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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.
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Vasos Coronarios , Estudio de Asociación del Genoma Completo , Humanos , Predisposición Genética a la Enfermedad/genética , Regulación de la Expresión Génica , Sitios de Carácter Cuantitativo/genéticaRESUMEN
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.
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Aterosclerosis , Enfermedad de la Arteria Coronaria , Infarto del Miocardio , Placa Aterosclerótica , Humanos , Estudio de Asociación del Genoma Completo , Aterosclerosis/genética , Enfermedad de la Arteria Coronaria/genética , Miocitos del Músculo Liso , Proteínas de Unión al Calcio/genéticaRESUMEN
Coronary artery calcification (CAC), a measure of subclinical atherosclerosis, predicts future symptomatic coronary artery disease (CAD). Identifying genetic risk factors for CAC may point to new therapeutic avenues for prevention. Currently, there are only four known risk loci for CAC identified from genome-wide association studies (GWAS) in the general population. Here we conducted the largest multi-ancestry GWAS meta-analysis of CAC to date, which comprised 26,909 individuals of European ancestry and 8,867 individuals of African ancestry. We identified 11 independent risk loci, of which eight were new for CAC and five had not been reported for CAD. These new CAC loci are related to bone mineralization, phosphate catabolism and hormone metabolic pathways. Several new loci harbor candidate causal genes supported by multiple lines of functional evidence and are regulators of smooth muscle cell-mediated calcification ex vivo and in vitro. Together, these findings help refine the genetic architecture of CAC and extend our understanding of the biological and potential druggable pathways underlying CAC.
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Aterosclerosis , Enfermedad de la Arteria Coronaria , Humanos , Aterosclerosis/genética , Población Negra/genética , Enfermedad de la Arteria Coronaria/genética , Estudio de Asociación del Genoma Completo , Factores de Riesgo , Pueblo Europeo/genéticaRESUMEN
BACKGROUND: Genome-wide association studies have identified hundreds of loci associated with common vascular diseases, such as coronary artery disease, myocardial infarction, and hypertension. However, the lack of mechanistic insights for many GWAS loci limits their translation into the clinic. Among these loci with unknown functions is UFL1-four-and-a-half LIM (LIN-11, Isl-1, MEC-3) domain 5 (FHL5; chr6q16.1), which reached genome-wide significance in a recent coronary artery disease/ myocardial infarction GWAS meta-analysis. UFL1-FHL5 is also associated with several vascular diseases, consistent with the widespread pleiotropy observed for GWAS loci. METHODS: We apply a multimodal approach leveraging statistical fine-mapping, epigenomic profiling, and ex vivo analysis of human coronary artery tissues to implicate FHL5 as the top candidate causal gene. We unravel the molecular mechanisms of the cross-phenotype genetic associations through in vitro functional analyses and epigenomic profiling experiments in coronary artery smooth muscle cells. RESULTS: We prioritized FHL5 as the top candidate causal gene at the UFL1-FHL5 locus through expression quantitative trait locus colocalization methods. FHL5 gene expression was enriched in the smooth muscle cells and pericyte population in human artery tissues with coexpression network analyses supporting a functional role in regulating smooth muscle cell contraction. Unexpectedly, under procalcifying conditions, FHL5 overexpression promoted vascular calcification and dysregulated processes related to extracellular matrix organization and calcium handling. Lastly, by mapping FHL5 binding sites and inferring FHL5 target gene function using artery tissue gene regulatory network analyses, we highlight regulatory interactions between FHL5 and downstream coronary artery disease/myocardial infarction loci, such as FOXL1 and FN1 that have roles in vascular remodeling. CONCLUSIONS: Taken together, these studies provide mechanistic insights into the pleiotropic genetic associations of UFL1-FHL5. We show that FHL5 mediates vascular disease risk through transcriptional regulation of downstream vascular remodeling gene programs. These transacting mechanisms may explain a portion of the heritable risk for complex vascular diseases.
