Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.</p

Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.</p

Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis

Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes remain controversial. Here, we perform an integrated meta-analysis of 22 scRNA-seq libraries to generate a comprehensive map of human atherosclerosis with 118,578 cells. Besides characterizing granular cell-type diversity and communication, we leverage this atlas to provide insights into smooth muscle cell (SMC) modulation. We integrate genome-wide association study data and uncover a critical role for modulated SMC phenotypes in CAD, myocardial infarction, and coronary calcification. Finally, we identify fibromyocyte/fibrochondrogenic SMC markers (LTBP1 and CRTAC1) as proxies of atherosclerosis progression and validate these through omics and spatial imaging analyses. Altogether, we create a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases.</p

PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics

Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields

Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes

Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis

Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes remain controversial. Here, we perform an integrated meta-analysis of 22 scRNA-seq libraries to generate a comprehensive map of human atherosclerosis with 118,578 cells. Besides characterizing granular cell-type diversity and communication, we leverage this atlas to provide insights into smooth muscle cell (SMC) modulation. We integrate genome-wide association study data and uncover a critical role for modulated SMC phenotypes in CAD, myocardial infarction, and coronary calcification. Finally, we identify fibromyocyte/fibrochondrogenic SMC markers (LTBP1 and CRTAC1) as proxies of atherosclerosis progression and validate these through omics and spatial imaging analyses. Altogether, we create a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases

L-type Calcium Channel, a direct target of aldosterone in cardiomyocytes

Ces dernières décennies ont mis à jour une implication pathologique nouvelle del’aldostérone, via le récepteur aux minéralocorticoïdes (RM) dans le coeur. L’ensemble desdonnées issues des études expérimentales et des essais cliniques suggère une association délétèreentre l’aldostérone et la survenue d’arythmies. L’utilisation d’antagonistes du RM prévient cesarythmies. Cependant, les voies de signalisations, comme les mécanismes moléculaires soustendantces effets bénéfiques du blocage des RM demeurent incertains. Nous avons accumulésdes preuves d’une modulation de la signalisation calcique dans le cardiomyocyte, et en particulierde l’influx calcique (Ca2+) au travers du canal Ca2+ de type L (LTCC). Celui-Ci pourrait être unecible primaire de l’aldostérone et du RM dans les cardiomyocytes ventriculaires. Toutefois, lesmécanismes par lesquels l’aldostérone et le RM régulent l’expression du LTCC restent à définir.Au cours de ces travaux menés sur cardiomyocytes de rats nouveau-Nés, nous avonsétudiés les évènements moléculaires par lesquels l’aldostérone exerce ses effets sur le CaV1.2,qui correspond à la sous-Unité principale du LTCC formant le pore du canal ; cette protéine estcodée par le CACNA1C. Par microscopie confocale, nous avons suivi en temps réel le traffickingnucléo-Cytoplasmique du RM couplé à la GFP en réponse à l’aldostérone, démontrant ainsi queles RM cardiaques sont fonctionnels. Le traitement durant 24 heures des cardiomyocytes avec del’aldostérone montre une augmentation dose-Dépendante des protéines et de l’ARN messager duCaV1.2. L’utilisation de la technique du gène rapporteur de la luciférase permet l’analyse del’activité du promoteur du CaCNA1C. Celui-Ci montre une activité transcriptionnelle dose ettemps dépendante en réponse à l’aldostérone. De plus, ces effets sont dépendant des RM carinhibés en présence de RU28318, un antagoniste sélectif du RM, ou par l’utilisation de siRNAdirigés contre le RM. L’analyse in silico de la séquence du promoteur du CaCNA1C nous a permisd’identifier cinq séquences putatives correspondant à des éléments de réponse auxglucocorticoïdes (GRE). La mutation du site le plus lointain du site d’initiation de la transcriptionne révèle aucun changement dans les réponses transcriptionnelles induites par un RM humainconstitutivement actif (hMRΔ5,6) ou dans les réponses doses-Dépendantes de l’aldostérone ou dela déxaméthasone, un glucocorticoïde de synthèse. La mutation des trois sites GRE putatifssuivants provoque une diminution des réponses au hMRΔ5,6 comme à l’aldostérone, alors que lesréponses à la déxaméthasone sont soit inchangées, soit augmentées. En contraste, la mutation dusite le plus proximal du promoteur augmente de façon importante l’activité transcriptionnelle dupromoteur en réponse au hMRΔ5,6, à l’aldostérone comme à la déxaméthasone.Ces résultats démontrent que le LTCC cardiaque constitue une cible directe del’aldostérone et du RM, et apportent de nouvelles perspectives quant aux conséquencesmoléculaires et fonctionnelles engendrées par l’activation délétère du système minéralocorticoïdedans la défaillance cardiaque.During the past decades, major novel pathogenic roles of the steroid hormone,aldosterone, via the Mineralocorticoid Receptor (MR) have been identified in heart. Collectively,experimental studies and clinical trials, suggest a detrimental association between aldosteroneand life threatening arrhythmias that may be prevented by MR blockade. However, the signalingpathways and underlying mechanisms still remain elusive. We have accumulated evidence thatmodulation of Ca2+ signaling, especially Ca2+ influx via L-Type Ca2+ channel (LTCC), might bethe primary aldosterone/MR target in ventricular cardiomyocytes. Yet, the molecularmechanisms by which MR regulates expression of LTCC remain to be defined. Here, weinvestigated, in primary cultures of neonatal rat ventricular myocytes, the molecular eventscritical for aldosterone-Mediated cardiac effects on CaV1.2, the pore-Forming main subunit ofLTCC, which is encoded by the CaCNA1C gene.We showed that cardiac MR are functional as demonstrated by aldosterone-Induced MRnucleocytoplasmic trafficking observed by time-Lapse imaging of transfected GFP-Labeled MRusing confocal microscopy. Aldosterone exposure for 24 hours, induced a dose-Dependentincrease in CaV1.2 expression at both mRNA and protein levels. Analysis of the CaCNA1Cpromoter activity using luciferase reporter assays, revealed a dose- and time-Dependent activationby aldosterone. These effects were inhibited in the presence of either RU28318, a selective MRantagonist, or MR siRNA. In silico analyze enabled us to identify five putative GlucocorticoidResponse Elements (GRE) within the CaCNA1C promoter sequence. The mutation of the mostdistal GRE from Transcription Start Site (TSS) did not altered responses either elicited by theconstitutively active human MR (hMRΔ5,6) or dose-Dependent effects of aldosterone anddexamethasone (a synthetic glucocorticoïd with minimal MR effect). Mutations of the three nextones decreased responses to hMRΔ5,6 and aldosterone, whereas dexamethasone responses wereeither unchanged or increased. In sharp contrast, the mutation of the most proximal GRE fromTSS, increased responses to hMRΔ5,6, aldosterone and dexamethasone.These results provide new insights into the molecular mechanisms associated with cardiacMR activation, and suggest that LTCC is a primary MR target, with subsequent molecular andfunctional consequences that could lead to MR-Related cardiac dysfunction

Multimaterial polarization maintaining optical fibers fabricated with the powder-in-tube technology

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Use of comprehensive two-dimensional gas chromatography for the broad screening of hazardous contaminants in urban wastewaters

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Fibre optique à maintien de polarisation fonctionnalisée avec une matrice vitreuse par l’exploitation de la technologie ’Poudre’

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