Publications by authors named "Nathan R Tucker"

35 Publications

Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses.

bioRxiv 2021 Jul 27. Epub 2021 Jul 27.

Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.
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http://dx.doi.org/10.1101/2021.07.27.453843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328056PMC
July 2021

COVID-19 and Cardiovascular Disease: From Bench to Bedside.

Circ Res 2021 04 15;128(8):1214-1236. Epub 2021 Apr 15.

Brigham and Women's Hospital, Harvard Medical School, Boston, MA (J.L.).

A pandemic of historic impact, coronavirus disease 2019 (COVID-19) has potential consequences on the cardiovascular health of millions of people who survive infection worldwide. Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19, can infect the heart, vascular tissues, and circulating cells through ACE2 (angiotensin-converting enzyme 2), the host cell receptor for the viral spike protein. Acute cardiac injury is a common extrapulmonary manifestation of COVID-19 with potential chronic consequences. This update provides a review of the clinical manifestations of cardiovascular involvement, potential direct SARS-CoV-2 and indirect immune response mechanisms impacting the cardiovascular system, and implications for the management of patients after recovery from acute COVID-19 infection.
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http://dx.doi.org/10.1161/CIRCRESAHA.121.317997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048382PMC
April 2021

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

Nat Med 2021 03 2;27(3):546-559. Epub 2021 Mar 2.

Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany.

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2TMPRSS2 cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
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http://dx.doi.org/10.1038/s41591-020-01227-zDOI Listing
March 2021

Epigenetic Analyses of Human Left Atrial Tissue Identifies Gene Networks Underlying Atrial Fibrillation.

Circ Genom Precis Med 2020 12 6;13(6):e003085. Epub 2020 Nov 6.

Cardiovascular Research Center, Massachusetts General Hospital, Boston (A.W.H., S.A.L., N.R.T., P.T.E.).

Background: Atrial fibrillation (AF) often arises from structural abnormalities in the left atria (LA). Annotation of the noncoding genome in human LA is limited, as are effects on gene expression and chromatin architecture. Many AF-associated genetic variants reside in noncoding regions; this knowledge gap impairs efforts to understand the molecular mechanisms of AF and cardiac conduction phenotypes.

Methods: We generated a model of the LA noncoding genome by profiling 7 histone post-translational modifications (active: H3K4me3, H3K4me2, H3K4me1, H3K27ac, H3K36me3; repressive: H3K27me3, H3K9me3), binding, and gene expression in samples from 5 individuals without structural heart disease or AF. We used MACS2 to identify peak regions (<0.01), applied a Markov model to classify regulatory elements, and annotated this model with matched gene expression data. We intersected chromatin states with expression quantitative trait locus, DNA methylation, and HiC chromatin interaction data from LA and left ventricle. Finally, we integrated genome-wide association data for AF and electrocardiographic traits to link disease-related variants to genes.

Results: Our model identified 21 epigenetic states, encompassing regulatory motifs, such as promoters, enhancers, and repressed regions. Genes were regulated by proximal chromatin states; repressive states were associated with a significant reduction in gene expression (<2×10). Chromatin states were differentially methylated, promoters were less methylated than repressed regions (<2×10). We identified over 15 000 LA-specific enhancers, defined by homeobox family motifs, and annotated several cardiovascular disease susceptibility loci. Intersecting AF and PR genome-wide association studies loci with long-range chromatin conformation data identified a gene interaction network dominated by , , , and .

Conclusions: Profiling the noncoding genome provides new insights into the gene expression and chromatin regulation in human LA tissue. These findings enabled identification of a gene network underlying AF; our experimental and analytic approach can be extended to identify molecular mechanisms for other cardiac diseases and traits.
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http://dx.doi.org/10.1161/CIRCGEN.120.003085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8240092PMC
December 2020

Epigenetic and Transcriptional Networks Underlying Atrial Fibrillation.

Circ Res 2020 06 18;127(1):34-50. Epub 2020 Jun 18.

From the Department of Medical Biology, Amsterdam University Medical Center, Academic Medical Center, The Netherlands (A.F.v.O., F.M.B., V.M.C.).

Genome-wide association studies have uncovered over a 100 genetic loci associated with atrial fibrillation (AF), the most common arrhythmia. Many of the top AF-associated loci harbor key cardiac transcription factors, including PITX2, TBX5, PRRX1, and ZFHX3. Moreover, the vast majority of the AF-associated variants lie within noncoding regions of the genome where causal variants affect gene expression by altering the activity of transcription factors and the epigenetic state of chromatin. In this review, we discuss a transcriptional regulatory network model for AF defined by effector genes in Genome-wide association studies loci. We describe the current state of the field regarding the identification and function of AF-relevant gene regulatory networks, including variant regulatory elements, dose-sensitive transcription factor functionality, target genes, and epigenetic states. We illustrate how altered transcriptional networks may impact cardiomyocyte function and ionic currents that impact AF risk. Last, we identify the need for improved tools to identify and functionally test transcriptional components to define the links between genetic variation, epigenetic gene regulation, and atrial function.
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http://dx.doi.org/10.1161/CIRCRESAHA.120.316574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8315291PMC
June 2020

Myocyte Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2 mediated myocarditis.

medRxiv 2020 Apr 14. Epub 2020 Apr 14.

Coronavirus disease 2019 (COVID-19) is a global pandemic caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 infection of host cells occurs predominantly via binding of the viral surface spike protein to the human angiotensin-converting enzyme 2 (ACE2) receptor. Hypertension and pre-existing cardiovascular disease are risk factors for morbidity from COVID-19, and it remains uncertain whether the use of angiotensin converting enzyme inhibitors (ACEi) or angiotensin receptor blockers (ARB) impacts infection and disease. Here, we aim to shed light on this question by assessing ACE2 expression in normal and diseased human myocardial samples profiled by bulk and single nucleus RNA-seq.
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http://dx.doi.org/10.1101/2020.04.09.20059204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7277016PMC
April 2020

Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction.

