Showing papers by "Mark Chaffin published in 2020"

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure.

Abstract: Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies.

Transcriptional and Cellular Diversity of the Human Heart

Abstract: 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...

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Abstract: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2 , TMPRSS2 , and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2 , TMPRSS2 , and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2 + TMPRSS2 + cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R , TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Abstract: Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies.Heart failure is a complex syndrome that is associated with many different underlying risk factors. Here, to increase power, the authors jointly analyse cases of heart failure of different aetiologies in a genome-wide association study and identify 11 loci of which ten had not been previously reported.

Analysis of cardiac magnetic resonance imaging in 36,000 individuals yields genetic insights into dilated cardiomyopathy

Abstract: Dilated cardiomyopathy (DCM) is an important cause of heart failure and the leading indication for heart transplantation. Many rare genetic variants have been associated with DCM, but common variant studies of the disease have yielded few associated loci. As structural changes in the heart are a defining feature of DCM, we report a genome-wide association study of cardiac magnetic resonance imaging (MRI)-derived left ventricular measurements in 36,041 UK Biobank participants, with replication in 2184 participants from the Multi-Ethnic Study of Atherosclerosis. We identify 45 previously unreported loci associated with cardiac structure and function, many near well-established genes for Mendelian cardiomyopathies. A polygenic score of MRI-derived left ventricular end systolic volume strongly associates with incident DCM in the general population. Even among carriers of TTN truncating mutations, this polygenic score influences the size and function of the human heart. These results further implicate common genetic polymorphisms in the pathogenesis of DCM.

A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease.

Abstract: Analyzing 12,361 all-cause cirrhosis cases and 790,095 controls from eight cohorts, we identify a common missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene (MARC1 p.A165T) that associates with protection from all-cause cirrhosis (OR 0.91, p = 2.3*10-11). This same variant also associates with lower levels of hepatic fat on computed tomographic imaging and lower odds of physician-diagnosed fatty liver as well as lower blood levels of alanine transaminase (-0.025 SD, 3.7*10-43), alkaline phosphatase (-0.025 SD, 1.2*10-37), total cholesterol (-0.030 SD, p = 1.9*10-36) and LDL cholesterol (-0.027 SD, p = 5.1*10-30) levels. We identified a series of additional MARC1 alleles (low-frequency missense p.M187K and rare protein-truncating p.R200Ter) that also associated with lower cholesterol levels, liver enzyme levels and reduced risk of cirrhosis (0 cirrhosis cases for 238 R200Ter carriers versus 17,046 cases of cirrhosis among 759,027 non-carriers, p = 0.04) suggesting that deficiency of the MARC1 enzyme may lower blood cholesterol levels and protect against cirrhosis.

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

Abstract: Supplemental Digital Content is available in the text.

Deep learning enables genetic analysis of the human thoracic aorta

Abstract: The aorta is the largest blood vessel in the body, and enlargement or aneurysm of the aorta can predispose to dissection, an important cause of sudden death. While rare syndromes have been identified that predispose to aortic aneurysm, the common genetic basis for the size of the aorta remains largely unknown. By leveraging a deep learning architecture that was originally developed to recognize natural images, we trained a model to evaluate the dimensions of the ascending and descending thoracic aorta in cardiac magnetic resonance imaging. After manual annotation of just 116 samples, we applied this model to 3,840,140 images from the UK Biobank. We then conducted a genome-wide association study in 33,420 individuals, revealing 68 loci associated with ascending and 35 with descending thoracic aortic diameter, of which 10 loci overlapped. Integration of common variation with transcriptome-wide analyses, rare-variant burden tests, and single nucleus RNA sequencing prioritized SVIL, a gene highly expressed in vascular smooth muscle, that was significantly associated with the diameter of the ascending and descending aorta. A polygenic score for ascending aortic diameter was associated with a diagnosis of thoracic aortic aneurysm in the remaining 391,251 UK Biobank participants who did not undergo imaging (HR = 1.44 per standard deviation; P = 3.7·10−12). Defining the genetic basis of the diameter of the aorta may enable the identification of asymptomatic individuals at risk for aneurysm or dissection and facilitate the prioritization of potential therapeutic targets for the prevention or treatment of aortic aneurysm. Finally, our results illustrate the potential for rapidly defining novel quantitative traits derived from a deep learning model, an approach that can be more broadly applied to biomedical imaging data.