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Enfermedad de la Arteria Coronaria , Hipertensión , Infarto del Miocardio , Humanos , Enfermedad de la Arteria Coronaria/genética , Enfermedad de la Arteria Coronaria/metabolismo , Estudio de Asociación del Genoma Completo , Remodelación Vascular , Infarto del Miocardio/metabolismo , Hipertensión/metabolismo , Miocitos del Músculo Liso/metabolismo , Polimorfismo de Nucleótido Simple , Predisposición Genética a la Enfermedad , Factores de Transcripción/metabolismo , Proteínas con Dominio LIM/genética , Proteínas con Dominio LIM/metabolismoRESUMEN
Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary arteries and 19% exhibited cell-type-specific expression. Colocalization analysis with GWAS identified subgroups of eGenes unique to CAD and blood pressure. Fine-mapping highlighted additional eGenes of interest, including TBX20 and IL5 . Splicing (s)QTLs for 1,690 genes were also identified, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing events to accurately identify disease-relevant gene expression. Our work provides the first human coronary artery eQTL resource from a patient sample and exemplifies the necessity of diverse study populations and multi-omic approaches to characterize gene regulation in critical disease processes.
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BACKGROUND: Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies have identified over 175 loci associated with CAD. The majority of these loci are in noncoding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we aimed to identify the subset of the CAD loci associated with the regulation of transcription in distinct SMC phenotypes. METHODS: We measured gene expression in SMCs isolated from the ascending aortas of 151 heart transplant donors of various genetic ancestries in quiescent or proliferative conditions and calculated the association of their expression and splicing with ~6.3 million imputed single-nucleotide polymorphism markers across the genome. RESULTS: We identified 4910 expression and 4412 splicing quantitative trait loci (sQTLs) representing regions of the genome associated with transcript abundance and splicing. A total of 3660 expression quantitative trait loci (eQTLs) had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 eQTLs were SMC-specific and sex-biased, respectively. We made these results available for public query on a user-friendly website. To identify the effector transcript(s) regulated by CAD loci, we used 4 distinct colocalization approaches. We identified 84 eQTL and 164 sQTL that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. One CAD locus colocalized with a sex-specific eQTL (TERF2IP), and another locus colocalized with SMC-specific eQTL (ALKBH8). The most significantly associated CAD locus, 9p21, was an sQTL for the long noncoding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. CONCLUSIONS: Collectively, our results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.
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Enfermedad de la Arteria Coronaria , Masculino , Femenino , Humanos , Enfermedad de la Arteria Coronaria/genética , Enfermedad de la Arteria Coronaria/metabolismo , Estudio de Asociación del Genoma Completo/métodos , Regulación de la Expresión Génica , Sitios de Carácter Cuantitativo , Predisposición Genética a la Enfermedad , Expresión Génica , Polimorfismo de Nucleótido Simple , Homólogo 8 de AlkB ARNt Metiltransferasa/genética , Homólogo 8 de AlkB ARNt Metiltransferasa/metabolismoRESUMEN
Coronary artery calcification (CAC) is a measure of atherosclerosis and a well-established predictor of coronary artery disease (CAD) events. Here we describe a genome-wide association study (GWAS) of CAC in 22,400 participants from multiple ancestral groups. We confirmed associations with four known loci and identified two additional loci associated with CAC (ARSE and MMP16), with evidence of significant associations in replication analyses for both novel loci. Functional assays of ARSE and MMP16 in human vascular smooth muscle cells (VSMCs) demonstrate that ARSE is a promoter of VSMC calcification and VSMC phenotype switching from a contractile to a calcifying or osteogenic phenotype. Furthermore, we show that the association of variants near ARSE with reduced CAC is likely explained by reduced ARSE expression with the G allele of enhancer variant rs5982944. Our study highlights ARSE as an important contributor to atherosclerotic vascular calcification, and a potential drug target for vascular calcific disease.
