozygous variant in RPL3L gene may act as a modifier gene. Further studies are needed to determine the role of these genes in CPVT.
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Affiliation(s)
- Hager Jaouadi
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05 Institut Pasteur de Tunis Tunis Tunisia
- Aix Marseille Université INSERM, Marseille Medical Genetics Marseille France
| | - Sonia Chabrak
- Faculty of Medicine of Tunis Université Tunis El Manar Tunis Tunisia
| | - Saida Lahbib
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05 Institut Pasteur de Tunis Tunis Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05 Institut Pasteur de Tunis Tunis Tunisia
| | - Stéphane Zaffran
- Aix Marseille Université INSERM, Marseille Medical Genetics Marseille France
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20
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Heliö K, Mäyränpää MI, Saarinen I, Ahonen S, Junnila H, Tommiska J, Weckström S, Holmström M, Toivonen M, Nikus K, Hathaway J, Siivonen P, Muona M, Sistonen J, Salmenperä P, Gentile M, Paananen J, Myllykangas S, Alastalo TP, Heliö T, Koskenvuo J. GRINL1A Complex Transcription Unit Containing GCOM1, MYZAP, and POLR2M Genes Associates with Fully Penetrant Recessive Dilated Cardiomyopathy. Front Genet 2021; 12:786705. [PMID: 34899865 PMCID: PMC8656111 DOI: 10.3389/fgene.2021.786705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Familial dilated cardiomyopathy (DCM) is a monogenic disorder typically inherited in an autosomal dominant pattern. We have identified two Finnish families with familial cardiomyopathy that is not explained by a variant in any previously known cardiomyopathy gene. We describe the cardiac phenotype related to homozygous truncating GCOM1 variants. Methods and Results: This study included two probands and their relatives. All the participants are of Finnish ethnicity. Whole-exome sequencing was used to test the probands; bi-directional Sanger sequencing was used to identify the GCOM1 variants in probands' family members. Clinical evaluation was performed, medical records and death certificates were obtained. Immunohistochemical analysis of myocardial samples was conducted. A homozygous GCOM1 variant was identified altogether in six individuals, all considered to be affected. None of the nine heterozygous family members fulfilled any cardiomyopathy criteria. Heart failure was the leading clinical feature, and the patients may have had a tendency for atrial arrhythmias. Conclusions: This study demonstrates the significance of GCOM1 variants as a cause of human cardiomyopathy and highlights the importance of searching for new candidate genes when targeted gene panels do not yield a positive outcome.
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Affiliation(s)
- Krista Heliö
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Mikko I Mäyränpää
- Department of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Inka Saarinen
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | - Saija Ahonen
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | - Heidi Junnila
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | | | - Sini Weckström
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Miia Holmström
- Department of Radiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Mia Toivonen
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | - Kjell Nikus
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Heart Center, Tampere University Hospital, Tampere, Finland
| | - Julie Hathaway
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | - Pauli Siivonen
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | - Mikko Muona
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | | | | | | | - Jussi Paananen
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
| | | | | | - Tiina Heliö
- Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Juha Koskenvuo
- Blueprint Genetics, A Quest Diagnostics Company, Espoo, Finland
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21
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Guo XJ, Qiu XB, Wang J, Guo YH, Yang CX, Li L, Gao RF, Ke ZP, Di RM, Sun YM, Xu YJ, Yang YQ. PRRX1 Loss-of-Function Mutations Underlying Familial Atrial Fibrillation. J Am Heart Assoc 2021; 10:e023517. [PMID: 34845933 PMCID: PMC9075371 DOI: 10.1161/jaha.121.023517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Atrial fibrillation (AF) is the most common form of clinical cardiac dysrhythmia responsible for thromboembolic cerebral stroke, congestive heart failure, and death. Aggregating evidence highlights the strong genetic basis of AF. Nevertheless, AF is of pronounced genetic heterogeneity, and in an overwhelming majority of patients, the genetic determinants underpinning AF remain elusive. Methods and Results By genome‐wide screening with polymorphic microsatellite markers and linkage analysis in a 4‐generation Chinese family affected with autosomal‐dominant AF, a novel locus for AF was mapped to chromosome 1q24.2–q25.1, a 3.20‐cM (≈4.19 Mbp) interval between markers D1S2851 and D1S218, with the greatest 2‐point logarithm of odds score of 4.8165 for the marker D1S452 at recombination fraction=0.00. Whole‐exome sequencing and bioinformatics analyses showed that within the mapping region, only the mutation in the paired related homeobox 1 (PRRX1) gene, NM_022716.4:c.319C>T;(p.Gln107*), cosegregated with AF in the family. In addition, sequencing analyses of PRRX1 in another cohort of 225 unrelated patients with AF revealed a new mutation, NM_022716.4:c.437G>T; (p.Arg146Ile), in a patient. The 2 mutations were absent in 908 control subjects. Biological analyses in HeLa cells demonstrated that the 2 mutants had significantly diminished transactivation on the target genes ISL1 and SHOX2 and markedly decreased ability to bind the promoters of ISL1 and SHOX2 (2 genes causally linked to AF), although with normal intracellular distribution. Conclusions This study first indicates that PRRX1 loss‐of‐function mutations predispose to AF, which provides novel insight into the molecular pathogenesis underpinning AF, implying potential implications for precisive prophylaxis and management of AF.