Nat Commun 2020 05 21;11(1):2542. Epub 2020 May 21.

Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.

The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease.
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http://dx.doi.org/10.1038/s41467-020-15706-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242331PMC
May 2020

Transcriptional and Cellular Diversity of the Human Heart.

Circulation 2020 08 14;142(5):466-482. Epub 2020 May 14.

Precision Cardiology Laboratory (N.R.T., M.C., S.J.F., A.W.H., A.-D.A., C.N.H., A.A., I.P., C.R., S.H.C., M.B., C.M.S., P.T.E.), Cambridge, MA.

Background: The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge of the intricate cellular milieu of the heart is critical to increase our understanding of cardiac homeostasis and pathology. As recent advances in low-input RNA sequencing have allowed definitions of cellular transcriptomes at single-cell resolution at scale, we have applied these approaches to assess the cellular and transcriptional diversity of the nonfailing human heart.

Methods: Microfluidic encapsulation and barcoding was used to perform single nuclear RNA sequencing with samples from 7 human donors, selected for their absence of overt cardiac disease. Individual nuclear transcriptomes were then clustered based on transcriptional profiles of highly variable genes. These clusters were used as the basis for between-chamber and between-sex differential gene expression analyses and intersection with genetic and pharmacologic data.

Results: We sequenced the transcriptomes of 287 269 single cardiac nuclei, revealing 9 major cell types and 20 subclusters of cell types within the human heart. Cellular subclasses include 2 distinct groups of resident macrophages, 4 endothelial subtypes, and 2 fibroblast subsets. Comparisons of cellular transcriptomes by cardiac chamber or sex reveal diversity not only in cardiomyocyte transcriptional programs but also in subtypes involved in extracellular matrix remodeling and vascularization. Using genetic association data, we identified strong enrichment for the role of cell subtypes in cardiac traits and diseases. Intersection of our data set with genes on cardiac clinical testing panels and the druggable genome reveals striking patterns of cellular specificity.

Conclusions: Using large-scale single nuclei RNA sequencing, we defined the transcriptional and cellular diversity in the normal human heart. Our identification of discrete cell subtypes and differentially expressed genes within the heart will ultimately facilitate the development of new therapeutics for cardiovascular diseases.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.119.045401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7666104PMC
August 2020

Identification of Functional Variant Enhancers Associated With Atrial Fibrillation.

Circ Res 2020 07 6;127(2):229-243. Epub 2020 Apr 6.

From the Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center, the Netherlands (A.F.v.O., F.M.B., K.v.D., P.B., V.M.C.).

Rationale: Genome-wide association studies have identified a large number of common variants (single-nucleotide polymorphisms) associated with atrial fibrillation (AF). These variants are located mainly in noncoding regions of the genome and likely include variants that modulate the function of transcriptional regulatory elements (REs) such as enhancers. However, the actual REs modulated by variants and the target genes of such REs remain to be identified. Thus, the biological mechanisms by which genetic variation promotes AF has thus far remained largely unexplored.

Objective: To identify REs in genome-wide association study loci that are influenced by AF-associated variants.

Methods And Results: We screened 2.45 Mbp of human genomic DNA containing 12 strongly AF-associated loci for RE activity using self-transcribing active regulatory region sequencing and a recently generated monoclonal line of conditionally immortalized rat atrial myocytes. We identified 444 potential REs, 55 of which contain AF-associated variants (<10). Subsequently, using an adaptation of the self-transcribing active regulatory region sequencing approach, we identified 24 variant REs with allele-specific regulatory activity. By mining available chromatin conformation data, the possible target genes of these REs were mapped. To define the physiological function and target genes of such REs, we deleted the orthologue of an RE containing noncoding variants in the (potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4) locus of the mouse genome. Mice heterozygous for the RE deletion showed bradycardia, sinus node dysfunction, and selective loss of expression.

Conclusions: We have identified REs at multiple genetic loci for AF and found that loss of an RE at the locus results in sinus node dysfunction and reduced gene expression. Our approach can be broadly applied to facilitate the identification of human disease-relevant REs and target genes at cardiovascular genome-wide association studies loci.
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http://dx.doi.org/10.1161/CIRCRESAHA.119.316006DOI Listing
July 2020

Long-range enhancer-promoter interactions prevent predisposition to atrial fibrillation.

Proc Natl Acad Sci U S A 2019 11 21;116(45):22692-22698. Epub 2019 Oct 21.

Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030;

Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia, is associated with noncoding sequence variants located in proximity to Cardiomyocyte-specific epigenomic and comparative genomics uncovered 2 AF-associated enhancers neighboring with varying conservation in mice. Chromosome conformation capture experiments in mice revealed that the promoter directly contacted the AF-associated enhancer regions. CRISPR/Cas9-mediated deletion of a 20-kb topologically engaged enhancer led to reduced transcription and AF predisposition. Allele-specific chromatin immunoprecipitation sequencing on hybrid heterozygous enhancer knockout mice revealed that long-range interaction of an AF-associated region with the promoter was required for maintenance of the c promoter chromatin state. Long-range looping was mediated by CCCTC-binding factor (CTCF), since genetic disruption of the intronic CTCF-binding site caused reduced expression, AF predisposition, and diminished active chromatin marks on AF risk variants located at 4q25 reside in genomic regions possessing long-range transcriptional regulatory functions directed at .
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http://dx.doi.org/10.1073/pnas.1907418116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842642PMC
November 2019

Genome-Wide Association Study-Driven Gene-Set Analyses, Genetic, and Functional Follow-Up Suggest GLIS1 as a Susceptibility Gene for Mitral Valve Prolapse.