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OBJECTIVES: Few machine learning (ML) models are successfully deployed in clinical practice. One of the common pitfalls across the field is inappropriate problem formulation: designing ML to fit the data rather than to address a real-world clinical pain point. METHODS: We introduce a practical toolkit for user-centred design consisting of four questions covering: (1) solvable pain points, (2) the unique value of ML (eg, automation and augmentation), (3) the actionability pathway and (4) the model's reward function. This toolkit was implemented in a series of six participatory design workshops with care managers in an academic medical centre. RESULTS: Pain points amenable to ML solutions included outpatient risk stratification and risk factor identification. The endpoint definitions, triggering frequency and evaluation metrics of the proposed risk scoring model were directly influenced by care manager workflows and real-world constraints. CONCLUSIONS: Integrating user-centred design early in the ML life cycle is key for configuring models in a clinically actionable way. This toolkit can guide problem selection and influence choices about the technical setup of the ML problem.
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Aprendizaje Automático , Diseño Centrado en el Usuario , Atención a la Salud , Humanos , Dolor , Flujo de TrabajoRESUMEN
Integration into host target DNA (tDNA), a hallmark of retroviral replication, is mediated by the intasome, a multimer of integrase (IN) assembled on viral DNA (vDNA) ends. To ascertain aspects of tDNA recognition during integration, we have solved the 3.5 Å resolution cryo-EM structure of the mouse mammary tumor virus (MMTV) strand transfer complex (STC) intasome. The tDNA adopts an A-like conformation in the region encompassing the sites of vDNA joining, which exposes the sugar-phosphate backbone for IN-mediated strand transfer. Examination of existing retroviral STC structures revealed conservation of A-form tDNA in the analogous regions of these complexes. Furthermore, analyses of sequence preferences in genomic integration sites selectively targeted by six different retroviruses highlighted consistent propensity for A-philic sequences at the sites of vDNA joining. Our structure additionally revealed several novel MMTV IN-DNA interactions, as well as contacts seen in prior STC structures, including conserved Pro125 and Tyr149 residues interacting with tDNA. In infected cells, Pro125 substitutions impacted the global pattern of MMTV integration without significantly altering local base sequence preferences at vDNA insertion sites. Collectively, these data advance our understanding of retroviral intasome structure and function, as well as factors that influence patterns of vDNA integration in genomic DNA.
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Integrasas , Integración Viral , Animales , Ratones , Integrasas/metabolismo , Retroviridae/genética , Retroviridae/metabolismo , ADN Viral/genética , ADN Viral/química , Conformación Molecular , Virus del Tumor Mamario del Ratón/genética , Virus del Tumor Mamario del Ratón/metabolismoRESUMEN
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.
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PURPOSE: To investigate existing studies examining the association between body mass index (BMI) and outcomes of anterior cruciate ligament reconstruction (ACLR) in adolescent patients. METHODS: A literature search was conducted on PubMed and Embase. Studies examining associations between BMI and outcomes after ACLR in adolescents were included. Quality assessment was performed. Data on patient age, sex, study design, time of follow-up, sample size, graft type, concomitant injuries (meniscal injury, surgical procedures), clinical outcomes (revision ACLR, postoperative weight gain, post-traumatic osteoarthritis [PTOA], range of motion [ROM]), and functional outcome (muscle strength) were extracted. RESULTS: Eleven papers of Levels II-IV evidence were included. Five studies found positive correlations between BMI and risk of concomitant meniscal injuries. Two of them reported young patients with elevated BMI having 1.6 times greater odds of requiring meniscectomy (P < .01) and 1.031 times greater odds of requiring concomitant surgeries (P = .011). One study showed significant positive association of postoperative weight gain by time (r = 0.28, P < .01), with smaller increase in the overweight and obese groups compared with the normal-weight group. One study demonstrated greater cartilage breakdown in young patients with overweight and obesity postsurgery, contributing to PTOA (r = 0.42, P = .009). There was no clinically important difference in postoperative ROM and muscle strength. Four studies reviewed the association between BMI and revision ACLR risk, but results were heterogeneous and a firm conclusion cannot be drawn. CONCLUSIONS: Adolescents with elevated BMI are more likely to have concomitant meniscal injuries and surgical procedures after ACL tear. There is some weak evidence of the association of elevated BMI with PTOA and slight postoperative weight gain post-ACLR. There may not be any clinically significant association of obesity with post-operative muscle strength and ROM, and current studies are inconclusive regarding the impact of BMI on revision ACLR risk. LEVEL OF EVIDENCE: Level IV, systematic review of Level II-IV studies.