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Affiliation(s)
- Xiao-Juan Guo
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Xing-Biao Qiu
- Department of Cardiology Shanghai Chest HospitalShanghai Jiao Tong University Shanghai China
| | - Jun Wang
- Department of Cardiology Shanghai Jing'an District Central HospitalFudan University Shanghai China
| | - Yu-Han Guo
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Chen-Xi Yang
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Li Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China Shanghai East HospitalTongji University School of Medicine Shanghai China.,Institute of Medical GeneticsTongji University Shanghai China
| | - Ri-Feng Gao
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Zun-Ping Ke
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Ruo-Min Di
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Yu-Min Sun
- Department of Cardiology Shanghai Jing'an District Central HospitalFudan University Shanghai China
| | - Ying-Jia Xu
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China
| | - Yi-Qing Yang
- Department of Cardiology and the Center for Complex Cardiac Arrhythmias of Minhang District Shanghai Fifth People's HospitalFudan University Shanghai China.,Cardiovascular Research Laboratory and Central Laboratory Shanghai Fifth People's HospitalFudan University Shanghai China
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22
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Skinnider MA, Scott NE, Prudova A, Kerr CH, Stoynov N, Stacey RG, Chan QWT, Rattray D, Gsponer J, Foster LJ. An atlas of protein-protein interactions across mouse tissues. Cell 2021; 184:4073-4089.e17. [PMID: 34214469 DOI: 10.1016/j.cell.2021.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the interactome has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood. Here, we develop a quantitative proteomic approach combining protein correlation profiling with stable isotope labeling of mammals (PCP-SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide a proteome-scale survey of interactome rewiring across mammalian tissues, revealing more than 125,000 unique interactions at a quality comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewired proteins are tightly regulated by multiple cellular mechanisms and are implicated in disease. Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.
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Affiliation(s)
- Michael A Skinnider
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nichollas E Scott
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Peter Doherty Institute, Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3000, Australia
| | - Anna Prudova
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Craig H Kerr
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikolay Stoynov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - R Greg Stacey
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Queenie W T Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David Rattray
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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23
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He Q, Li Z, Lei X, Zou Q, Yu H, Ding Y, Xu G, Zhu W. The underlying molecular mechanisms and prognostic factors of RNA binding protein in colorectal cancer: a study based on multiple online databases. Cancer Cell Int 2021; 21:325. [PMID: 34193169 PMCID: PMC8244213 DOI: 10.1186/s12935-021-02031-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/19/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND RNA binding protein (RBP) is an active factor involved in the occurrence and development of colorectal cancer (CRC). Therefore, the potential mechanism of RBP in CRC needs to be clarified by dry-lab analyses or wet-lab experiments. METHODS The differential RBP gene obtained from the GEPIA 2 (Gene Expression Profiling Interactive Analysis 2) were performed functional enrichment analysis. Then, the alternative splicing (AS) events related to survival were acquired by univariate regression analysis, and the correlation between RBP and AS was analyzed by R software. The online databases were conducted to analyze the mutation and methylation of RBPs in CRC. Moreover, 5 key RBP signatures were obtained through univariate and multivariate Cox regression analysis and established as RBP prognosis model. Subsequently, the above model was verified through another randomized group of TCGA CRC cohorts. Finally, multiple online databases and qRT-PCR analysis were carried to further confirm the expression of the above 5 RBP signatures in CRC. RESULTS Through a comprehensive bioinformatics analysis, it was revealed that RBPs had genetic and epigenetic changes in CRC. We obtained 300 differentially expressed RBPs in CRC samples. The functional analysis suggested that they mainly participated in spliceosome. Then, a regulatory network for RBP was established to participate in AS and DDX39B was detected to act as a potentially essential factor in the regulation of AS in CRC. Our analysis discovered that 11 differentially expressed RBPs with a mutation frequency higher than 5%. Furthermore, we found that 10 differentially expressed RBPs had methylation sites related to the prognosis of CRC, and a prognostic model was constructed by the 5 RBP signatures. In another randomized group of TCGA CRC cohorts, the prognostic performance of the 5 RBP signatures was verified. CONCLUSION The potential mechanisms that regulate the aberrant expression of RBPs in the development of CRC was explored, a network that regulated AS was established, and the RBP-related prognosis model was constructed and verified, which could improve the individualized prognosis prediction of CRC.
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Affiliation(s)
- Qinglian He
- Department of Pathology, Guangdong Medical University, No.1 Xincheng Road, Dongguan, 523808, Guangdong Province, China
| | - Ziqi Li
- Department of Pathology, Guangdong Medical University, No.1 Xincheng Road, Dongguan, 523808, Guangdong Province, China
| | - Xue Lei
- Department of Pathology, Guangdong Medical University, No.1 Xincheng Road, Dongguan, 523808, Guangdong Province, China
| | - Qian Zou
- Department of Pathology, Guangdong Medical University, No.1 Xincheng Road, Dongguan, 523808, Guangdong Province, China
| | - Haibing Yu
- School of Public Health, Guangdong Medical University, Dongguan, 523808, Guangdong Province, China
| | - Yuanlin Ding
- School of Public Health, Guangdong Medical University, Dongguan, 523808, Guangdong Province, China
| | - Guangxian Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, Institute of Clinical Laboratory, Guangdong Medical University, Dongguan, 523808, Guangdong Province, China
| | - Wei Zhu
- Department of Pathology, Guangdong Medical University, No.1 Xincheng Road, Dongguan, 523808, Guangdong Province, China.
