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Mangum KD, Li Q, Bauer TM, Wolf SJ, Shadiow J, Moon JY, Barrett EC, Joshi AD, Ahmed Z, Wasikowski R, Boyer K, Obi AT, Davis FM, Chang L, Tsoi LC, Gudjonsson J, Gallagher KA. Epigenetic Alteration of Smooth Muscle Cells Regulates Endothelin-Dependent Blood Pressure and Hypertensive Arterial Remodeling. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.09.24310178. [PMID: 39040193 PMCID: PMC11261912 DOI: 10.1101/2024.07.09.24310178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Long-standing hypertension (HTN) affects multiple organ systems and leads to pathologic arterial remodeling, which is driven largely by smooth muscle cell (SMC) plasticity. Although genome wide association studies (GWAS) have identified numerous variants associated with changes in blood pressure in humans, only a small percentage of these variants actually cause HTN. In order to identify relevant genes important in SMC function in HTN, we screened three separate human GWAS and Mendelian randomization studies to identify SNPs located within non-coding gene regions, focusing on genes encoding epigenetic enzymes, as these have been recently identified to control SMC fate in cardiovascular disease. We identified SNPs rs62059712 and rs74480102 in the promoter of the human JMJD3 gene and show that the minor C allele increases JMJD3 transcription in SMCs via increased SP1 binding to the JMJD3 promoter. Using our novel SMC-specific Jmjd3-deficient murine model ( Jmjd3 flox/flox Myh11 CreERT ), we show that loss of Jmjd3 in SMCs results in HTN, mechanistically, due to decreased EDNRB expression and a compensatory increase in EDNRA expression. As a translational corollary, through single cell RNA-sequencing (scRNA-seq) of human arteries, we found strong correlation between JMJD3 and EDNRB expression in SMCs. Further, we identified that JMJD3 is required for SMC-specific gene expression, and loss of JMJD3 in SMCs in the setting of HTN results in increased arterial remodeling by promoting the SMC synthetic phenotype. Our findings link a HTN-associated human DNA variant with regulation of SMC plasticity, revealing therapeutic targets that may be used in the screening and/or personalized treatment of HTN.
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Nejad SH, Azzam O, Schlaich MP. Recent developments in the management of resistant hypertension: focus on endothelin receptor antagonists. Future Cardiol 2024:1-11. [PMID: 38953510 DOI: 10.1080/14796678.2024.2367390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
Resistant hypertension is characterized by the inability of guideline-recommended triple combination therapy to control blood pressure (BP) to target. It is associated with a significantly increased risk of adverse outcomes. Despite abundant preclinical evidence supporting the critical role of the endothelin pathway in resistant hypertension (RH), clinical implementation of endothelin antagonists for the treatment of hypertension was hindered by various factors. Recently, the novel dual endothelin-receptor antagonist aprocitentan was tested in individuals with resistant hypertension in the PRECISION trial and provided compelling evidence supporting both short and longer-term safety and clinically meaningful and sustained BP lowering efficacy. These findings resulted in the recent regulatory approval of aprocitentan by the FDA. Aprocitentan may be a particularly useful antihypertensive option for individuals with advanced age, chronic kidney disease, and albuminuria.
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Affiliation(s)
- Sayeh Heidari Nejad
- Dobney Hypertension Centre, Medical School - Royal Perth Hospital Unit & RPH Research Foundation, The University of Western Australia, Perth, Western Australia, Australia
| | - Omar Azzam
- Dobney Hypertension Centre, Medical School - Royal Perth Hospital Unit & RPH Research Foundation, The University of Western Australia, Perth, Western Australia, Australia
- Department of Nephrology, Royal Perth Hospital, Perth, Australia
| | - Markus P Schlaich
- Dobney Hypertension Centre, Medical School - Royal Perth Hospital Unit & RPH Research Foundation, The University of Western Australia, Perth, Western Australia, Australia
- Department of Nephrology, Royal Perth Hospital, Perth, Australia
- Department of Cardiology, Royal Perth Hospital, Perth, Australia
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Kiskin FN, Yang Y, Yang H, Zhang JZ. Cracking the code of the cardiovascular enigma: hPSC-derived endothelial cells unveil the secrets of endothelial dysfunction. J Mol Cell Cardiol 2024; 192:65-78. [PMID: 38761989 DOI: 10.1016/j.yjmcc.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Endothelial dysfunction is a central contributor to the development of most cardiovascular diseases and is characterised by the reduced synthesis or bioavailability of the vasodilator nitric oxide together with other abnormalities such as inflammation, senescence, and oxidative stress. The use of patient-specific and genome-edited human pluripotent stem cell-derived endothelial cells (hPSC-ECs) has shed novel insights into the role of endothelial dysfunction in cardiovascular diseases with strong genetic components such as genetic cardiomyopathies and pulmonary arterial hypertension. However, their utility in studying complex multifactorial diseases such as atherosclerosis, metabolic syndrome and heart failure poses notable challenges. In this review, we provide an overview of the different methods used to generate and characterise hPSC-ECs before comprehensively assessing their effectiveness in cardiovascular disease modelling and high-throughput drug screening. Furthermore, we explore current obstacles that will need to be overcome to unleash the full potential of hPSC-ECs in facilitating patient-specific precision medicine. Addressing these challenges holds great promise in advancing our understanding of intricate cardiovascular diseases and in tailoring personalised therapeutic strategies.