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Lesiones del Ligamento Cruzado Anterior , Osteoartritis , Lesiones de Menisco Tibial , Adolescente , Humanos , Lesiones del Ligamento Cruzado Anterior/complicaciones , Lesiones del Ligamento Cruzado Anterior/cirugía , Índice de Masa Corporal , Lesiones de Menisco Tibial/complicaciones , Lesiones de Menisco Tibial/cirugía , Sobrepeso/complicaciones , Osteoartritis/complicaciones , Obesidad/complicaciones , Aumento de PesoRESUMEN
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell-type-specific elements and transcription factors, and prioritized functional CAD risk variants. We identified elements in smooth muscle cell transition states (for example, fibromyocytes) and functional variants predicted to alter smooth muscle cell- and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single-nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.
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Enfermedad de la Arteria Coronaria , Estudio de Asociación del Genoma Completo , Cromatina/genética , Enfermedad de la Arteria Coronaria/genética , Enfermedad de la Arteria Coronaria/metabolismo , Humanos , Polimorfismo de Nucleótido Simple/genética , Factores de Transcripción/genéticaRESUMEN
BACKGROUND AND AIMS: The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets. METHODS: Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further exploration and analysis of this and other cardiovascular single-cell datasets. RESULTS: We revealed distinct derivations of fibroblast-like cells from smooth muscle cells (SMCs), and showed the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several avenues for future pharmacological development for precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows lay scientists to explore this and other datasets and compare scRNA-seq tools without prior coding knowledge. CONCLUSIONS: This publicly available workflow and application will allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. Our analysis pipeline provides many hypothesis-generating tools to unravel the etiology of coronary artery disease. We also highlight potential mechanisms for several drugs in the atherosclerotic cellular environment. Future releases of PlaqView will feature more scRNA-seq and scATAC-seq atherosclerosis-related datasets to provide a critical resource for the field, and to promote data harmonization and biological interpretation.
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Enfermedad de la Arteria Coronaria , Preparaciones Farmacéuticas , Enfermedad de la Arteria Coronaria/tratamiento farmacológico , Enfermedad de la Arteria Coronaria/genética , Perfilación de la Expresión Génica , Humanos , RNA-Seq , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Programas Informáticos , Flujo de TrabajoRESUMEN
Lentiviral DNA integration favors transcriptionally active chromatin. We previously showed that the interaction of human immunodeficiency virus type 1 (HIV-1) capsid with cleavage and polyadenylation specificity factor 6 (CPSF6) localizes viral preintegration complexes (PICs) to nuclear speckles for integration into transcriptionally active speckle-associated domains (SPADs). In the absence of the capsid-CPSF6 interaction, PICs uncharacteristically accumulate at the nuclear periphery and target heterochromatic lamina-associated domains (LADs) for integration. The integrase-binding protein lens epithelium-derived growth factor (LEDGF)/p75 in contrast to CPSF6 predominantly functions to direct HIV-1 integration to interior regions of transcription units. Though CPSF6 and LEDGF/p75 can reportedly interact with the capsid and integrase proteins of both primate and nonprimate lentiviruses, the extents to which these different viruses target SPADs versus LADs, as well as their dependencies on CPSF6 and LEDGF/p75 for integration targeting, are largely unknown. Here, we mapped 5,489,157 primate and nonprimate lentiviral integration sites in HEK293T and Jurkat T cells as well as derivative cells that were knocked out or knocked down for host factor expression. Despite marked preferences of all lentiviruses to target genes for integration, nonprimate lentiviruses only marginally favored SPADs, with corresponding upticks