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24
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Thorolfsdottir RB, Sveinbjornsson G, Aegisdottir HM, Benonisdottir S, Stefansdottir L, Ivarsdottir EV, Halldorsson GH, Sigurdsson JK, Torp-Pedersen C, Weeke PE, Brunak S, Westergaard D, Pedersen OB, Sorensen E, Nielsen KR, Burgdorf KS, Banasik K, Brumpton B, Zhou W, Oddsson A, Tragante V, Hjorleifsson KE, Davidsson OB, Rajamani S, Jonsson S, Torfason B, Valgardsson AS, Thorgeirsson G, Frigge ML, Thorleifsson G, Norddahl GL, Helgadottir A, Gretarsdottir S, Sulem P, Jonsdottir I, Willer CJ, Hveem K, Bundgaard H, Ullum H, Arnar DO, Thorsteinsdottir U, Gudbjartsson DF, Holm H, Stefansson K. Genetic insight into sick sinus syndrome. Eur Heart J 2021; 42:1959-1971. [PMID: 36282123 PMCID: PMC8140484 DOI: 10.1093/eurheartj/ehaa1108] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/24/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Aims The aim of this study was to use human genetics to investigate the pathogenesis of sick sinus syndrome (SSS) and the role of risk factors in its development. Methods and results We performed a genome-wide association study of 6469 SSS cases and 1 000 187 controls from deCODE genetics, the Copenhagen Hospital Biobank, UK Biobank, and the HUNT study. Variants at six loci associated with SSS, a reported missense variant in MYH6, known atrial fibrillation (AF)/electrocardiogram variants at PITX2, ZFHX3, TTN/CCDC141, and SCN10A and a low-frequency (MAF = 1.1–1.8%) missense variant, p.Gly62Cys in KRT8 encoding the intermediate filament protein keratin 8. A full genotypic model best described the p.Gly62Cys association (P = 1.6 × 10−20), with an odds ratio (OR) of 1.44 for heterozygotes and a disproportionally large OR of 13.99 for homozygotes. All the SSS variants increased the risk of pacemaker implantation. Their association with AF varied and p.Gly62Cys was the only variant not associating with any other arrhythmia or cardiovascular disease. We tested 17 exposure phenotypes in polygenic score (PGS) and Mendelian randomization analyses. Only two associated with the risk of SSS in Mendelian randomization, AF, and lower heart rate, suggesting causality. Powerful PGS analyses provided convincing evidence against causal associations for body mass index, cholesterol, triglycerides, and type 2 diabetes (P > 0.05). Conclusion We report the associations of variants at six loci with SSS, including a missense variant in KRT8 that confers high risk in homozygotes and points to a mechanism specific to SSS development. Mendelian randomization supports a causal role for AF in the development of SSS.
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Affiliation(s)
| | | | | | | | | | | | | | - Jon K Sigurdsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Christian Torp-Pedersen
- Department of Clinical Research and Cardiology, Nordsjaelland Hospital, Dyrehavevej 29, Hillerød 3400, Denmark
| | - Peter E Weeke
- Department of Cardiology, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Ole B Pedersen
- Department of Clinical Immunology, Naestved Hospital, Ringstedgade 77B, Naestved 4700, Denmark
| | - Erik Sorensen
- Department of Clinical Immunology, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital North, Urbansgade 36, Aalborg 9000, Denmark
| | - Kristoffer S Burgdorf
- Department of Clinical Immunology, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, Copenhagen 2200, Denmark
| | - Ben Brumpton
- Department of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Prinsesse Kristinas gate 3, Trondheim 7030, Norway
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA
| | - Asmundur Oddsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | - Kristjan E Hjorleifsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E California Blvd. MC 305-16, Pasadena, CA 91125, USA
| | | | | | - Stefan Jonsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Bjarni Torfason
- Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland.,Department of Cardiothoracic Surgery, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Atli S Valgardsson
- Department of Cardiothoracic Surgery, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Michael L Frigge
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | | | - Anna Helgadottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | | | - Patrick Sulem
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland.,Department of Immunology, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA.,Department of Internal Medicine: Cardiology, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109 -5368, USA.,Department of Human Genetics, University of Michigan, 4909 Buhl Building, 1241 E. Catherine St., Ann Arbor, MI 48109 -5618, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, Trondheim 7491, Norway.,Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Postboks 8905, Trondheim 7491, Norway.,HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Forskningsveien 2, Levanger 7600, Norway
| | - Henning Bundgaard
- Department of Cardiology, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Henrik Ullum
- Department of Clinical Immunology, Copenhagen University Hospital, Blegdamsvej 9, Copenhagen 2100, Denmark.,Statens Serum Institut, Artillerivej 5, Copenhagen 2300, Denmark
| | - David O Arnar
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Hringbraut, Reykjavik 101, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Hjardarhagi 4, Reykjavik 107, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Sturlugata 8, Reykjavik 101, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland
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25
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Victorino J, Alvarez-Franco A, Manzanares M. Functional genomics and epigenomics of atrial fibrillation. J Mol Cell Cardiol 2021; 157:45-55. [PMID: 33887329 DOI: 10.1016/j.yjmcc.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023]
Abstract
Atrial fibrillation is a progressive cardiac arrhythmia that increases the risk of hospitalization and adverse cardiovascular events. Despite years of study, we still do not have a full comprehension of the molecular mechanism responsible for the disease. The recent implementation of large-scale approaches in both patient samples, population studies and animal models has helped us to broaden our knowledge on the molecular drivers responsible for AF and on the mechanisms behind disease progression. Understanding genomic and epigenomic changes that take place during chronification of AF will prove essential to design novel treatments leading to improved patient care.
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Affiliation(s)
- Jesus Victorino
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Spain
| | - Alba Alvarez-Franco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain; Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.
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26
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Atrial fibrillation-a complex polygenetic disease. Eur J Hum Genet 2020; 29:1051-1060. [PMID: 33279945 PMCID: PMC8298566 DOI: 10.1038/s41431-020-00784-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/19/2022] Open
Abstract
Atrial fibrillation (AF) is the most common type of arrhythmia. Epidemiological studies have documented a substantial genetic component. More than 160 genes have been associated with AF during the last decades. Some of these were discovered by classical linkage studies while the majority relies on functional studies or genome-wide association studies. In this review, we will evaluate the genetic basis of AF and the role of both common and rare genetic variants in AF. Rare variants in multiple ion-channel genes as well as gap junction and transcription factor genes have been associated with AF. More recently, a growing body of evidence has implicated structural genes with AF. An increased burden of atrial fibrosis in AF patients compared with non-AF patients has also been reported. These findings challenge our traditional understanding of AF being an electrical disease. We will focus on several quantitative landmark papers, which are transforming our understanding of AF by implicating atrial cardiomyopathies in the pathogenesis. This new AF research field may enable better diagnostics and treatment in the future.