Monogenic and Polygenic Contributions to Atrial Fibrillation Risk: Results From a National Biobank.

Abstract: Rationale: Genome-wide association studies have identified over 100 genetic loci for atrial fibrillation (AF); recent work described an association between loss-of-function (LOF) variants in TTN an...

Genome-wide polygenic score, clinical risk factors, and long-term trajectories of coronary artery disease

Abstract: Objective: To determine the relationship of a genome-wide polygenic score for coronary artery disease (GPSCAD) with lifetime trajectories of CAD risk, directly compare its predictive capacity to tr...

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

Abstract: 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.

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

Abstract: 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.

Identification of Functional Variant Enhancers Associated With Atrial Fibrillation.

Abstract: 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 m...

Genetic Variation in Cardiometabolic Traits and Medication Targets and the Risk of Hypertensive Disorders of Pregnancy.

Abstract: August 18, 2020 711

Rare Genetic Variation Underlying Human Diseases and Traits: Results from 200,000 Individuals in the UK Biobank

Abstract: Background Many human diseases are known to have a genetic contribution. While genome-wide studies have identified many disease-associated loci, it remains challenging to elucidate causal genes. In contrast, exome sequencing provides an opportunity to identify new disease genes and large-effect variants of clinical relevance. We therefore sought to determine the contribution of rare genetic variation in a curated set of human diseases and traits using a unique resource of 200,000 individuals with exome sequencing data from the UK Biobank. Methods and Results We included 199,832 participants with a mean age of 68 at follow-up. Exome-wide gene-based tests were performed for 64 diseases and 23 quantitative traits using a mixed-effects model, testing rare loss-of-function and damaging missense variants. We identified 51 known and 23 novel associations with 26 diseases and traits at a false-discovery-rate of 1%. There was a striking risk associated with many Mendelian disease genes including: MYPBC3 with over a 100-fold increased odds of hypertrophic cardiomyopathy, PKD1 with a greater than 25-fold increased odds of chronic kidney disease, and BRCA2, BRCA1, ATM and PALB2 with 3 to 10-fold increased odds of breast cancer. Notable novel findings included an association between GIGYF1 and type 2 diabetes (OR 5.6, P=5.35×10−8), elevated blood glucose, and lower insulin-like-growth-factor-1 levels. Rare variants in CCAR2 were also associated with diabetes risk (OR 13, P=8.5×10−8), while COL9A3 was associated with cataract (OR 3.4, P=6.7×10−8). Notable associations for blood lipids and hypercholesterolemia included NR1H3, RRBP1, GIGYF1, SCGN, APH1A, PDE3B and ANGPTL8. A number of novel genes were associated with height, including DTL, PIEZO1, SCUBE3, PAPPA and ADAMTS6, while BSN was associated with body-mass-index. We further assessed putatively pathogenic variants in known Mendelian cardiovascular disease genes and found that between 1.3 and 2.3% of the population carried likely pathogenic variants in known cardiomyopathy, arrhythmia or hypercholesterolemia genes. Conclusions Large-scale population sequencing identifies known and novel genes harboring high-impact variation for human traits and diseases. A number of novel findings, including GIGYF1,represent interesting potential therapeutic targets. Exome sequencing at scale can identify a meaningful proportion of the population that carries a pathogenic variant underlying cardiovascular disease.