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Affiliation(s)
- Fedir N Kiskin
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Yuan Yang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Hao Yang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Joe Z Zhang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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4
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Biswas PK, Park J. Applications, challenges, and prospects of induced pluripotent stem cells for vascular disease. Mol Cells 2024; 47:100077. [PMID: 38825189 PMCID: PMC11260847 DOI: 10.1016/j.mocell.2024.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/04/2024] Open
Abstract
Vascular disease, including heart disease, stroke, and peripheral arterial disease, is one of the leading causes of death and disability and represents a significant global health issue. Since the development of human induced pluripotent stem cells (hiPSCs) in 2007, hiPSCs have provided unique and tremendous opportunities for studying human pathophysiology, disease modeling, and drug discovery in the field of regenerative medicine. In this review, we discuss vascular physiology and related diseases, the current methods for generating vascular cells (eg, endothelial cells, smooth muscle cells, and pericytes) from hiPSCs, and describe the opportunities and challenges to the clinical applications of vascular organoids, tissue-engineered blood vessels, and vessels-on-a-chip. We then explore how hiPSCs can be used to study and treat inherited vascular diseases and discuss the current challenges and future prospects. In the future, it will be essential to develop vascularized organoids or tissues that can simultaneously undergo shear stress and cyclic stretching. This development will not only increase their maturity and function but also enable effective and innovative disease modeling and drug discovery.
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Affiliation(s)
- Polash Kumar Biswas
- Department of Physiology, College of Medicine, Hallym University, Chuncheon-si, Gangwon-do 24252, South Korea
| | - Jinkyu Park
- Department of Physiology, College of Medicine, Hallym University, Chuncheon-si, Gangwon-do 24252, South Korea; Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale School of Medicine, New Haven, CT 06511, USA.
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5
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Katz AE, Gupte T, Ganesh SK. From Atherosclerosis to Spontaneous Coronary Artery Dissection: Defining a Clinical and Genetic Risk Spectrum for Myocardial Infarction. Curr Atheroscler Rep 2024; 26:331-340. [PMID: 38761354 DOI: 10.1007/s11883-024-01208-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2024] [Indexed: 05/20/2024]
Abstract
PURPOSE OF REVIEW Spontaneous coronary artery dissection (SCAD) has been increasingly recognized as a significant cause of acute myocardial infarction (AMI) in young and middle-aged women and arises through mechanisms independent of atherosclerosis. SCAD has a multifactorial etiology that includes environmental, individual, and genetic factors distinct from those typically associated with coronary artery disease. Here, we summarize the current understanding of the genetic factors contributing to the development of SCAD and highlight those factors which differentiate SCAD from atherosclerotic coronary artery disease. RECENT FINDINGS Recent studies have revealed several associated variants with varying effect sizes for SCAD, giving rise to a complex genetic architecture. Associated genes highlight an important role for arterial cells and their extracellular matrix in the pathogenesis of SCAD, as well as notable genetic overlap between SCAD and other systemic arteriopathies such as fibromuscular dysplasia and vascular connective tissue diseases. Further investigation of individual variants (including in the associated gene PHACTR1) along with polygenic score analysis have demonstrated an inverse genetic relationship between SCAD and atherosclerosis as distinct causes of AMI. SCAD represents an increasingly recognized cause of AMI with opposing clinical and genetic risk factors from that of AMI due to atherosclerosis, and it is often associated with complex underlying genetic conditions. Genetic study of SCAD on a larger scale and with more diverse cohorts will not only further our evolving understanding of a newly defined genetic spectrum for AMI, but it will also inform the clinical utility of integrating genetic testing in AMI prevention and management moving forward.
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Affiliation(s)
- Alexander E Katz
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Trisha Gupte
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Santhi K Ganesh
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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Hemerich D, Svenstrup V, Obrero VD, Preuss M, Moscati A, Hirschhorn JN, Loos RJF. An integrative framework to prioritize genes in more than 500 loci associated with body mass index. Am J Hum Genet 2024; 111:1035-1046. [PMID: 38754426 PMCID: PMC11179420 DOI: 10.1016/j.ajhg.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Obesity is a major risk factor for a myriad of diseases, affecting >600 million people worldwide. Genome-wide association studies (GWASs) have identified hundreds of genetic variants that influence body mass index (BMI), a commonly used metric to assess obesity risk. Most variants are non-coding and likely act through regulating genes nearby. Here, we apply multiple computational methods to prioritize the likely causal gene(s) within each of the 536 previously reported GWAS-identified BMI-associated loci. We performed summary-data-based Mendelian randomization (SMR), FINEMAP, DEPICT, MAGMA, transcriptome-wide association studies (TWASs), mutation significance cutoff (MSC), polygenic priority score (PoPS), and the nearest gene strategy. Results of each method were weighted based on their success in identifying genes known to be implicated in obesity, ranking all prioritized genes according to a confidence score (minimum: 0; max: 28). We identified 292 high-scoring genes (≥11) in 264 loci, including genes known to play a role in body weight regulation (e.g., DGKI, ANKRD26, MC4R, LEPR, BDNF, GIPR, AKT3, KAT8, MTOR) and genes related to comorbidities (e.g., FGFR1, ISL1, TFAP2B, PARK2, TCF7L2, GSK3B). For most of the high-scoring genes, however, we found limited or no evidence for a role in obesity, including the top-scoring gene BPTF. Many of the top-scoring genes seem to act through a neuronal regulation of body weight, whereas others affect peripheral pathways, including circadian rhythm, insulin secretion, and glucose and carbohydrate homeostasis. The characterization of these likely causal genes can increase our understanding of the underlying biology and offer avenues to develop therapeutics for weight loss.