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27
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Weng LC, Hall AW, Choi SH, Jurgens SJ, Haessler J, Bihlmeyer NA, Grarup N, Lin H, Teumer A, Li-Gao R, Yao J, Guo X, Brody JA, Müller-Nurasyid M, Schramm K, Verweij N, van den Berg ME, van Setten J, Isaacs A, Ramírez J, Warren HR, Padmanabhan S, Kors JA, de Boer RA, van der Meer P, Sinner MF, Waldenberger M, Psaty BM, Taylor KD, Völker U, Kanters JK, Li M, Alonso A, Perez MV, Vaartjes I, Bots ML, Huang PL, Heckbert SR, Lin HJ, Kornej J, Munroe PB, van Duijn CM, Asselbergs FW, Stricker BH, van der Harst P, Kääb S, Peters A, Sotoodehnia N, Rotter JI, Mook-Kanamori DO, Dörr M, Felix SB, Linneberg A, Hansen T, Arking DE, Kooperberg C, Benjamin EJ, Lunetta KL, Ellinor PT, Lubitz SA. Genetic Determinants of Electrocardiographic P-Wave Duration and Relation to Atrial Fibrillation. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2020; 13:387-395. [PMID: 32822252 PMCID: PMC7578098 DOI: 10.1161/circgen.119.002874] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The P-wave duration (PWD) is an electrocardiographic measurement that represents cardiac conduction in the atria. Shortened or prolonged PWD is associated with atrial fibrillation (AF). We used exome-chip data to examine the associations between common and rare variants with PWD. METHODS Fifteen studies comprising 64 440 individuals (56 943 European, 5681 African, 1186 Hispanic, 630 Asian) and ≈230 000 variants were used to examine associations with maximum PWD across the 12-lead ECG. Meta-analyses summarized association results for common variants; gene-based burden and sequence kernel association tests examined low-frequency variant-PWD associations. Additionally, we examined the associations between PWD loci and AF using previous AF genome-wide association studies. RESULTS We identified 21 common and low-frequency genetic loci (14 novel) associated with maximum PWD, including several AF loci (TTN, CAND2, SCN10A, PITX2, CAV1, SYNPO2L, SOX5, TBX5, MYH6, RPL3L). The top variants at known sarcomere genes (TTN, MYH6) were associated with longer PWD and increased AF risk. However, top variants at other loci (eg, PITX2 and SCN10A) were associated with longer PWD but lower AF risk. CONCLUSIONS Our results highlight multiple novel genetic loci associated with PWD, and underscore the shared mechanisms of atrial conduction and AF. Prolonged PWD may be an endophenotype for several different genetic mechanisms of AF.
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Affiliation(s)
- Lu-Chen Weng
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Amelia Weber Hall
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Seung Hoan Choi
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Sean J. Jurgens
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
| | - Jeffrey Haessler
- Fred Hutchinson Cancer Rsrch Ctr, Division of Public Health Sciences, Seattle WA
| | - Nathan A. Bihlmeyer
- McKusick-Nathans Dept of Genetic Medicine, Johns Hopkins Univ School of Med, Baltimore, MD
| | - Niels Grarup
- Novo Nordisk Foundation Ctr for Basic Metabolic Rsrch, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Honghuang Lin
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
- Section of Computational Biomedicine, Dept of Med, Boston Univ School of Med, Boston, MA
| | - Alexander Teumer
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Inst for Community Med, Univ Medicine Greifswald, Greifswald, Germany
| | - Ruifang Li-Gao
- Dept of Clinical Epidemiology, Leiden Univ Medical Ctr, the Netherlands
| | - Jie Yao
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
| | - Xiuqing Guo
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Dept of Pediatrics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Jennifer A. Brody
- Cardiovascular Health Rsrch Unit, Dept of Med, Dept of Epidemiology, Univ of Washington
| | - Martina Müller-Nurasyid
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- Inst of Genetic Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
| | - Katharina Schramm
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- Inst of Genetic Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
| | - Niek Verweij
- Genomics plc, Oxford, UK
- Dept of Cardiology, Univ of Groningen & Univ Medical Ctr, Groningen
| | - Marten E. van den Berg
- Dept of Epidemiology, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
| | - Jessica van Setten
- Dept of Cardiology, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
| | - Aaron Isaacs
- CARIM School for Cardiovascular Diseases, Maastricht Univ, Maastricht, the Netherlands
- Dept of Physiology, Maastricht Univ, Maastricht, the Netherlands
| | - Julia Ramírez
- Nat Inst for Health Rsrch, Barts Cardiovascular Biomedical Rsrch Ctr, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
- William Harvey Rsrch Inst, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
| | - Helen R. Warren
- Nat Inst for Health Rsrch, Barts Cardiovascular Biomedical Rsrch Ctr, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
- William Harvey Rsrch Inst, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
| | - Sandosh Padmanabhan
- Inst of Cardiovascular & Medical Sciences, College of Medical, Veterinary & Life Sciences, Univ of Glasgow, Glasgow, UK
| | - Jan A. Kors
- Dept of Med Informatics, Erasmus Univ Medical Ctr, Rotterdam, the Netherlands
| | | | | | - Moritz F. Sinner
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
| | - Melanie Waldenberger
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
- Inst of Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
- Rsrch unit of Molecular Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
| | - Bruce M. Psaty
- Cardiovascular Health Rsrch Unit, Depts of Med, Epidemiology & Health Services, Dept of Epidemiology, Univ of Washington
- Kaiser Permanente Washington Health Rsrch Inst, Seattle, WA
| | - Kent D. Taylor
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Dept of Pediatrics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Uwe Völker
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Interfaculty Inst for Genetics & Functional Genomics, Univ Medicine Greifswald, Greifswald, Germany
| | - Jørgen K. Kanters
- Lab of Experimental Cardiology, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Man Li