Circ Genom Precis Med 2019 05;12(5):e002497

INSERM, UMR970, Paris Cardiovascular Research Center, France (M.Y., A.G., S.K., A.A.H., X.J., N.B.-N.).

Background Mitral valve prolapse (MVP) is a common heart valve disease, the most frequent indication for valve repair or replacement. MVP is characterized by excess extracellular matrix secretion and cellular disorganization, which leads to bulky valves that are unable to coapt correctly during ventricular systole resulting in mitral regurgitation, and it is associated with sudden cardiac death. Here we aim to characterize globally the biological mechanisms underlying genetic susceptibility to MVP to better characterize its triggering mechanisms. Methods We applied i-GSEA4GWAS and DEPICT, two pathway enrichment tools to MVP genome-wide association studies. We followed-up the association with MVP in an independent dataset of cases and controls. This research was conducted using the UK Biobank Resource. Immunohistochemistry staining for Glis1 (GLIS family zinc finger 1) was conducted in developing heart of mice. Knockdown of Glis1 using morpholinos was performed in zebrafish animals 72 hours postfertilization. Results We show that genes at risk loci are involved in biological functions relevant to actin filament organization, cytoskeleton biology, and cardiac development. The enrichment for positive regulation of transcription, cell proliferation, and migration motivated the follow-up of GLIS1, a transcription factor from the Krüppel-like zinc finger family. In combination with previously available data, we now report a genome-wide significant association with MVP (odds ratio, 1.20; P=4.36×10), indicating that Glis1 is expressed during embryonic development predominantly in nuclei of endothelial and interstitial cells of mitral valves in mouse. We also show that Glis1 knockdown causes atrioventricular regurgitation in developing hearts in zebrafish. Conclusions Our findings define globally molecular and cellular mechanisms underlying common genetic susceptibility to MVP and implicate established and unprecedented mechanisms. Through the GLIS1 association and function, we point at regulatory functions during cardiac development as common mechanisms to mitral valve degeneration.
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http://dx.doi.org/10.1161/CIRCGEN.119.002497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532425PMC
May 2019

Cardioprotective Effects of MTSS1 Enhancer Variants.

Circulation 2019 04;139(17):2073-2076

Division of Cardiovascular Medicine and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia (M.P.P., X.W., R.H., J.B., K.B.M., K.M., T.P.C.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.118.037939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510256PMC
April 2019

Association Between Titin Loss-of-Function Variants and Early-Onset Atrial Fibrillation.

JAMA 2018 12;320(22):2354-2364

Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania.

Importance: Atrial fibrillation (AF) is the most common arrhythmia affecting 1% of the population. Young individuals with AF have a strong genetic association with the disease, but the mechanisms remain incompletely understood.

Objective: To perform large-scale whole-genome sequencing to identify genetic variants related to AF.

Design, Setting, And Participants: The National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine Program includes longitudinal and cohort studies that underwent high-depth whole-genome sequencing between 2014 and 2017 in 18 526 individuals from the United States, Mexico, Puerto Rico, Costa Rica, Barbados, and Samoa. This case-control study included 2781 patients with early-onset AF from 9 studies and identified 4959 controls of European ancestry from the remaining participants. Results were replicated in the UK Biobank (346 546 participants) and the MyCode Study (42 782 participants).

Exposures: Loss-of-function (LOF) variants in genes at AF loci and common genetic variation across the whole genome.

Main Outcomes And Measures: Early-onset AF (defined as AF onset in persons <66 years of age). Due to multiple testing, the significance threshold for the rare variant analysis was P = 4.55 × 10-3.

Results: Among 2781 participants with early-onset AF (the case group), 72.1% were men, and the mean (SD) age of AF onset was 48.7 (10.2) years. Participants underwent whole-genome sequencing at a mean depth of 37.8 fold and mean genome coverage of 99.1%. At least 1 LOF variant in TTN, the gene encoding the sarcomeric protein titin, was present in 2.1% of case participants compared with 1.1% in control participants (odds ratio [OR], 1.76 [95% CI, 1.04-2.97]). The proportion of individuals with early-onset AF who carried a LOF variant in TTN increased with an earlier age of AF onset (P value for trend, 4.92 × 10-4), and 6.5% of individuals with AF onset prior to age 30 carried a TTN LOF variant (OR, 5.94 [95% CI, 2.64-13.35]; P = 1.65 × 10-5). The association between TTN LOF variants and AF was replicated in an independent study of 1582 patients with early-onset AF (cases) and 41 200 control participants (OR, 2.16 [95% CI, 1.19-3.92]; P = .01).

Conclusions And Relevance: In a case-control study, there was a statistically significant association between an LOF variant in the TTN gene and early-onset AF, with the variant present in a small percentage of participants with early-onset AF (the case group). Further research is necessary to understand whether this is a causal relationship.
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http://dx.doi.org/10.1001/jama.2018.18179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436530PMC
December 2018

Multi-ethnic genome-wide association study for atrial fibrillation.

Nat Genet 2018 06 11;50(9):1225-1233. Epub 2018 Jun 11.

Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Atrial fibrillation (AF) affects more than 33 million individuals worldwide and has a complex heritability. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.
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http://dx.doi.org/10.1038/s41588-018-0133-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136836PMC
June 2018

Common and Rare Coding Genetic Variation Underlying the Electrocardiographic PR Interval.