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Affiliation(s)
- Daiane Hemerich
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Bristol Myers Squibb, Summit, NJ, USA
| | - Victor Svenstrup
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Virginia Diez Obrero
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arden Moscati
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Regeneron Genetics Center, Tarrytown, NY, USA
| | - Joel N Hirschhorn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Eltabbakh A, Khudair A, Khudair A, Fredericks S. Spontaneous coronary artery dissection and fibromuscular dysplasia: insights into recent developments. Front Cardiovasc Med 2024; 11:1409278. [PMID: 38883987 PMCID: PMC11176522 DOI: 10.3389/fcvm.2024.1409278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
Spontaneous coronary artery dissection (SCAD), an uncommon cause of acute coronary syndrome, continues to be a poorly understood disease predominantly affecting females. It is characterized by an abrupt separation in the coronary arterial wall due to intramural bleeding. Fibromuscular dysplasia (FMD) is a non-atherosclerotic arteriopathy manifesting in medium and small-sized arteries. It is a concomitant disease found among SCAD patients. In some studies, FMD prevalence in SCAD patients ranges between 25%-86%, which can be explained through varying screening techniques or modalities. The potential association has been elucidated in some studies; notably, not only has a genetic link been recently delineated between SCAD and FMD, but there is data to suggest that FMD not only can predispose to SCAD but can also be a potential predictor of its recurrence. However, a clear-cut correlation between the two has still not been established due to conflicting reports in the literature. To further dive into its pathology, it is crucial to highlight the importance of systematic screening in SCAD in order to identify associated risk factors and to be used as a method of FMD detection in such patients. Together, the two pathologies pose unique challenges in understanding its pathophysiology, diagnosis and management, as there is no clear evidence of a definitive treatment plan for patients with SCAD and FMD. A potentially beneficial modality of management is physical exercise, which is currently understudied in the long-term approach to treatment for patients with concomitant SCAD and FMD. Limited research in this field brings disadvantages to the understanding of the association between these two diseases, in order to give rise to better management recommendations. This mini-review aims to highlight the recent developments in the association between SCAD and FMD, its potential genetic association and some insights in screening, diagnosis, and management.
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Affiliation(s)
- Ayah Eltabbakh
- Department of Medicine, Royal College of Surgeons in Ireland-Bahrain, Busaiteen, Bahrain
| | - Ahmed Khudair
- Department of Medicine, Royal College of Surgeons in Ireland-Bahrain, Busaiteen, Bahrain
| | - Aiman Khudair
- Department of Medicine, Royal College of Surgeons in Ireland-Bahrain, Busaiteen, Bahrain
| | - Salim Fredericks
- Department of Medicine, Royal College of Surgeons in Ireland-Bahrain, Busaiteen, Bahrain
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Wang Y, Hu X, Wang X, Li L, Lou P, Liu Z. Exploring the Two-Way Link between Migraines and Venous Thromboembolism: A Bidirectional Two-Sample Mendelian Randomization Study. Thromb Haemost 2024. [PMID: 38657649 DOI: 10.1055/a-2313-0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
BACKGROUND The objective of this study is to utilize Mendelian randomization to scrutinize the mutual causality between migraine and venous thromboembolism (VTE) thereby addressing the heterogeneity and inconsistency that were observed in prior observational studies concerning the potential interrelation of the two conditions. METHODS Employing a bidirectional Mendelian randomization approach, the study explored the link between migraine and VTE, incorporating participants of European descent from a large-scale meta-analysis. An inverse-variance weighted (IVW) regression model, with random-effects, leveraging single nucleotide polymorphisms (SNPs) as instrumental variables was utilized to endorse the mutual causality between migraine and VTE. SNP heterogeneity was evaluated using Cochran's Q-test and to account for multiple testing, correction was implemented using the intercept of the MR-Egger method, and a leave-one-out analysis. RESULTS The IVW model unveiled a statistically considerable causal link between migraine and the development of VTE (odds ratio [OR] = 96.155, 95% confidence interval [CI]: 4.342-2129.458, p = 0.004), implying that migraine poses a strong risk factor for VTE development. Conversely, both IVW and simple model outcomes indicated that VTE poses as a weaker risk factor for migraine (IVW OR = 1.002, 95% CI: 1.000-1.004, p = 0.016). The MR-Egger regression analysis denoted absence of evidence for genetic pleiotropy among the SNPs while the durability of our Mendelian randomization results was vouched by the leave-one-out sensitivity analysis. CONCLUSION The findings of this Mendelian randomization assessment provide substantiation for a reciprocal causative association between migraine and VTE within the European population.
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Affiliation(s)
- Yang Wang
- Vascular Surgery, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Xiaofang Hu
- Department of Neurology, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Xiaoqing Wang
- Interventional Department, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Lili Li
- Interventional Department, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Peng Lou
- Vascular Surgery, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Zhaoxuan Liu
- Vascular Surgery, Shandong First Medical University affiliated Central Hospital, Jinan, China
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Zalaquett NG, Salameh E, Kim JM, Ghanbarian E, Tawk K, Abouzari M. The Dawn and Advancement of the Knowledge of the Genetics of Migraine. J Clin Med 2024; 13:2701. [PMID: 38731230 PMCID: PMC11084801 DOI: 10.3390/jcm13092701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Background: Migraine is a prevalent episodic brain disorder known for recurrent attacks of unilateral headaches, accompanied by complaints of photophobia, phonophobia, nausea, and vomiting. Two main categories of migraine are migraine with aura (MA) and migraine without aura (MO). Main body: Early twin and population studies have shown a genetic basis for these disorders, and efforts have been invested since to discern the genes involved. Many techniques, including candidate-gene association studies, loci linkage studies, genome-wide association, and transcription studies, have been used for this goal. As a result, several genes were pinned with concurrent and conflicting data among studies. It is important to understand the evolution of techniques and their findings. Conclusions: This review provides a chronological understanding of the different techniques used from the dawn of migraine genetic investigations and the genes linked with the migraine subtypes.