- Division of Nephrology & Hypertensions, Dept of Internal Med, Univ of Utah School of Med, Salt Lake City, UT
| | - Alvaro Alonso
- Dept of Epidemiology, Rollins School of Public Health, Emory Univ, Atlanta, GA
| | | | - Ilonca Vaartjes
- Julius Ctr for Health Sciences & Primary Care, Univ Medical Ctr Utrecht, Utrecht Univ, the Netherlands
| | - Michiel L. Bots
- Julius Ctr for Health Sciences & Primary Care, Univ Medical Ctr Utrecht, Utrecht Univ, the Netherlands
| | | | - Susan R. Heckbert
- Cardiovascular Health Rsrch Unit, Dept of Epidemiology, Univ of Washington
| | - Henry J. Lin
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Dept of Pediatrics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Jelena Kornej
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
| | - Patricia B. Munroe
- Nat Inst for Health Rsrch, Barts Cardiovascular Biomedical Rsrch Ctr, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
- William Harvey Rsrch Inst, Barts & The London School of Med & Dentistry, Queen Mary Univ of London, London
| | - Cornelia M. van Duijn
- Dept of Epidemiology, Erasmus Univ Medical Ctr, Rotterdam, the Netherlands
- Nuffield Dept of Population Health, Medical Sciences Division, St. Cross College, Oxford Univ, Oxford
| | - Folkert W. Asselbergs
- Dept of Cardiology, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
- Health Data Rsrch UK & Inst of Health Informatics, Faculty of Population Health Sciences, Univ College London, London, UK
- Inst of Cardiovascular Science, Faculty of Population Health Sciences, Univ College London, London, UK
| | - Bruno H. Stricker
- Dept of Internal Medicine, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
- Dept of Med Informatics, Erasmus MC, Medical Ctr Rotterdam, Division of Heart & Lungs, Univ of Utrecht, Univ Medical Ctr Utrecht
- Inspectorate of Health Care
| | - Pim van der Harst
- Dept of Cardiology, Univ of Groningen & Univ Medical Ctr, Groningen
- Durrer Ctr for Cardiogenetic Rsrch, ICIN-Netherlands Heart Inst, Utrecht, the Netherlands
- Dept of Genetics, Univ of Groningen & Univ Medical Ctr, Groningen
| | - Stefan Kääb
- Dept of Internal Med I (Cardiology), Hospital of the Ludwig-Maximilians-Univ (LMU) Munich, Munich
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
| | - Annette Peters
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Munich Heart Alliance, Munich
- Inst of Epidemiology, Helmholtz Zentrum München - German Rsrch Ctr for Environmental Health, Neuherberg, Germany
- German Ctr for Diabetes Rsrch, Neuherberg, Germany
| | - Nona Sotoodehnia
- Cardiovascular Health Rsrch Unit, Dept of Med, Dept of Epidemiology, Univ of Washington
| | - Jerome I. Rotter
- The Inst for Translational Genomics & Population Sciences at Harbor-UCLA Medical Ctr, Torrance
- Depts of Pediatrics & Human Genetics, David Geffen School of Med at UCLA, Los Angeles, CA
| | - Dennis O. Mook-Kanamori
- Dept of Clinical Epidemiology, Leiden Univ Medical Ctr, the Netherlands
- Dept of Public Health & Primary Care, Leiden Univ Medical Ctr, the Netherlands
| | - Marcus Dörr
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Dept of Internal Med B, Univ Medicine Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- DZHK (German Ctr for Cardiovascular Rsrch), partner site Greifswald
- Dept of Internal Med B, Univ Medicine Greifswald, Greifswald, Germany
| | - Allan Linneberg
- Ctr for Clinical Rsrch & Prevention, Bispebjerg & Frederiksberg Hospital, Copenhagen, Denamrk
- Dept of Clinical Med, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Ctr for Basic Metabolic Rsrch, Faculty of Health & Med Sciences, Univ of Copenhagen, Copenhagen, Denmark
| | - Dan E. Arking
- McKusick-Nathans Dept of Genetic Medicine, Johns Hopkins Univ School of Med, Baltimore, MD
| | - Charles Kooperberg
- Fred Hutchinson Cancer Rsrch Ctr, Division of Public Health Sciences, Seattle WA
| | - Emelia J. Benjamin
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
- Dept of Epidemiology, Boston Univ School of Public Health, Boston, MA
- Dept of Med, Boston Univ School of Med, Boston, MA
| | - Kathryn L. Lunetta
- Boston Univ & NHLBI’s Framingham Heart Study, Framingham
- Dept of Biostatistics, Boston Univ School of Public Health, Boston, MA
| | - Patrick T. Ellinor
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
- Cardiac Arrhythmia Service, MGH, Boston
| | - Steven A. Lubitz
- Cardiovascular Rsrch Ctr, MGH, Boston
- Cardiovascular Disease Initiative, The Broad Inst of MIT & Harvard, Cambridge, MA
- Cardiac Arrhythmia Service, MGH, Boston
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28
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Xu C, Zhang R, Xia Y, Xiong L, Yang W, Wang P. Annotation of susceptibility SNPs associated with atrial fibrillation. Aging (Albany NY) 2020; 12:16981-16998. [PMID: 32902410 PMCID: PMC7521544 DOI: 10.18632/aging.103615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/18/2020] [Indexed: 01/24/2023]
Abstract
OBJECTIVE Genome-wide association studies (GWAS) and the candidate gene based association studies have identified a panel of variants associated with atrial fibrillation (AF), however, most of the identified single nucleotide polymorphisms (SNPs) were found located within intergenic or intronic genomic regions, and whether the positive SNPs have a real biological function is unknown, and the real disease causing gene need to be studied. RESULTS The current results of the genetic studies including common variants identified by GWAS (338 index SNPs) and candidate gene based association studies (40 SNPs) were summarized. CONCLUSION Our study suggests the relationship between genetic variants and possible targeted genes, and provides insight into potential genetic pathways underlying AF incidence and development. The results may provide an encyclopedia of AF susceptibility SNPs and shed light on the functional mechanisms of AF variants identified through genetic studies. METHODS We summarized AF susceptibility SNPs identified by GWAS and candidate gene based association studies, and give a comprehensive functional annotation of all these AF susceptibility loci. by genomic annotation, microRNA binding prediction, promoter activity analysis, enhancer activity analysis, transcription factors binding activity prediction, expression quantitative trait loci (eQTL) analysis, long-range transcriptional regulatory function analysis, gene ontology and pathway enrichment analysis.