Circ Genom Precis Med 2018 05;11(5):e002037

Section of Computational Biomedicine (H.L.) and Section of Cardiovascular Medicine (E.J.B.), Department of Medicine, Boston University School of Medicine, MA. National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, MA (H.L., E.J.B.). Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, The Netherlands (J.v.S., F.W.A.). Icelandic Heart Association, Kopavogur (A.V.S., V.G.). Faculty of Medicine, University of Iceland, Reykjavik (A.V.S., V.G.). Predoctoral Training Program in Human Genetics, McKusick-Nathans Institute of Genetic Medicine (N.A.B.) and McKusick-Nathans Institute of Genetic Medicine (D.E.A.), Johns Hopkins University School of Medicine, Baltimore, MD. William Harvey Research Institute (H.R.W., P.B.M.) and NIHR Barts Cardiovascular Research Unit (H.R.W., P.B.M.), Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom. Cardiovascular Health Research Unit, Department of Medicine (J.A.B., J.C.B., C.M.S.), Department of Biostatistics (K.M.R.), Cardiovascular Health Research Unit, Division of Cardiology, Departments of Medicine and Epidemiology (N.S.), Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services (B.M.P.), and Cardiovascular Health Research Unit, Department of Epidemiology (S.R.H.), University of Washington, Seattle. Center for Human Genetic Research (F. Radmanesh, J.R.) and Cardiovascular Research Center (P.L.H., L.-C.W., H.S.J., W.H., A.H., N.R.T., P.T.E., S.A.L.), Massachusetts General Hospital, Boston. Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA (L.-C.W., P.T.E., S.A.L.). Department of Cardiovascular Sciences, University of Leicester, United Kingdom (L.H., C.P.N., N.J.S.). NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, United Kingdom (L.H., C.P.N., N.J.S.). The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences (N.G., J.B.-J., O. Pedersen, T.H.), Laboratory of Experimental Cardiology (J.K.K.), and Department of Clinical Medicine, Faculty of Health and Medical Sciences (A.L.), University of Copenhagen, Denmark. Department of Medicine I, University Hospital Munich, Ludwig Maximilian's University Munich, Germany (M.M.-N., M.F.S., S.K.). Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Germany (K.S.). DZHK (German Cardiovascular Research Centre), Partner Site: Munich Heart Alliance, Germany (M.M.-N., M.F.S., A.P., T.M., S.K.). Institute of Genetic Epidemiology (M.M.-N., K.S.), Institute of Epidemiology II (A.P., M.W.), Research Unit of Molecular Epidemiology (M.W.), and Institute of Human Genetics (T.M.), Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany. Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine (T.B., J.M., C.H.) and Usher Institute of Population Health Sciences and Informatics (I.R.), University of Edinburgh, United Kingdom. University of Groningen, University Medical Center Groningen, Department of Cardiology, The Netherlands (N.V., R.A.d.B., P.v.d.M., P.v.d.H.). Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA (H.J.L., Y.-D.I.C., J.Y., X.G., K.D.T., J.I.R.). Department of Clinical Epidemiology (R.L.-G., D.O.M.-K.) and Department of Cardiology (S.T., J.W.J.), Leiden University Medical Center, The Netherlands. Department of Medical Informatics (M.E.v.d.B.), Human Genomics Facility (F. Rivadeneira), Human Genotyping Facility (A.U.), and Department of Epidemiology (M.E., B.H. Stricker), Erasmus MC, University Medical Center Rotterdam, The Netherlands. Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Germany (S.W., G.H., U.V.). DZHK (German Cardiovascular Research Centre), Partner Site Greifswald, Germany (S.W., H.V., S.B.F., U.V., M.D.). Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA (J.H., C.K.). Department of Clinical Chemistry, Fimlab Laboratories and Faculty of Medicine and Life Sciences (L.-P.L., T.L.) and Department of Clinical Physiology, Tampere University Hospital and Faculty of Medicine and Life Sciences (M.K.), University of Tampere, Finland. Department of Data Science (H.M.) and Physiology and Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson. Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD (T.B.H., L.J.L.). Division of Nephrology and Hypertension, Internal Medicine, School of Medicine, University of Utah, Salt Lake City (M.L.). Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA (A.A.). Epidemiological Cardiology Research Center (EPICARE), Wake Forest School of Medicine, Winston Salem, NC (E.Z.S.). Medical Research Institute (J.M.C.) and Division of Population Health Sciences (B.H. Smith), Ninewells Hospital and Medical School, University of Dundee, United Kingdom. Department of Medical Informatics (J.A.K.) and Genetic Epidemiology Unit, Department of Epidemiology (C.M.v.D.), Erasmus MC, Rotterdam, The Netherlands. TCM Clinical Basis Institute, Zhejiang Chinese Medicine University, Hangzhou, China (Z.X., C.W.). Division of Cardiology, Department of Medicine, UPMC Heart and Vascular Institute, University of Pittsburgh, PA (J.W.M.). German Center for Diabetes Research, Neuherberg, Germany (A.P.). Institute of Human Genetics, Technische Universität München, Germany (T.M.). Research Centre for Prevention and Health, Capital Region of Denmark, Copenhagen (A.L.). Department of Clinical Experimental Research, Rigshospitalet, Denmark (A.L.). British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland (S.P.). Institute for Community Medicine (H.V.) and Department of Internal Medicine B (S.B.F., M.D.), University Medicine Greifswald, Germany. Department of Twin Research and Genetic Epidemiology, King's College London, United Kingdom (M.M., T.D.S.). Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands (M.L.B.). Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, CA (M.P.). Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, and Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Finland (O.T.R.). Kaiser Permanente Washington Health Research Institute, Kaiser Foundation Health Plan of Washington, Seattle (B.M.P., S.R.H.). Faculty of Medicine, University of Split, Croatia (O. Polasek). Cardiogenetics Lab, Genetics and Molecular Cell Sciences Research Centre, Cardiovascular and Cell Sciences Institute, St George's, University of London, Cranmer Terrace, United Kingdom (B.P.P., Y.J.). Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, The Netherlands (F.W.A.). Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom (F.W.A.). Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, United Kingdom; CARIM School for Cardiovascular Diseases, Maastricht Centre for Systems Biology (MaCSBio) and Department of Biochemistry, Maastricht University, The Netherlands (A.I.).