in LAD-proximal integration. While LEDGF/p75 knockout disrupted the intragenic integration profiles of all lentiviruses similarly, CPSF6 depletion specifically counteracted SPAD integration targeting by primate lentiviruses. CPSF6 correspondingly failed to appreciably interact with nonprimate lentiviral capsids. We conclude that primate lentiviral capsid proteins evolved to interact with CPSF6 to optimize PIC localization for integration into transcriptionally active SPADs.IMPORTANCE Integration is the defining step of the retroviral life cycle and underlies the inability to cure HIV/AIDS through the use of intensified antiviral therapy. The reservoir of latent, replication-competent proviruses that forms early during HIV infection reseeds viremia when patients discontinue medication. HIV cure research is accordingly focused on the factors that guide provirus formation and associated chromatin environments that regulate transcriptional reactivation, and studies of orthologous infectious agents such as nonprimate lentiviruses can inform basic principles of HIV biology. HIV-1 utilizes the integrase-binding protein LEDGF/p75 and the capsid interactor CPSF6 to target speckle-associated domains (SPADs) for integration. However, the extent to which these two host proteins regulate integration of other lentiviruses is largely unknown. Here, we mapped millions of retroviral integration sites in cell lines that were depleted for LEDGF/p75 and/or CPSF6. Our results reveal that primate lentiviruses uniquely target SPADs for integration in a CPSF6-dependent manner.
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Lentivirus/genética , Primates/genética , Integración Viral/genética , Factores de Escisión y Poliadenilación de ARNm/genética , Animales , Gatos/genética , Gatos/virología , Bovinos/genética , Bovinos/virología , Línea Celular , Evolución Molecular , Células HEK293 , Caballos/genética , Caballos/virología , Humanos , Péptidos y Proteínas de Señalización Intercelular/genética , Células Jurkat , Macaca mulatta/genética , Macaca mulatta/virología , Ratones/genética , Ratones/virología , Primates/virología , Replicación ViralRESUMEN
Coronary artery disease is a complex cardiovascular disease involving an interplay of genetic and environmental influences over a lifetime. Although considerable progress has been made in understanding lifestyle risk factors, genetic factors identified from genome-wide association studies may capture additional hidden risk undetected by traditional clinical tests. These genetic discoveries have highlighted many candidate genes and pathways dysregulated in the vessel wall, including those involving smooth muscle cell phenotypic modulation and injury responses. Here, we summarize experimental evidence for a few genome-wide significant loci supporting their roles in smooth muscle cell biology and disease. We also discuss molecular quantitative trait locus mapping as a powerful discovery and fine-mapping approach applied to smooth muscle cell and coronary artery disease-relevant tissues. We emphasize the critical need for alternative genetic strategies, including cis/trans-regulatory network analysis, genome editing, and perturbations, as well as single-cell sequencing in smooth muscle cell tissues and model organisms, under both normal and disease states. By integrating multiple experimental and analytical modalities, these multidimensional datasets should improve the interpretation of coronary artery disease genome-wide association studies and molecular quantitative trait locus signals and inform candidate targets for therapeutic intervention or risk prediction.
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Enfermedad de la Arteria Coronaria/genética , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Músculo Liso Vascular/patología , Sitios de Carácter Cuantitativo/genética , Enfermedad de la Arteria Coronaria/patología , Vasos Coronarios/metabolismo , Vasos Coronarios/patología , Humanos , Estilo de Vida , Músculo Liso Vascular/metabolismo , Miocitos del Músculo Liso/metabolismo , Fenotipo , Polimorfismo de Nucleótido Simple/genética , Medición de Riesgo , Sensibilidad y EspecificidadRESUMEN
Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.