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Affiliation(s)
- Chengqi Xu
- College of Life Science and Technology, Center for Human Genome Research and Cardio-X Institute, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Rongfeng Zhang
- Department of Cardiology, First Affiliated Hospital of Dalian Medical University, Dalian 116011, P. R. China
| | - Yunlong Xia
- Department of Cardiology, First Affiliated Hospital of Dalian Medical University, Dalian 116011, P. R. China
| | - Liang Xiong
- Department of Clinical Laboratory, Liyuan Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430077, P. R. China
| | - Wei Yang
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun 130041, P. R. China
| | - Pengyun Wang
- Department of Clinical Laboratory, Liyuan Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430077, P. R. China
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29
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Wu SH, Wang XH, Xu YJ, Gu JN, Yang CX, Qiao Q, Guo XJ, Guo YH, Qiu XB, Jiang WF, Yang YQ. ISL1 loss-of-function variation causes familial atrial fibrillation. Eur J Med Genet 2020; 63:104029. [PMID: 32771629 DOI: 10.1016/j.ejmg.2020.104029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 02/08/2023]
Abstract
Atrial fibrillation (AF) represents the most frequent form of sustained cardiac rhythm disturbance, affecting approximately 1% of the general population worldwide, and confers a substantially enhanced risk of cerebral stroke, heart failure, and death. Increasing epidemiological studies have clearly demonstrated a strong genetic basis for AF, and variants in a wide range of genes, including those coding for ion channels, gap junction channels, cardiac structural proteins and transcription factors, have been identified to underlie AF. Nevertheless, the genetic pathogenesis of AF is complex and still far from completely understood. Here, whole-exome sequencing and bioinformatics analyses of a three-generation family with AF were performed, and after filtering variants by multiple metrics, we identified a heterozygous variant in the ISL1 gene (encoding a transcription factor critical for embryonic cardiogenesis and postnatal cardiac remodeling), NM_002202.2: c.481G > T; p.(Glu161*), which was validated by Sanger sequencing and segregated with autosome-dominant AF in the family with complete penetrance. The nonsense variant was absent from 284 unrelated healthy individuals used as controls. Functional assays with a dual-luciferase reporter assay system revealed that the truncating ISL1 protein lost transcriptional activation on the verified target genes MEF2C and NKX2-5. Additionally, the variant nullified the synergistic transactivation between ISL1 and TBX5 as well as GATA4, two other transcription factors that have been implicated in AF. The findings suggest ISL1 as a novel gene contributing to AF, which adds new insight to the genetic mechanisms underpinning AF, implying potential implications for genetic testing and risk stratification of the AF family members.
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Affiliation(s)
- Shao-Hui Wu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Hua Wang
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Jia-Ning Gu
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Chen-Xi Yang
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Qi Qiao
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Xiao-Juan Guo
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yu-Han Guo
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Xing-Biao Qiu
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Feng Jiang
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China; Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China; Central Laboratory, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China.
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30
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Abstract
Atrial fibrillation is a common heart rhythm disorder that leads to an increased risk for stroke and heart failure. Atrial fibrillation is a complex disease with both environmental and genetic risk factors that contribute to the arrhythmia. Over the last decade, rapid progress has been made in identifying the genetic basis for this common condition. In this review, we provide an overview of the primary types of genetic analyses performed for atrial fibrillation, including linkage studies, genome-wide association studies, and studies of rare coding variation. With these results in mind, we aim to highlighting the existing knowledge gaps and future directions for atrial fibrillation genetics research.
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Affiliation(s)
- Carolina Roselli
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, MA, USA
- Department of Cardiology, University of Groningen, University Medical Center Groningen Groningen, the Netherlands
| | - Michiel Rienstra
- Department of Cardiology, University of Groningen, University Medical Center Groningen Groningen, the Netherlands
| | - Patrick T. Ellinor
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, MA, USA
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31
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Ang YS, Rajamani S, Haldar SM, Hüser J. A New Therapeutic Framework for Atrial Fibrillation Drug Development. Circ Res 2020; 127:184-201. [DOI: 10.1161/circresaha.120.316576] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Atrial fibrillation (AF) is a highly prevalent cardiac arrhythmia and cause of significant morbidity and mortality. Its increasing prevalence in aging societies constitutes a growing challenge to global healthcare systems. Despite substantial unmet needs in AF prevention and treatment, drug developments hitherto have been challenging, and the current pharmaceutical pipeline is nearly empty. In this review, we argue that current drugs for AF are inadequate because of an oversimplified system for patient classification and the development of drugs that do not interdict underlying disease mechanisms. We posit that an improved understanding of AF molecular pathophysiology related to the continuous identification of novel disease-modifying drug targets and an increased appreciation of patient heterogeneity provide a new framework to personalize AF drug development. Together with recent innovations in diagnostics, remote rhythm monitoring, and big data capabilities, we anticipate that adoption of a new framework for patient subsegmentation based on pathophysiological, genetic, and molecular subsets will improve success rates of clinical trials and advance drugs that reduce the individual patient and public health burden of AF.