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Affiliation(s)
- Nader G. Zalaquett
- Faculty of Medicine, American University of Beirut, Beirut 1107, Lebanon
| | - Elio Salameh
- Faculty of Medicine, American University of Beirut, Beirut 1107, Lebanon
| | - Jonathan M. Kim
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, CA 92697, USA
| | - Elham Ghanbarian
- Department of Neurology, University of California, Irvine, CA 92617, USA
| | - Karen Tawk
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, CA 92697, USA
| | - Mehdi Abouzari
- Department of Otolaryngology-Head and Neck Surgery, University of California, Irvine, CA 92697, USA
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Tremmel R, Martínez Pereyra V, Broders I, Schaeffeler E, Hoffmann P, Nöthen MM, Bekeredjian R, Sechtem U, Schwab M, Ong P. Genetic associations of cardiovascular risk genes in European patients with coronary artery spasm. Clin Res Cardiol 2024:10.1007/s00392-024-02446-x. [PMID: 38635033 DOI: 10.1007/s00392-024-02446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Coronary artery spasm (CAS) is a frequent finding in patients presenting with angina pectoris. Although the pathogenesis of CAS is incompletely understood, previous studies suggested a genetic contribution. Our study aimed to elucidate genetic variants in a cohort of European patients with angina and unobstructed coronary arteries who underwent acetylcholine (ACh) provocation testing. METHODS A candidate association analysis of 208 genes previously associated with cardiovascular conditions was performed using genotyped and imputed variants in patients grouped in epicardial (focal, diffuse) CAS (n = 119) and microvascular CAS (n = 87). Patients with a negative ACh test result (n = 45) served as controls. RESULTS We found no association below the genome-wide significance threshold of p < 5 × 10-8, thus not confirming variants in ALDH2, NOS3, and ROCK2 previously reported in CAS patients of Asian ancestry. However, the analysis identified suggestive associations (p < 10-05) for the groups of focal epicardial CAS (CDH13) and diffuse epicardial CAS (HDAC9, EDN1). Downstream analysis of the potential EDN1 risk locus showed that CAS patients have significantly increased plasma endothelin-1 levels (ET-1) compared to controls. An EDN1 haplotype comprising rs9349379 and rs2070698 was significantly associated to ET-1 levels (p = 0.01). CONCLUSIONS In summary, we suggest EDN1 as potential genetic risk loci for patients with diffuse epicardial CAS, and European ancestry. Plasma ET-1 levels may serve as a potential cardiac marker.
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Affiliation(s)
- Roman Tremmel
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Valeria Martínez Pereyra
- Department of Cardiology and Angiology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Incifer Broders
- Department of Cardiology and Angiology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Raffi Bekeredjian
- Department of Cardiology and Angiology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Udo Sechtem
- Department of Cardiology and Angiology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- Departments of Clinical Pharmacology, and Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
- University of Tübingen, Tübingen, Germany
| | - Peter Ong
- Department of Cardiology and Angiology, Robert-Bosch-Hospital, Auerbachstr. 110, 70376, Stuttgart, Germany.
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11
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Alireza Z, Maleeha M, Kaikkonen M, Fortino V. Enhancing prediction accuracy of coronary artery disease through machine learning-driven genomic variant selection. J Transl Med 2024; 22:356. [PMID: 38627847 PMCID: PMC11020205 DOI: 10.1186/s12967-024-05090-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Machine learning (ML) methods are increasingly becoming crucial in genome-wide association studies for identifying key genetic variants or SNPs that statistical methods might overlook. Statistical methods predominantly identify SNPs with notable effect sizes by conducting association tests on individual genetic variants, one at a time, to determine their relationship with the target phenotype. These genetic variants are then used to create polygenic risk scores (PRSs), estimating an individual's genetic risk for complex diseases like cancer or cardiovascular disorders. Unlike traditional methods, ML algorithms can identify groups of low-risk genetic variants that improve prediction accuracy when combined in a mathematical model. However, the application of ML strategies requires addressing the feature selection challenge to prevent overfitting. Moreover, ensuring the ML model depends on a concise set of genomic variants enhances its clinical applicability, where testing is feasible for only a limited number of SNPs. In this study, we introduce a robust pipeline that applies ML algorithms in combination with feature selection (ML-FS algorithms), aimed at identifying the most significant genomic variants associated with the coronary artery disease (CAD) phenotype. The proposed computational approach was tested on individuals from the UK Biobank, differentiating between CAD and non-CAD individuals within this extensive cohort, and benchmarked against standard PRS-based methodologies like LDpred2 and Lassosum. Our strategy incorporates cross-validation to ensure a more robust evaluation of genomic variant-based prediction models. This method is commonly applied in machine learning strategies but has often been neglected in previous studies assessing the predictive performance of polygenic risk scores. Our results demonstrate that the ML-FS algorithm can identify panels with as few as 50 genetic markers that can achieve approximately 80% accuracy when used in combination with known risk factors. The modest increase in accuracy over PRS performances is noteworthy, especially considering that PRS models incorporate a substantially larger number of genetic variants. This extensive variant selection can pose practical challenges in clinical settings. Additionally, the proposed approach revealed novel CAD-genetic variant associations.
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Affiliation(s)
- Z Alireza
- Institute of Biomedicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - M Maleeha
- Institute of Biomedicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - M Kaikkonen
- A.I.Virtanen Institute, University of Eastern Finland, 70210, Kuopio, Finland
| | - V Fortino
- Institute of Biomedicine, University of Eastern Finland, 70210, Kuopio, Finland.
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12
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Schiffrin EL, Pollock DM. Endothelin System in Hypertension and Chronic Kidney Disease. Hypertension 2024; 81:691-701. [PMID: 38059359 PMCID: PMC10954415 DOI: 10.1161/hypertensionaha.123.21716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
ET (endothelin) is a powerful vasoconstrictor 21-amino acid peptide present in many tissues, which exerts many physiological functions across the body and participates as a mediator in many pathological conditions. ETs exert their effects through ETA and ETB receptors, which can be blocked by selective receptor antagonists. ETs were shown to play important roles among others, in systemic hypertension, particularly when resistant or difficult to control, and in pulmonary hypertension, atherosclerosis, cardiac hypertrophy, subarachnoid hemorrhage, chronic kidney disease, diabetic cardiovascular disease, scleroderma, some cancers, etc. To date, ET antagonists are only approved for the treatment of primary pulmonary hypertension and recently for IgA nephropathy and used in the treatment of digital ulcers in scleroderma. However, they may soon be approved for the treatment of patients with resistant hypertension and different types of nephropathy. Here, the role of ETs is reviewed with a special emphasis on participation in and treatment of hypertension and chronic kidney disease.