Background: Electrical conduction from the cardiac sinoatrial node to the ventricles is critical for normal heart function. Genome-wide association studies have identified more than a dozen common genetic loci that are associated with PR interval. However, it is unclear whether rare and low-frequency variants also contribute to PR interval heritability.

Methods: We performed large-scale meta-analyses of the PR interval that included 83 367 participants of European ancestry and 9436 of African ancestry. We examined both common and rare variants associated with the PR interval.

Results: We identified 31 genetic loci that were significantly associated with PR interval after Bonferroni correction (<1.2×10), including 11 novel loci that have not been reported previously. Many of these loci are involved in heart morphogenesis. In gene-based analysis, we found that multiple rare variants at (=5.9×10) and (=1.1×10) were associated with PR interval. locus also was implicated in the common variant analysis, whereas was a novel locus.

Conclusions: We identified common variants at 11 novel loci and rare variants within 2 gene regions that were significantly associated with PR interval. Our findings provide novel insights to the current understanding of atrioventricular conduction, which is critical for cardiac activity and an important determinant of health.
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http://dx.doi.org/10.1161/CIRCGEN.117.002037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951629PMC
May 2018

Response by Ma et al to Letter Regarding Article, "Novel Mutation in (Filamin C) Causes Familial Restrictive Cardiomyopathy".

Circ Genom Precis Med 2018 04;11(4):e002140

Cardiovascular Research Center, Massachusetts General Hospital, Boston (N.R.T., P.T.E.); and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA (N.R.T., P.T.E.).

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http://dx.doi.org/10.1161/CIRCGEN.118.002140DOI Listing
April 2018

Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects.

Circ Genom Precis Med 2018 03;11(3):e001901

From the Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia (R.H., M.P.M., J.B., K.B.M., T.P.C.); Cardiovascular Research Center (N.R.T., V.A.P., P.T.E.) and Center for Human Genetic Research and Cardiovascular Research Center (C.N.-C.), Massachusetts General Hospital, Boston; Department of Statistics, University of Illinois at Urbana-Champaign (S.D.Z.); Heidelberg University Hospital, Germany (B.M., H.A.K.); Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, Germany (F.R., M.S.); INSERM UMRS1166-IACN, Hôpital Pitié-Salpêtrière, Paris, France (E.V., F.C.); Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, MA (H.L.); Department of Epidemiology, University of Washington, Seattle (N.L.S.); Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, the Netherlands (J.F.F.); Boston University School of Medicine, MA (R.S.V.); Department of Cardiology, University of Groningen, University Medical Center Groningen, the Netherlands (P.v.d.H.); Medical and Population Genetics Program, Broad Institute, Cambridge, MA (C.N.-C.); Center for Applied Genomics, Children's Hospital of Philadelphia, PA (J.L., C.E.K., H.H.); Center for Bioinformatics and Computational Biology, University of Maryland, College Park (S.H.); Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, CA (E.A.A.); Department of Cardiovascular Medicine, Cleveland Clinic, OH (C.S.M., W.H.W.T.); and Howard Hughes Medical Institute and Cincinnati Children's Hospital Medical Center, OH (M.M., J.D.M.).

Background: Inhibition of PKC-α (protein kinase C-α) enhances contractility and cardioprotection in animal models, but effects in humans are unknown. Genotypes at rs9912468 strongly associate with expression in the left ventricle, enabling genetic approaches to measure effects of reduced PKC-α in human populations.

Methods And Results: We analyzed the expression quantitative trait locus for marked by rs9912468 using 313 left ventricular specimens from European Ancestry patients. The forward strand minor allele (G) at rs9912468 is associated with reduced PKC-α transcript abundance (1.7-fold reduction in minor allele homozygotes, =1×10). This association was cardiac specific in expression quantitative trait locus data sets that span 16 human tissues. Cardiac epigenomic data revealed a predicted enhancer in complete (=1.0) linkage disequilibrium with rs9912468 within intron 2 of We cloned this region and used reporter constructs to verify cardiac-specific enhancer activity in vitro in cardiac and noncardiac cells and in vivo in zebrafish. The enhancer contains 2 common genetic variants and 4 haplotypes; the haplotype correlated with the rs9912468 PKC-α-lowering allele (G) showed lowest activity. In contrast to previous reports in animal models, the PKC-α-lowering allele is associated with adverse left ventricular remodeling (higher mass, larger diastolic dimension), reduced fractional shortening, and higher risk of dilated cardiomyopathy in human populations.

Conclusions: These findings support PKC-α as a regulator of the human heart but suggest that PKC-α inhibition may adversely affect the left ventricle depending on timing and duration. Pharmacological studies in human subjects are required to discern potential benefits and harms of PKC-α inhibitors as an approach to treat heart disease.
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http://dx.doi.org/10.1161/CIRCGEN.117.001901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858599PMC
March 2018

Novel Mutation in (Filamin C) Causes Familial Restrictive Cardiomyopathy.