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Affiliation(s)
- Yen-Sin Ang
- From Amgen Research, Cardiometabolic Disorders, South San Francisco, CA (Y.-S.A., S.R., S.M.H.)
| | - Sridharan Rajamani
- From Amgen Research, Cardiometabolic Disorders, South San Francisco, CA (Y.-S.A., S.R., S.M.H.)
| | - Saptarsi M. Haldar
- From Amgen Research, Cardiometabolic Disorders, South San Francisco, CA (Y.-S.A., S.R., S.M.H.)
- Gladstone Institutes, San Francisco, CA (S.M.H.)
- Department of Medicine, Cardiology Division, UCSF School of Medicine, San Francisco, CA (S.M.H.)
| | - Jörg Hüser
- Bayer AG, Pharma-RD-PCR TA Cardiovascular Disease, Wuppertal, Germany (J.H.)
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32
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Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis. Hum Genet 2020; 139:1443-1454. [PMID: 32514796 PMCID: PMC7519902 DOI: 10.1007/s00439-020-02188-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
Dilated cardiomyopathy (DCM) belongs to the most frequent forms of cardiomyopathy mainly characterized by cardiac dilatation and reduced systolic function. Although most cases of DCM are classified as sporadic, 20–30% of cases show a heritable pattern. Familial forms of DCM are genetically heterogeneous, and mutations in several genes have been identified that most commonly play a role in cytoskeleton and sarcomere-associated processes. Still, a large number of familial cases remain unsolved. Here, we report five individuals from three independent families who presented with severe dilated cardiomyopathy during the neonatal period. Using whole-exome sequencing (WES), we identified causative, compound heterozygous missense variants in RPL3L (ribosomal protein L3-like) in all the affected individuals. The identified variants co-segregated with the disease in each of the three families and were absent or very rare in the human population, in line with an autosomal recessive inheritance pattern. They are located within the conserved RPL3 domain of the protein and were classified as deleterious by several in silico prediction software applications. RPL3L is one of the four non-canonical riboprotein genes and it encodes the 60S ribosomal protein L3-like protein that is highly expressed only in cardiac and skeletal muscle. Three-dimensional homology modeling and in silico analysis of the affected residues in RPL3L indicate that the identified changes specifically alter the interaction of RPL3L with the RNA components of the 60S ribosomal subunit and thus destabilize its binding to the 60S subunit. In conclusion, we report that bi-allelic pathogenic variants in RPL3L are causative of an early-onset, severe neonatal form of dilated cardiomyopathy, and we show for the first time that cytoplasmic ribosomal proteins are involved in the pathogenesis of non-syndromic cardiomyopathies.
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33
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Kember RL, Levin MG, Cousminer DL, Tsao N, Judy R, Schur GM, Lubitz SA, Ellinor PT, McCormack SE, Grant SF, Rader DJ, Voight BF, Damrauer SM. Genetically Determined Birthweight Associates With Atrial Fibrillation: A Mendelian Randomization Study. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2020; 13:e002553. [PMID: 32340472 PMCID: PMC7299774 DOI: 10.1161/circgen.119.002553] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Atrial fibrillation is a common cardiovascular disorder, characterized by irregular electrical activity in the upper chambers of the heart. Both chronic cardiometabolic risk factors and genetics have been shown to contribute to the development of atrial fibrillation. Birthweight has also been associated with risk of atrial fibrillation. METHODS In the current study, we utilized a genetic approach to study the effect of birthweight on atrial fibrillation. We used 2-sample Mendelian randomization to consider the impact of birthweight on incident atrial fibrillation using summary data from the Early Growth Genetics Consortium GWAS of birthweight and a large biobank-based GWAS of atrial fibrillation. RESULTS Using the framework of 2-sample Mendelian randomization, we found that a 1-SD genetic elevation of birthweight was associated with increased risk of atrial fibrillation (odds ratio, 1.27 [95% CI, 1.14-1.41]; P=1×10-5) with sensitivity analyses demonstrating robustness of this result. CONCLUSIONS Our findings clarify the directionality of the relationship between birthweight and atrial fibrillation, supporting the growing body of evidence that intrauterine growth has a lifelong impact on cardiovascular health.
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Affiliation(s)
- Rachel L. Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania;,Corporal Michael J. Crescenz VA Medical Center
| | - Michael G. Levin
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania;,Corporal Michael J. Crescenz VA Medical Center
| | - Diana L. Cousminer
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania;,Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA;,Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Noah Tsao
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania
| | - Gayatri M. Schur
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Steven A. Lubitz
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston;,Program in Medical and Population Genetics, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Patrick T. Ellinor
- Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston;,Program in Medical and Population Genetics, The Broad Institute of MIT & Harvard, Cambridge, MA
| | - Shana E. McCormack
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania;,Division of Endocrinology & Diabetes, Children’s Hospital of Philadelphia
| | - Struan F.A. Grant
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania;,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania;,Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA;,Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | - Daniel J. Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania;,Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Benjamin F. Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania;,Departments of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania;,Institute for Translational Medicine and Therapeutics, University of Pennsylvania
| | - Scott M. Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania;,Corporal Michael J. Crescenz VA Medical Center
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34
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Ford D. Ribosomal heterogeneity - A new inroad for pharmacological innovation. Biochem Pharmacol 2020; 175:113874. [PMID: 32105657 DOI: 10.1016/j.bcp.2020.113874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
The paradigm of ribosome usage in protein translation has shifted from a stance proposed as scientists began to unpick the genetic code that each mRNA was partnered by its own, unique ribosome to a rapid reversal of this view that ribosomes are completely interchangeable and simply recruited to mRNAs from a completely homogenous cellular pool. Evidence that the ribosomal proteome, ribosomal gene transcriptome and ribosome protein and RNA modifications differ between cells and tissues points to the fact that ribosomes are heterogeneous in their composition and have a degree of specialisation in their function. It has also been posited that the tissue-specificity of ribosome diseases provides an indication of functional ribosome heterogeneity, but there are substantial caveats to this interpretation. Only now have proteomic technologies developed to a level enabling accurate stoichiometric comparison of the abundance of specific ribosomal proteins in actively translating ribosomes and to measure protein in non-denatured ribosomes. This poises the field for the provocation that ribosome heterogeneity offers a novel and powerful inroad for the pharmacological targeting of disease. Such ribosome-targeted treatments may extend beyond specific ribosomopathies through strategies such as targeting features of ribosomes that are unique to diseased cells, particularly cancer cells, or to activated immune cells, as well as augmenting the action of other drugs through weakening the production of new proteins in target tissues. We may also be able to harness the potential power in ribosome diversity and specialism to better tune synthetic biology for the production of pharmaceutical proteins.