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Coronary artery disease (CAD) is the leading cause of mortality worldwide and poses a considerable public health burden. Recent genome-wide association studies (GWAS) have revealed >100 genetic loci associated with CAD susceptibility in humans. While a number of these loci harbor gene targets of currently approved therapies, such as statins and PCSK9 inhibitors, the majority of the annotated genes at these loci encode for proteins involved in vessel wall function with no known drugs available. Importantly many of the associated genes linked to vascular (smooth muscle, endothelial, and macrophage) cell processes are now organized into distinct functional pathways, e.g., vasodilation, growth factor responses, extracellular matrix and plaque remodeling, and inflammation. In this mini-review, we highlight the most recently identified loci that have predicted roles in the vessel wall and provide genetic context for pre-existing therapies as well as new drug targets informed from GWAS. With the development of new modalities to target these pathways, (e.g., antisense oligonucleotides, CRISPR/Cas9, and RNA interference) as well as the computational frameworks to prioritize or reposition therapeutics, there is great opportunity to close the gap from initial genetic discovery to clinical translation for many patients affected by this common disease.
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BACKGROUND: The objectives were to evaluate the effectiveness of an infection control bundle in controlling the meticillin resistant Staphylococcus aureus (MRSA) transmission in residential care homes for the elderly (RCHEs) in Hong Kong. METHODS: This was a two-arm cluster randomised controlled trial. Infection control bundles focused on hand hygiene (HH), environmental hygiene, and modified contact precautions were applied to the intervention arm. Nasal swabs from residents; staff HH compliance and effectiveness; and environmental hygiene were assessed by microbiological sampling or observation at the baseline and quarterly after the intervention. RESULTS: A total of 2776 residents from 36 RCHEs were recruited. The overall MRSA prevalence was 20.4% (95% confidence interval, 18.9%-21.9%). The intervention elicited an immediate effect of 2.4% absolute decrease in the prevalence and 3.7% in the intra-facility transmission, though the difference between the two arms was insignificant. Staff HH compliance increased substantially from 5.9% to 45.6% post-intervention (p < 0.001). CONCLUSIONS: We initiated the infection control culture into the RCHEs and gained their acceptance. However, this behavioural change takes time to emerge. Our study shows that relying on the bundle alone could not bring sustainable MRSA reduction. Administrative control for strengthening infection control infrastructure is important for continuous compliance and improvement.
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The aim was to assess the self-efficacy and health outcomes of an adopted Arthritis Self-Management Programme (ASMP) among osteoarthritic knee sufferers in Hong Kong at 1 year. An experimental study with 95 participants assigned randomly to the intervention (n=45) or control group (n=50). Seventy-seven (81.1%) participants joined at least one out of three follow-ups in the 12 month period. Participants in the intervention group received a 6-week ASMP with an added exercise component in two general clinics. Outcome measures included arthritis self-efficacy (ASE) and health outcomes including pain and fatigue rating, self-rated health, daily activities limitation and number of unplanned arthritis-related medical consultations. Mean change (12 months minus baseline) and the effect size of the outcome measures were calculated by Mann-Whitney U test and nQuery Advisor 4.0. At 12 months, there were significant reductions of current pain (p=0.0001), pain at night (p=0.001), pain during walking (p=0.01) and number of unplanned arthritis-related medical consultations (p=0.03) and a significant increase in ASE for pain (p=0.01) and other symptoms (p=0.02) and self-rated health (p=0.04) among the intervention group but not for the control group. However, there were similarities in outcome measures of pain while switching from a sitting to a standing position, fatigue rating and physical functional limitation (p=0.15; p=0.22 and p=0.91, respectively) for both groups. Our findings add to the evidence that the modified arthritis empowering programme improved perception of control of osteoarthritis and three health outcomes after 12 months of treatment.