Circ Cardiovasc Genet 2017 Dec;10(6)

From the Cardiovascular Research Center, Massachusetts General Hospital, Charlestown (N.R.T., M.A.M., D.H., J.Y., V.A.P., R.W.M., S.C., E.D., D.J.M., M.L., S.A.L., I.J.D., P.T.E.); Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA (N.R.T., J.Y., V.A.P., S.A.L., H.L., P.T.E.); Department of Medicine I, Klinikum Grosshadern, University of Munich (LMU), Germany (S.C.); German Centre for Cardiovascular Research, Partner site Munich, Germany (S.C.); Division of Cardiology (M.A.S., D.J.M., N.S.S., M.L., S.A.L., I.J.D., P.T.E.) and Department of Pathology, Center for Systems Biology (J.R.S.), Massachusetts General Hospital, Boston; and Computational Biomedicine Section, Department of Medicine, Boston University School of Medicine, MA (H.L.).

Background: Restrictive cardiomyopathy (RCM) is a rare cardiomyopathy characterized by impaired diastolic ventricular function resulting in a poor clinical prognosis. Rarely, heritable forms of RCM have been reported, and mutations underlying RCM have been identified in genes that govern the contractile function of the cardiomyocytes.

Methods And Results: We evaluated 8 family members across 4 generations by history, physical examination, electrocardiography, and echocardiography. Affected individuals presented with a pleitropic syndrome of progressive RCM, atrioventricular septal defects, and a high prevalence of atrial fibrillation. Exome sequencing of 5 affected members identified a single novel missense variant in a highly conserved residue of FLNC (filamin C; p.V2297M). encodes filamin C-a protein that acts as both a scaffold for the assembly and organization of the central contractile unit of striated muscle and also as a mechanosensitive signaling molecule during cell migration and shear stress. Immunohistochemical analysis of FLNC localization in cardiac tissue from an affected family member revealed a diminished localization at the z disk, whereas traditional localization at the intercalated disk was preserved. Stem cell-derived cardiomyocytes mutated to carry the effect allele had diminished contractile activity when compared with controls.

Conclusion: We have identified a novel variant in as pathogenic variant for familial RCM-a finding that further expands on the genetic basis of this rare and morbid cardiomyopathy.
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http://dx.doi.org/10.1161/CIRCGENETICS.117.001780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802346PMC
December 2017

Diminished Expression Is Associated With Increased Risk of Atrial Fibrillation and Shortening of the Cardiac Action Potential.

Circ Cardiovasc Genet 2017 Oct;10(5)

From the Cardiovascular Research Center (N.R.T., E.V.D., R.R.C., J.Y., W.J.H., H.S.J., V.A.P., L.-C.W., R.W.M., J.L.-M., S.A.L., D.J.M., P.T.E.) and Department of Surgery (G.V.), Massachusetts General Hospital, Boston; National Heart, Lung and Blood Institute's and Boston University's Framingham Heart, MA (H.L., E.J.B., K.L.L.); Computational Biomedicine Section (H.L.), Cardiology Section (E.J.B.), and Preventive Medicine Section (E.J.B.), Department of Medicine, Boston University School of Medicine, MA; Department of Medicine I, University Hospital Munich, Campus Grosshadern, Ludwig-Maximilians-University, Germany (M.F.S.); Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge (M.I., L.M.); Department of Epidemiology (E.J.B.) and Department of Biostatistics (K.L.L.), Boston University School of Public Health, MA; and Program in Medical and Populations Genetics, Broad Institute, Cambridge, MA (S.A.L., D.J.M., P.T.E.).

Background: Atrial fibrillation (AF) affects over 33 million individuals worldwide. Genome-wide association studies have identified at least 30 AF loci, but the mechanisms through which individual variants lead to altered disease risk have remained unclear for the majority of these loci. At the 1q24 locus, we hypothesized that the transcription factor could be a strong candidate gene as it is expressed in the pulmonary veins, a source of AF in many individuals. We sought to identify the molecular mechanism, whereby variation at 1q24 may lead to AF susceptibility.

Methods And Results: We sequenced a ≈158 kb region encompassing in 962 individuals with and without AF. We identified a broad region of association with AF at the 1q24 locus. Using in silico prediction and functional validation, we identified an enhancer that interacts with the promoter of in cells of cardiac lineage. Within this enhancer, we identified a single-nucleotide polymorphism, rs577676, which alters enhancer activity in a mouse atrial cell line and in embryonic zebrafish and differentially regulates expression in human left atria. We found that suppression of in human embryonic stem cell-derived cardiomyocytes and embryonic zebrafish resulted in shortening of the atrial action potential duration, a hallmark of AF.

Conclusions: We have identified a functional genetic variant that alters expression, ultimately resulting in electrophysiological alterations in atrial myocytes that may promote AF.
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http://dx.doi.org/10.1161/CIRCGENETICS.117.001902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679717PMC
October 2017

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation.

Nat Genet 2017 Jun 17;49(6):946-952. Epub 2017 Apr 17.

Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität, Munich, Germany.

Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death. Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups. To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery.
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http://dx.doi.org/10.1038/ng.3843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585859PMC
June 2017

A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a.

Am J Hum Genet 2016 Dec 17;99(6):1281-1291. Epub 2016 Nov 17.

Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

The most significantly associated genetic locus for atrial fibrillation (AF) is in chromosomal region 4q25, where four independent association signals have been identified. Although model-system studies suggest that altered PITX2c expression might underlie the association, the link between specific variants and the direction of effect on gene expression remains unknown for all four signals. In the present study, we analyzed the AF-associated region most proximal to PITX2 at 4q25. First, we identified candidate regulatory variants that might confer AF risk through a combination of mammalian conservation, DNase hypersensitivity, and histone modification from ENCODE and the Roadmap Epigenomics Project, as well as through in vivo analysis of enhancer activity in embryonic zebrafish. Within candidate regions, we then identified a single associated SNP, rs2595104, which displayed dramatically reduced enhancer activity with the AF risk allele. CRISPR-Cas9-mediated deletion of the rs2595104 region and editing of the rs2595104 risk allele in human stem-cell-derived cardiomyocytes resulted in diminished PITX2c expression in comparison to that of the non-risk allele. This differential activity was mediated by activating enhancer binding protein 2 alpha (TFAP2a), which bound robustly to the non-risk allele at rs2595104, but not to the risk allele, in cardiomyocytes. In sum, we found that the AF-associated SNP rs2595104 altered PITX2c expression via interaction with TFAP2a. Such a pathway could ultimately contribute to AF susceptibility at the PITX2 locus associated with AF.
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http://dx.doi.org/10.1016/j.ajhg.2016.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142106PMC
December 2016

Mutation of a common amino acid in NKX2.5 results in dilated cardiomyopathy in two large families.

BMC Med Genet 2016 Nov 17;17(1):83. Epub 2016 Nov 17.

Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.

Background: The genetic basis for dilated cardiomyopathy (DCM) can be difficult to determine, particularly in familial cases with complex phenotypes. Next generation sequencing may be useful in the management of such cases.

Methods: We report two large families with pleiotropic inherited cardiomyopathy. In addition to DCM, the phenotypes included atrial and ventricular septal defects, cardiac arrhythmia and sudden death. Probands underwent whole exome sequencing to identify potentially causative variants.

Results: Each whole exome sequence yielded over 18,000 variants. We identified distinct mutations affecting a common amino acid in NKX2.5. Segregation analysis of the families support the pathogenic role of these variants.

Conclusion: Our study emphasizes the utility of next generation sequencing in identifying causative mutations in complex inherited cardiac disease. We also report a novel pathogenic NKX2.5 mutation.
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http://dx.doi.org/10.1186/s12881-016-0347-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114776PMC
November 2016

PHACTR1 Is a Genetic Susceptibility Locus for Fibromuscular Dysplasia Supporting Its Complex Genetic Pattern of Inheritance.

PLoS Genet 2016 Oct 28;12(10):e1006367. Epub 2016 Oct 28.

INSERM, UMR970 Paris Cardiovascular Research Center (PARCC), Paris F-75015, FRANCE.

Fibromuscular dysplasia (FMD) is a nonatherosclerotic vascular disease leading to stenosis, dissection and aneurysm affecting mainly the renal and cerebrovascular arteries. FMD is often an underdiagnosed cause of hypertension and stroke, has higher prevalence in females (~80%) but its pathophysiology is unclear. We analyzed ~26K common variants (MAF>0.05) generated by exome-chip arrays in 249 FMD patients and 689 controls. We replicated 13 loci (P<10-4) in 402 cases and 2,537 controls and confirmed an association between FMD and a variant in the phosphatase and actin regulator 1 gene (PHACTR1). Three additional case control cohorts including 512 cases and 669 replicated this result and overall reached the genomic level of significance (OR = 1.39, P = 7.4×10-10, 1,154 cases and 3,895 controls). The top variant, rs9349379, is intronic to PHACTR1, a risk locus for coronary artery disease, migraine, and cervical artery dissection. The analyses of geometrical parameters of carotids from ~2,500 healthy volunteers indicate higher intima media thickness (P = 1.97×10-4) and wall to lumen ratio (P = 0.002) in rs9349379-A carriers, suggesting indices of carotid hypertrophy previously described in carotids of FMD patients. Immunohistochemistry detected PHACTR1 in endothelium and smooth muscle cells of FMD and normal human carotids. The expression of PHACTR1 by genotypes in primary human fibroblasts showed higher expression in rs9349379-A carriers (N = 86, P = 0.003). Phactr1 knockdown in zebrafish resulted in dilated vessels indicating subtle impaired vascular development. We report the first susceptibility locus for FMD and provide evidence for a complex genetic pattern of inheritance and indices of shared pathophysiology between FMD and other cardiovascular and neurovascular diseases.
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http://dx.doi.org/10.1371/journal.pgen.1006367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5085032PMC
October 2016

Gain-of-function mutations in GATA6 lead to atrial fibrillation.

Heart Rhythm 2017 02 15;14(2):284-291. Epub 2016 Oct 15.

Cardiovascular Research Center and; Cardiac Arrhythmia Service, Massachusetts General Hospital, Boston, Massachusetts. Electronic address:

Background: The genetic basis of atrial fibrillation (AF) and congenital heart disease remains incompletely understood.

Objective: We sought to determine the causative mutation in a family with AF, atrial septal defects, and ventricular septal defects.

Methods: We evaluated a pedigree with 16 family members, 1 with an atrial septal defect, 1 with a ventricular septal defect, and 3 with AF; we performed whole exome sequencing in 3 affected family members. Given that early-onset AF was prominent in the family, we then screened individuals with early-onset AF, defined as an age of onset <66 years, for mutations in GATA6. Variants were functionally characterized using reporter assays in a mammalian cell line.

Results: Exome sequencing in 3 affected individuals identified a conserved mutation, R585L, in the transcription factor gene GATA6. In the Massachusetts General Hospital Atrial Fibrillation (MGH AF) Study, the mean age of AF onset was 47.1 ± 10.9 years; 79% of the participants were men; and there was no evidence of structural heart disease. We identified 3 GATA6 variants (P91S, A177T, and A543G). Using wild-type and mutant GATA6 constructs driving atrial natriuretic peptide promoter reporter, we found that 3 of the 4 variants had a marked upregulation of luciferase activity (R585L: 4.1-fold, P < .0001; P91S: 2.5-fold, P = .0002; A177T; 1.7-fold, P = .03). In addition, when co-overexpressed with GATA4 and MEF2C, GATA6 variants exhibited upregulation of the alpha myosin heavy chain and atrial natriuretic peptide reporter activity.