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Affiliation(s)
- Dianne Ford
- Northumbria University, Northumberland Building, Northumberland Road, Newcastle upon Tyne, NE1 8ST, United Kingdom.
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Thomas AM, Cabrera CP, Finlay M, Lall K, Nobles M, Schilling RJ, Wood K, Mein CA, Barnes MR, Munroe PB, Tinker A. Differentially expressed genes for atrial fibrillation identified by RNA sequencing from paired human left and right atrial appendages. Physiol Genomics 2019; 51:323-332. [PMID: 31172864 PMCID: PMC6732415 DOI: 10.1152/physiolgenomics.00012.2019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 11/22/2022] Open
Abstract
Atrial fibrillation is a significant worldwide contributor to cardiovascular morbidity and mortality. Few studies have investigated the differences in gene expression between the left and right atrial appendages, leaving their characterization largely unexplored. In this study, differential gene expression was investigated in atrial fibrillation and sinus rhythm using left and right atrial appendages from the same patients. RNA sequencing was performed on the left and right atrial appendages from five sinus rhythm (SR) control patients and five permanent AF case patients. Differential gene expression in both the left and right atrial appendages was analyzed using the Bioconductor package edgeR. A selection of differentially expressed genes, with relevance to atrial fibrillation, were further validated using quantitative RT-PCR. The distribution of the samples assessed through principal component analysis showed distinct grouping between left and right atrial appendages and between SR controls and AF cases. Overall 157 differentially expressed genes were identified to be downregulated and 90 genes upregulated in AF. Pathway enrichment analysis indicated a greater involvement of left atrial genes in the Wnt signaling pathway whereas right atrial genes were involved in clathrin-coated vesicle and collagen formation. The differing expression of genes in both left and right atrial appendages indicate that there are different mechanisms for development, support and remodeling of AF within the left and right atria.
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Affiliation(s)
- Alison M Thomas
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Claudia P Cabrera
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Malcolm Finlay
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Barts Heart Centre, St. Bartholomew's Hospital, London, United Kingdom
| | - Kulvinder Lall
- Barts Heart Centre, St. Bartholomew's Hospital, London, United Kingdom
| | - Muriel Nobles
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | | | - Kristie Wood
- Barts and London Genome Centre, School of Medicine and Dentistry, Blizard Institute, London, United Kingdom
| | - Charles A Mein
- Barts and London Genome Centre, School of Medicine and Dentistry, Blizard Institute, London, United Kingdom
| | - Michael R Barnes
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, London, United Kingdom
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Andrew Tinker
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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Genuth NR, Barna M. The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life. Mol Cell 2018; 71:364-374. [PMID: 30075139 DOI: 10.1016/j.molcel.2018.07.018get] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 05/27/2023]
Abstract
The ribosome has recently transitioned from being viewed as a passive, indiscriminate machine to a more dynamic macromolecular complex with specialized roles in the cell. Here, we discuss the historical milestones from the discovery of the ribosome itself to how this ancient machinery has gained newfound appreciation as a more regulatory participant in the central dogma of gene expression. The first emerging examples of direct changes in ribosome composition at the RNA and protein level, coupled with an increased awareness of the role individual ribosomal components play in the translation of specific mRNAs, is opening a new field of study centered on ribosome-mediated control of gene regulation. In this Perspective, we discuss our current understanding of the known functions for ribosome heterogeneity, including specialized translation of individual transcripts, and its implications for the regulation and expression of key gene regulatory networks. In addition, we suggest what the crucial next steps are to ascertain the extent of ribosome heterogeneity and specialization and its importance for regulation of the proteome within subcellular space, across different cell types, and during multi-cellular organismal development.
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Affiliation(s)
- Naomi R Genuth
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA; Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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Genuth NR, Barna M. The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life. Mol Cell 2018; 71:364-374. [PMID: 30075139 PMCID: PMC6092941 DOI: 10.1016/j.molcel.2018.07.018] [Citation(s) in RCA: 259] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 12/24/2022]
Abstract
The ribosome has recently transitioned from being viewed as a passive, indiscriminate machine to a more dynamic macromolecular complex with specialized roles in the cell. Here, we discuss the historical milestones from the discovery of the ribosome itself to how this ancient machinery has gained newfound appreciation as a more regulatory participant in the central dogma of gene expression. The first emerging examples of direct changes in ribosome composition at the RNA and protein level, coupled with an increased awareness of the role individual ribosomal components play in the translation of specific mRNAs, is opening a new field of study centered on ribosome-mediated control of gene regulation. In this Perspective, we discuss our current understanding of the known functions for ribosome heterogeneity, including specialized translation of individual transcripts, and its implications for the regulation and expression of key gene regulatory networks. In addition, we suggest what the crucial next steps are to ascertain the extent of ribosome heterogeneity and specialization and its importance for regulation of the proteome within subcellular space, across different cell types, and during multi-cellular organismal development.
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Affiliation(s)
- Naomi R Genuth
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA; Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Maria Barna
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA; Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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