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Affiliation(s)
- Ernesto L. Schiffrin
- Lady Davis Institute for Medical Research, and Department of Medicine, Sir Mortimer B. Davis-Jewish General Hospital, McGill University
| | - David M. Pollock
- Section of Cardio-Renal Physiology and Medicine, Department of Medicine, Division of Nephrology, University of Alabama at Birmingham, Birmingham, AL
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13
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Pepin ME, Gupta RM. The Role of Endothelial Cells in Atherosclerosis: Insights from Genetic Association Studies. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:499-509. [PMID: 37827214 PMCID: PMC10988759 DOI: 10.1016/j.ajpath.2023.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
Endothelial cells (ECs) mediate several biological functions that are relevant to atherosclerosis and coronary artery disease (CAD), regulating an array of vital processes including vascular tone, wound healing, reactive oxygen species, shear stress response, and inflammation. Although which of these functions is linked causally with CAD development and/or progression is not yet known, genome-wide association studies have implicated more than 400 loci associated with CAD risk, among which several have shown EC-relevant functions. Given the arduous process of mechanistically interrogating single loci to CAD, high-throughput variant characterization methods, including pooled Clustered Regularly Interspaced Short Palindromic Repeats screens, offer exciting potential to rapidly accelerate the discovery of bona fide EC-relevant genetic loci. These discoveries in turn will broaden the therapeutic avenues for CAD beyond lipid lowering and behavioral risk modification to include EC-centric modalities of risk prevention and treatment.
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Affiliation(s)
- Mark E Pepin
- Cardiovascular Disease Initiative, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Divisions of Genetics and Cardiovascular Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Rajat M Gupta
- Cardiovascular Disease Initiative, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts; Divisions of Genetics and Cardiovascular Medicine, Brigham & Women's Hospital, Boston, Massachusetts.
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14
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Li J, Zhu J, Gray O, Sobreira DR, Wu D, Huang RT, Miao B, Sakabe NJ, Krause MD, Kaikkonen MU, Romanoski CE, Nobrega MA, Fang Y. Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells. J Cell Biol 2024; 223:e202211125. [PMID: 38231044 PMCID: PMC10794123 DOI: 10.1083/jcb.202211125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 10/05/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Vascular homeostasis and pathophysiology are tightly regulated by mechanical forces generated by hemodynamics. Vascular disorders such as atherosclerotic diseases largely occur at curvatures and bifurcations where disturbed blood flow activates endothelial cells while unidirectional flow at the straight part of vessels promotes endothelial health. Integrated analysis of the endothelial transcriptome, the 3D epigenome, and human genetics systematically identified the SNP-enriched cistrome in vascular endothelium subjected to well-defined atherosclerosis-prone disturbed flow or atherosclerosis-protective unidirectional flow. Our results characterized the endothelial typical- and super-enhancers and underscored the critical regulatory role of flow-sensitive endothelial super-enhancers. CRISPR interference and activation validated the function of a previously unrecognized unidirectional flow-induced super-enhancer that upregulates antioxidant genes NQO1, CYB5B, and WWP2, and a disturbed flow-induced super-enhancer in endothelium which drives prothrombotic genes EDN1 and HIVEP in vascular endothelium. Our results employing multiomics identify the cis-regulatory architecture of the flow-sensitive endothelial epigenome related to atherosclerosis and highlight the regulatory role of super-enhancers in mechanotransduction mechanisms.
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Affiliation(s)
- Jin Li
- Committee on Molecular Metabolism and Nutrition, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Jiayu Zhu
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Olivia Gray
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Débora R. Sobreira
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - David Wu
- Committee on Molecular Metabolism and Nutrition, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Ru-Ting Huang
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Bernadette Miao
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Noboru J. Sakabe
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Matthew D. Krause
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Minna U. Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Casey E. Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Marcelo A. Nobrega
- Department of Human Genetics, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
| | - Yun Fang
- Committee on Molecular Metabolism and Nutrition, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Department of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL, USA
- Committee on Molecular Medicine, The University of Chicago, Chicago, IL, USA
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15
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Stein AP, Harder J, Holmes HR, Merz CNB, Pepine CJ, Keeley EC. Single Nucleotide Polymorphisms in Coronary Microvascular Dysfunction. J Am Heart Assoc 2024; 13:e032137. [PMID: 38348798 PMCID: PMC11010085 DOI: 10.1161/jaha.123.032137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/09/2024] [Indexed: 02/21/2024]
Abstract
Coronary microvascular dysfunction is an underdiagnosed pathologic process that is associated with adverse clinical outcomes. There are data to suggest that coronary microvascular dysfunction, in some cases, may be genetically determined. We present an updated review of single nucleotide polymorphisms in coronary microvascular dysfunction.