Transcriptional and Cellular Diversity of the Human Heart

Abstract: Introduction 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, here we have applied these approaches to assess the cellular and transcriptional diversity of the non-failing human heart. Methods Microfluidic encapsulation and barcoding was used to perform single nuclear RNA sequencing with samples from seven human donors, selected for their absence of overt cardiac disease. Individual nuclear transcriptomes were then clustered based upon 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 a total of 9 major cell types and 20 subclusters of cell types within the human heart. Cellular subclasses include two distinct groups of resident macrophages, four endothelial subtypes, and two fibroblasts 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. Finally, intersection of our dataset 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 have 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.

Rare variants lowering the levels of coagulation factor X are protective against ischemic heart disease

Abstract: Coagulation factor X (FX) is a serine protease playing a pivotal role in the clotting process. It exerts its function by catalyzing thrombin formation, ultimately leading to the generation of fibrin from fibrinogen to produce a stable clot (Figure 1A). This mechanism prevents excessive blood loss after injury; however, it can also cause the generation of pathologic thrombi in blood vessels, blocking blood flow to a tissue and eventually resulting in ischemia and tissue death. An example is the acute coronary syndrome (ACS), the most severe complication of coronary artery disease (CAD). ACS commonly results from atherosclerotic plaque rupture, followed by platelet and coagulation cascade activation, which leads to a thrombus formation in the coronary arteries. Since activated FX (FXa) is central in the coagulation cascade, being involved in the initiation, amplification, and propagation phases of clot formation (Figure 1A), its specific inhibition was demonstrated to be effective in the prevention/treatment of life-threatening thrombi formation in arterial atherothrombotic diseases and venous thromboembolism. FXa inhibitors (i.e. rivaroxaban, apixaban, edoxaban) were proven to reduce the risk of stroke and systemic embolism in patients with nonvalvular atrial fibrillation, and to treat and/or prevent deepvenous thrombosis and pulmonary embolism. Rivaroxaban was shown to reduce the risk of major cardiovascular events in patients with a recent ACS when co-administered with antiplatelet therapies. Recently, the association between rivaroxaban and aspirin was proposed to improve cardiovascular outcomes even in patients with stable atherosclerotic vascular disease. Therefore, growing evidence emphasizes the role of FXa in the modulation of the residual cardiovascular risk in ischemic heart disease. Besides coagulation, FX is implicated in inflammation, tissue fibrosis, and vascular remodeling through the interaction with protease-activated receptors (PAR). PAR belong to a family of seven-transmembrane, G proteincoupled receptors that are activated by different serine proteases by specific N-terminal cleavage. FXa activates PAR-1 and PAR-2, expressed in endothelial cells (EC), dendritic cells, leukocytes, fibroblasts, and vascular smooth muscle cells (VSMC). Recent findings suggested that FXa and its major receptor, PAR-2, play an important role in the pathophysiology of inflammatory diseases, including atherosclerosis (Figure 1B-C). In this frame, Hara and colleagues demonstrated that the administration of rivaroxaban reduces atherosclerotic plaque progression in ApoE-deficient mice by decreasing lipid deposition, macrophage accumulation, and MMP-9 expression within plaques. This indicates that FXa inhibition may attenuate plaque progression/destabilization beyond the influence on the coagulation pathway. Importantly, the inflammation response was also affected: after treatment, expression levels of TNF-α, Cox-2, iNOS, MCP-1, and IL-1B were significantly reduced in atherosclerotic plaques and macrophages. Consistently, FXa proteolytic activities were found significantly increased in early atherosclerotic lesions compared to lesions at a later stage, suggesting an important role for this protease also in the initial development of atherosclerosis. Naturally occurring DNA variants affecting the expression/activity of drug protein targets can give insights in the therapeutic treatment directed against such gene products. Mutations lowering the expression of a drugtarget gene are hence particularly interesting, because they may mimic the effect of pharmacological inhibition. According to this notion, variants disrupting