Conclusion: Overall, we found gain-of-function mutations in GATA6 in both a family with early-onset AF and atrioventricular septal defects as well as in a family with sporadic, early-onset AF.
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http://dx.doi.org/10.1016/j.hrthm.2016.10.014DOI Listing
February 2017

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures.

Elife 2016 05 10;5. Epub 2016 May 10.

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.

Genetic variants identified by genome-wide association studies explain only a modest proportion of heritability, suggesting that meaningful associations lie 'hidden' below current thresholds. Here, we integrate information from association studies with epigenomic maps to demonstrate that enhancers significantly overlap known loci associated with the cardiac QT interval and QRS duration. We apply functional criteria to identify loci associated with QT interval that do not meet genome-wide significance and are missed by existing studies. We demonstrate that these 'sub-threshold' signals represent novel loci, and that epigenomic maps are effective at discriminating true biological signals from noise. We experimentally validate the molecular, gene-regulatory, cellular and organismal phenotypes of these sub-threshold loci, demonstrating that most sub-threshold loci have regulatory consequences and that genetic perturbation of nearby genes causes cardiac phenotypes in mouse. Our work provides a general approach for improving the detection of novel loci associated with complex human traits.
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http://dx.doi.org/10.7554/eLife.10557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862755PMC
May 2016

Common variation in atrial fibrillation: navigating the path from genetic association to mechanism.

Cardiovasc Res 2016 Apr 4;109(4):493-501. Epub 2016 Jan 4.

Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA

Atrial fibrillation (AF) is the most common cardiac arrhythmia with well-established clinical and genetic risk components. Genome-wide association studies (GWAS) have identified 17 independent susceptibility signals for AF at 14 genomic regions, but the mechanisms through which these loci confer risk to AF remain largely undefined. This problem is not unique to AF, as the field of functional genomics, which attempts to bridge this gap from genotype to phenotype, has only uncovered the mechanisms for a handful of GWAS loci. Recent functional genomic studies have made great strides towards translating genetic discoveries to an underlying mechanism, but the large-scale application of these techniques to AF has remain limited. These advances, as well as the continued unresolved challenges for both common variation in AF and the functional genomics field in general, will be the subject of the following review.
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http://dx.doi.org/10.1093/cvr/cvv283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4777911PMC
April 2016

Integrating genetic, transcriptional, and functional analyses to identify 5 novel genes for atrial fibrillation.

Circulation 2014 Oct 14;130(15):1225-35. Epub 2014 Aug 14.

Background: Atrial fibrillation (AF) affects >30 million individuals worldwide and is associated with an increased risk of stroke, heart failure, and death. AF is highly heritable, yet the genetic basis for the arrhythmia remains incompletely understood.

Methods And Results: To identify new AF-related genes, we used a multifaceted approach, combining large-scale genotyping in 2 ethnically distinct populations, cis-eQTL (expression quantitative trait loci) mapping, and functional validation. Four novel loci were identified in individuals of European descent near the genes NEURL (rs12415501; relative risk [RR]=1.18; 95% confidence interval [CI], 1.13-1.23; P=6.5×10(-16)), GJA1 (rs13216675; RR=1.10; 95% CI, 1.06-1.14; P=2.2×10(-8)), TBX5 (rs10507248; RR=1.12; 95% CI, 1.08-1.16; P=5.7×10(-11)), and CAND2 (rs4642101; RR=1.10; 95% CI, 1.06-1.14; P=9.8×10(-9)). In Japanese, novel loci were identified near NEURL (rs6584555; RR=1.32; 95% CI, 1.26-1.39; P=2.0×10(-25)) and CUX2 (rs6490029; RR=1.12; 95% CI, 1.08-1.16; P=3.9×10(-9)). The top single-nucleotide polymorphisms or their proxies were identified as cis-eQTLs for the genes CAND2 (P=2.6×10(-19)), GJA1 (P=2.66×10(-6)), and TBX5 (P=1.36×10(-5)). Knockdown of the zebrafish orthologs of NEURL and CAND2 resulted in prolongation of the atrial action potential duration (17% and 45%, respectively).

Conclusions: We have identified 5 novel loci for AF. Our results expand the diversity of genetic pathways implicated in AF and provide novel molecular targets for future biological and pharmacological investigation.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.114.009892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190011PMC
October 2014

Emerging directions in the genetics of atrial fibrillation.

Circ Res 2014 Apr;114(9):1469-82

From the Cardiovascular Research Center, Massachusetts General Hospital, Boston.

Atrial fibrillation (AF) is the most common arrhythmia and is associated with increased morbidity. As the population ages and the prevalence of AF continues to rise, the socioeconomic consequences of AF will become increasingly burdensome. Although there are well-defined clinical risk factors for AF, a significant heritable component is also recognized. To identify the molecular basis for the heritability of AF, investigators have used a combination of classical Mendelian genetics, candidate gene screening, and genome-wide association studies. However, these avenues have, as yet, failed to define the majority of the heritability of AF. The goal of this review is to describe the results from both candidate gene and genome-wide studies, as well as to outline potential future avenues for creating a more complete understanding of AF genetics. Ultimately, a more comprehensive view of the genetic underpinnings for AF will lead to the identification of novel molecular pathways and improved risk prediction of this complex arrhythmia.
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http://dx.doi.org/10.1161/CIRCRESAHA.114.302225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040146PMC
April 2014
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