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Affiliation(s)
| | | | | | - C. Noel Bairey Merz
- Barbra Streisand Women’s Heart CenterSmidt Heart Institute, Cedars‐Sinai Medical CenterLos AngelesCAUSA
| | - Carl J. Pepine
- Department of MedicineUniversity of FloridaGainesvilleFLUSA
- Division of Cardiovascular MedicineUniversity of FloridaGainesvilleFLUSA
| | - Ellen C. Keeley
- Department of MedicineUniversity of FloridaGainesvilleFLUSA
- Division of Cardiovascular MedicineUniversity of FloridaGainesvilleFLUSA
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16
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Castillejo-López C, Bárcenas-Walls JR, Cavalli M, Larsson A, Wadelius C. A regulatory element associated to NAFLD in the promoter of DIO1 controls LDL-C, HDL-C and triglycerides in hepatic cells. Lipids Health Dis 2024; 23:48. [PMID: 38365720 PMCID: PMC10870585 DOI: 10.1186/s12944-024-02029-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified genetic variants linked to fat metabolism and related traits, but rarely pinpoint causative variants. This limitation arises from GWAS not considering functional implications of noncoding variants that can affect transcription factor binding and potentially regulate gene expression. The aim of this study is to investigate a candidate noncoding functional variant within a genetic locus flagged by a GWAS SNP associated with non-alcoholic fatty liver disease (NAFLD), a condition characterized by liver fat accumulation in non-alcohol consumers. METHODS CRISPR-Cas9 gene editing in HepG2 cells was used to modify the regulatory element containing the candidate functional variant linked to NAFLD. Global gene expression in mutant cells was assessed through RT-qPCR and targeted transcriptomics. A phenotypic assay measured lipid droplet accumulation in the CRISPR-Cas9 mutants. RESULTS The candidate functional variant, rs2294510, closely linked to the NAFLD-associated GWAS SNP rs11206226, resided in a regulatory element within the DIO1 gene's promoter region. Altering this element resulted in changes in transcription factor binding sites and differential expression of candidate target genes like DIO1, TMEM59, DHCR24, and LDLRAD1, potentially influencing the NAFLD phenotype. Mutant HepG2 cells exhibited increased lipid accumulation, a hallmark of NAFLD, along with reduced LDL-C, HDL-C and elevated triglycerides. CONCLUSIONS This comprehensive approach, that combines genome editing, transcriptomics, and phenotypic assays identified the DIO1 promoter region as a potential enhancer. Its activity could regulate multiple genes involved in the NAFLD phenotype or contribute to defining a polygenic risk score for enhanced risk assessment in NAFLD patients.
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Affiliation(s)
- Casimiro Castillejo-López
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC
| | - José Ramón Bárcenas-Walls
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University Hospital, 751 85, Uppsala, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 751 08 , Uppsala, Sweden, Box 815, Husargatan 3, BMC.
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17
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Zhang Y, Gao Y, Li F, Qi Q, Li Q, Gu Y, Zheng Z, Hu B, Wang T, Zhang E, Xu H, Liu L, Tian T, Jin G, Yan C. Long non-coding RNA NRAV in the 12q24.31 risk locus drives gastric cancer development through glucose metabolism reprogramming. Carcinogenesis 2024; 45:23-34. [PMID: 37950445 DOI: 10.1093/carcin/bgad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/24/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) serve as vital candidates to mediate cancer risk. Here, we aimed to identify the risk single-nucleotide polymorphisms (SNPs)-induced lncRNAs and to investigate their roles in gastric cancer (GC) development. Through integrating the differential expression analysis of lncRNAs in GC tissues and expression quantitative trait loci analysis in normal stomach tissues and GC tissues, as well as genetic association analysis based on GC genome-wide association studies and an independent validation study, we identified four lncRNA-related SNPs consistently associated with GC risk, including SNHG7 [odds ratio (OR) = 1.16, 95% confidence interval (CI): 1.09-1.23], NRAV (OR = 1.11, 95% CI: 1.05-1.17), LINC01082 (OR = 1.16, 95% CI: 1.08-1.22) and FENDRR (OR = 1.16, 95% CI: 1.07-1.25). We further found that a functional SNP rs6489786 at 12q24.31 increases binding of MEOX1 or MEOX2 at a distal enhancer and results in up-regulation of NRAV. The functional assays revealed that NRAV accelerates GC cell proliferation while inhibits GC cell apoptosis. Mechanistically, NRAV decreases the expression of key subunit genes through the electron transport chain, thereby driving the glucose metabolism reprogramming from aerobic respiration to glycolysis. These findings suggest that regulating lncRNA expression is a crucial mechanism for risk-associated variants in promoting GC development.
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Affiliation(s)
- Yan Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Yun Gao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Fengyuan Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Qi
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qian Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuanliang Gu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhonghua Zheng
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Beiping Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tianpei Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Public Health Institute of Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Liu
- Institute of Digestive Endoscopy, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
- Public Health Institute of Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
- Research Center for Clinical Oncology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Immunology, Key Laboratory of Immunological Environment and Disease, Nanjing Medical University, Nanjing, China
- The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Wuxi, China
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18
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Boye C, Kalita CA, Findley AS, Alazizi A, Wei J, Wen X, Pique-Regi R, Luca F. Characterization of caffeine response regulatory variants in vascular endothelial cells. eLife 2024; 13:e85235. [PMID: 38334359 PMCID: PMC10901511 DOI: 10.7554/elife.85235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/08/2024] [Indexed: 02/10/2024] Open
Abstract
Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype-environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 6 variants that regulate the gene expression response to caffeine (GxE, false discovery rate [FDR] < 5%). When overlapping our GxE results with expression quantitative trait loci colocalized with coronary artery disease and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Anthony S Findley
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
- Department of Biology, University of Rome Tor VergataRomeItaly
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19
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Verma G, Rebholz-Schuhmann D, Madden MG. Enabling personalised disease diagnosis by combining a patient's time-specific gene expression profile with a biomedical knowledge base. BMC Bioinformatics 2024; 25:62. [PMID: 38326757 PMCID: PMC10848462 DOI: 10.1186/s12859-024-05674-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/25/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Recent developments in the domain of biomedical knowledge bases (KBs) open up new ways to exploit biomedical knowledge that is available in the form of KBs. Significant work has been done in the direction of biomedical KB creation and KB completion, specifically, those having gene-disease associations and other related entities. However, the use of such biomedical KBs in combination with patients' temporal clinical data still largely remains unexplored, but has the potential to immensely benefit medical diagnostic decision support systems. RESULTS We propose two new algorithms, LOADDx and SCADDx, to combine a patient's gene expression data with gene-disease association and other related information available in the form of a KB, to assist personalized disease diagnosis. We have tested both of the algorithms on two KBs and on four real-world gene expression datasets of respiratory viral infection caused by Influenza-like viruses of 19 subtypes. We also compare the performance of proposed algorithms with that of five existing state-of-the-art machine learning algorithms (k-NN, Random Forest, XGBoost, Linear SVM, and SVM with RBF Kernel) using two validation approaches: LOOCV and a single internal validation set. Both SCADDx and LOADDx outperform the existing algorithms when evaluated with both validation approaches. SCADDx is able to detect infections with up to 100% accuracy in the cases of Datasets 2 and 3. Overall, SCADDx and LOADDx are able to detect an infection within 72 h of infection with 91.38% and 92.66% average accuracy respectively considering all four datasets, whereas XGBoost, which performed best among the existing machine learning algorithms, can detect the infection with only 86.43% accuracy on an average. CONCLUSIONS We demonstrate how our novel idea of using the most and least differentially expressed genes in combination with a KB can enable identification of the diseases that a patient is most likely to have at a particular time, from a KB with thousands of diseases. Moreover, the proposed algorithms can provide a short ranked list of the most likely diseases for each patient along with their most affected genes, and other entities linked with them in the KB, which can support health care professionals in their decision-making.