the protein function of two drug-target genes, PCSK9 and NPC1L1, were demonstrated to be associated with a lower risk of CAD, and clinical trials testing the inhibition of their protein products proved consistent with the genetic findings. Here, we aimed at evaluating whether rare variants leading to decreased FX levels are associated with a lower risk of ischemic heart disease. We were able to show, for the first time, that rare damaging variants in the F10 gene are associated with reduced MI risk, thus providing a genetic support to the working hypothesis of clinical trials showing that FX inhibition may be beneficial for the treatment of ischemic heart disease. The study was conducted on an Italian cohort collected by “The Atherosclerosis, Thrombosis, and Vascular Biology Italian Study Group” (ATVB). The cohort is composed of 2,008 patients with early-onset MI (first event before 45 years) and an equal number of controls, matched for sex, age, and geographical origin. The clinical characteristics of the population are shown in the Online Supplementary Table S1. Whole-exome sequencing was performed on the ATVB cohort at the Broad Institute (Boston, MA, USA). Exome capture, sequencing, and data processing were previously described.Overall, sequencing of the FX gene (F10) was successful for 1,791 cases and 1,750 controls. No null variants (nonsense, frameshift, splicing) were present in the cohort, in line with the constraint score reported in GnomAD repository (https://gnomad.broadinstitute.org/), i.e. the ratio of the observed/expected (o/e) number of loss-of-function (LoF) variants in the gene (o/e=0.6, 90% CI: 0.38-0.97), which indicates a certain degree of LoF mutation intolerance for F10. Conversely, 34 different rare missense variants (listed in the Online Supplementary Table S2) and 20 low-frequency synonymous variants were identified. A total of 86 subjects carried one missense variant in the heterozygous state, including 32 MI cases (1.8%), and 54 controls (3.1%). The 34 missense variants were analyzed using five algorithms, with the aim of predicting their damaging effect (for details, see the Online Supplementary Materials and Methods). Only five were predicted as damaging by all software (Online Supplementary Table S2). In parallel, we searched these 34 missense variants in publicly-available databases, finding that that five variations (p.E54G, p.G134R, p.E142K, p.G192R, p.G420R) had already been described in patients affected by FX deficiency (Online Supplementary Table S2). Interestingly, only three of these (p.E54G, p.G134R, p.G420R) were predicted as damaging by all algorithms, whereas the variants p.E142K and p.G192R were recognized as pathogenic only by three and one software, respectively. We therefore performed an initial analysis including all variants identified as disruptive by all five algorithms, plus those previously annotated as pathogenic in FX deficiency. When restricting the analysis to this set, we observed an enrichment in the burden of potentially deleterious variants among controls: in fact, 1.48% of controls carried at least one such rare mutation compared to only 0.78% of cases, (P=0.046, OR=0.51, 95% CI: 0.26-0.99) (Figure 2A). This result highlighted a reduced risk of MI in subjects carrying a F10 deleterious mutation. When considering a broader set of variants (all the identified missense variants), we still observed a significant

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

Abstract: 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 ...

Analysis of cardiac magnetic resonance imaging traits in 29,000 individuals reveals shared genetic basis with dilated cardiomyopathy

Abstract: Dilated cardiomyopathy (DCM) is an important cause of heart failure and the leading indication for heart transplantation. Many rare genetic variants have been associated with DCM, but common variant studies of the disease have yielded few associated loci. As structural changes in the heart are a defining feature of DCM, we conducted a genome-wide association study (GWAS) of cardiac magnetic resonance imaging (MRI)-derived left ventricular measurements in 29,041 UK Biobank participants. 26 novel loci were associated with cardiac structure and function. These loci were found near 17 genes previously shown to cause Mendelian cardiomyopathies. A polygenic score of left ventricular end systolic volume was associated with incident DCM in previously disease-free individuals (hazard ratio = 1.54 per one standard deviation increase in the polygenic score, P = 2.1×10−16). Even among carriers of truncating mutations in TTN, the polygenic score influenced the size and function of the heart. These results further implicate common genetic polymorphisms in DCM pathogenesis.