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Affiliation(s)
- Ghanshyam Verma
- Insight Centre for Data Analytics, School of Computer Science, University of Galway, Galway, Ireland.
- School of Computer Science, University of Galway, Galway, Ireland.
| | | | - Michael G Madden
- Insight Centre for Data Analytics, School of Computer Science, University of Galway, Galway, Ireland
- School of Computer Science, University of Galway, Galway, Ireland
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20
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Fatima L, Goyal A, Yakkali S, Jain H, Raza FA, Peer T, Kanagala SG, Sohail AH, Malik J. Precision medicine in Myocardial Infarction With Non-obstructive Coronary Disease (MINOCA): A comprehensive review. Curr Probl Cardiol 2024; 49:102185. [PMID: 37925046 DOI: 10.1016/j.cpcardiol.2023.102185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023]
Abstract
Cardiovascular diseases, particularly myocardial infarction (MI), are a significant cause of mortality globally. Traditional MIs are commonly linked to substantial coronary artery blockage. However, a distinct subset of patients experience MI with non-obstructive coronary arteries, known as MINOCA. Imaging techniques, such as invasive coronary angiograms, are employed to diagnose MI or assess predisposition to one. Coronary angiograms help visualize vessel blockages; however, these blockages are absent in MINOCA cases, posing a diagnostic challenge. Precision medicine aims to introduce new diagnostic tools to assist in early diagnosis and further management of MINOCA. As percutaneous coronary intervention (PCI) does not benefit MINOCA patients, medical management tailored to the specific pathophysiological mechanism of MINOCA is employed. For example, if MINOCA is attributed to plaque disruption with or without plaque thrombus formation, the fundamental treatments may include statins, agents that modulate the renin-angiotensin system (RAS), and antiplatelet therapies. On the other hand, if coronary artery spasm is identified as the primary cause, essential intervention involves the use of calcium channel blockers. This approach has been previously utilized in patients with vasospastic angina and could be utilized in MINOCA, although research specific to MINOCA is ongoing. Therefore, the handling of MINOCA underscores the necessity for a tailored therapeutic strategy that corresponds to the underlying physiological mechanism responsible for the patient's clinical symptoms. Ongoing research initiatives are directed at expanding the availability of these treatments, uncovering new biomarkers, creating advanced diagnostic instruments, and establishing a more individualized approach for managing MINOCA patients.
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Affiliation(s)
- Laveeza Fatima
- Department of Internal Medicine, Allama Iqbal Medical College, Lahore, Pakistan.
| | - Aman Goyal
- Department of Internal Medicine, Seth GS Medical College and KEM Hospital, Mumbai, India
| | - Shreyas Yakkali
- Department of Internal Medicine, Jacobi Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA
| | - Hritvik Jain
- All India Institute of Medical Sciences (AIIMS)-Jodhpur, Jodhpur, Rajasthan, India
| | - Fatima Ali Raza
- Department of Internal Medicine, Karachi Medical and Dental College, Karachi, Pakistan
| | - Taha Peer
- Undergraduate student, University of California Los Angeles (UCLA), California, LA, USA
| | - Sai Gautham Kanagala
- Department of Internal Medicine, Metropolitan Hospital Center, NY, New York, USA
| | - Amir H Sohail
- Department of Surgery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jahanzeb Malik
- Department of Cardiovascular Medicine, Cardiovascular Analytics Group, Islamabad, Pakistan
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21
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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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22
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Schnitzler GR, Kang H, Fang S, Angom RS, Lee-Kim VS, Ma XR, Zhou R, Zeng T, Guo K, Taylor MS, Vellarikkal SK, Barry AE, Sias-Garcia O, Bloemendal A, Munson G, Guckelberger P, Nguyen TH, Bergman DT, Hinshaw S, Cheng N, Cleary B, Aragam K, Lander ES, Finucane HK, Mukhopadhyay D, Gupta RM, Engreitz JM. Convergence of coronary artery disease genes onto endothelial cell programs. Nature 2024; 626:799-807. [PMID: 38326615 PMCID: PMC10921916 DOI: 10.1038/s41586-024-07022-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Linking variants from genome-wide association studies (GWAS) to underlying mechanisms of disease remains a challenge1-3. For some diseases, a successful strategy has been to look for cases in which multiple GWAS loci contain genes that act in the same biological pathway1-6. However, our knowledge of which genes act in which pathways is incomplete, particularly for cell-type-specific pathways or understudied genes. Here we introduce a method to connect GWAS variants to functions. This method links variants to genes using epigenomics data, links genes to pathways de novo using Perturb-seq and integrates these data to identify convergence of GWAS loci onto pathways. We apply this approach to study the role of endothelial cells in genetic risk for coronary artery disease (CAD), and discover 43 CAD GWAS signals that converge on the cerebral cavernous malformation (CCM) signalling pathway. Two regulators of this pathway, CCM2 and TLNRD1, are each linked to a CAD risk variant, regulate other CAD risk genes and affect atheroprotective processes in endothelial cells. These results suggest a model whereby CAD risk is driven in part by the convergence of causal genes onto a particular transcriptional pathway in endothelial cells. They highlight shared genes between common and rare vascular diseases (CAD and CCM), and identify TLNRD1 as a new, previously uncharacterized member of the CCM signalling pathway. This approach will be widely useful for linking variants to functions for other common polygenic diseases.
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Affiliation(s)
- Gavin R Schnitzler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Helen Kang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Shi Fang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ramcharan S Angom
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL, USA
| | - Vivian S Lee-Kim
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - X Rosa Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Ronghao Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Tony Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Katherine Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Shamsudheen K Vellarikkal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Aurelie E Barry
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Oscar Sias-Garcia
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
| | - Glen Munson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Tung H Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Drew T Bergman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Stephen Hinshaw
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan Cheng
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brian Cleary
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Faculty of Computing and Data Sciences, Departments of Biology and Biomedical Engineering, Biological Design Center, and Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Krishna Aragam
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL, USA
| | - Rajat M Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA.
- Divisions of Genetics and Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
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23
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Quertermous T, Li DY, Weldy CS, Ramste M, Sharma D, Monteiro JP, Gu W, Worssam MD, Palmisano BT, Park CY, Cheng P. Genome-Wide Genetic Associations Prioritize Evaluation of Causal Mechanisms of Atherosclerotic Disease Risk. Arterioscler Thromb Vasc Biol 2024; 44:323-327. [PMID: 38266112 PMCID: PMC10857784 DOI: 10.1161/atvbaha.123.319480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/28/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE The goal of this review is to discuss the implementation of genome-wide association studies to identify causal mechanisms of vascular disease risk. APPROACH AND RESULTS The history of genome-wide association studies is described, the use of imputation and the creation of consortia to conduct meta-analyses with sufficient power to arrive at consistent associated loci for vascular disease. Genomic methods are described that allow the identification of causal variants and causal genes and how they impact the disease process. The power of single-cell analyses to promote genome-wide association studies of causal gene function is described. CONCLUSIONS Genome-wide association studies represent a paradigm shift in the study of cardiovascular disease, providing identification of genes, cellular phenotypes, and disease pathways that empower the future of targeted drug development.
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Affiliation(s)
- Thomas Quertermous
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Daniel Yuhang Li
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Chad S Weldy
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Markus Ramste
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Disha Sharma
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - João P Monteiro
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Wenduo Gu
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Matthew D Worssam
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Brian T Palmisano
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Chong Y Park
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
| | - Paul Cheng
- Division of Cardiovascular Medicine, Stanford University School of Medicine, CA
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24
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Zhu QM, Hsu YHH, Lassen FH, MacDonald BT, Stead S, Malolepsza E, Kim A, Li T, Mizoguchi T, Schenone M, Guzman G, Tanenbaum B, Fornelos N, Carr SA, Gupta RM, Ellinor PT, Lage K. Protein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease. Commun Biol 2024; 7:87. [PMID: 38216744 PMCID: PMC10786878 DOI: 10.1038/s42003-023-05705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interaction proteomics for 11 CAD-risk genes to map their protein-protein interactions (PPIs) in human vascular cells and elucidate their roles in CAD. The resulting PPI networks contain interactions that are outside of known biology in the vasculature and are enriched for genes involved in immunity-related and arterial-wall-specific mechanisms. Several PPI networks derived from smooth muscle cells are significantly enriched for genetic variants associated with CAD and related vascular phenotypes. Furthermore, the networks identify 61 genes that are found in genetic loci associated with risk of CAD, prioritizing them as the causal candidates within these loci. These findings indicate that the PPI networks we have generated are a rich resource for guiding future research into the molecular pathogenesis of CAD.
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Affiliation(s)
- Qiuyu Martin Zhu
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Yu-Han H Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Frederik H Lassen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bryan T MacDonald
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie Stead
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edyta Malolepsza
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taibo Li
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Taiji Mizoguchi
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Monica Schenone
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaelen Guzman
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Tanenbaum
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rajat M Gupta
- Divisions of Cardiovascular Medicine and Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative & Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
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25
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Shrestha S, Wiener HW, Kajimoto H, Srinivasasainagendra V, Ledee D, Chowdhury S, Cui J, Chen JY, Beckley MA, Padilla LA, Dahdah N, Tiwari HK, Portman MA. Pharmacogenomics of intravenous immunoglobulin response in Kawasaki disease. Front Immunol 2024; 14:1287094. [PMID: 38259468 PMCID: PMC10800400 DOI: 10.3389/fimmu.2023.1287094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Kawasaki disease (KD) is a diffuse vasculitis in children. Response to high dose intravenous gamma globulin (IVIG), the primary treatment, varies according to genetic background. We sought to identify genetic loci, which associate with treatment response using whole genome sequencing (WGS). Method We performed WGS in 472 KD patients with 305 IVIG responders and 167 non-responders defined by AHA clinical criteria. We conducted logistic regression models to test additive genetic effect in the entire cohort and in four subgroups defined by ancestry information markers (Whites, African Americans, Asians, and Hispanics). We performed functional mapping and annotation using FUMA to examine genetic variants that are potentially involved IVIG non-response. Further, we conducted SNP-set [Sequence] Kernel Association Test (SKAT) for all rare and common variants. Results Of the 43,288,336 SNPs (23,660,970 in intergenic regions, 16,764,594 in introns and 556,814 in the exons) identified, the top ten hits associated with IVIG non-response were in FANK1, MAP2K3:KCNJ12, CA10, FRG1DP, CWH43 regions. When analyzed separately in ancestry-based racial subgroups, SNPs in several novel genes were associated. A total of 23 possible causal genes were pinpointed by positional and chromatin mapping. SKAT analysis demonstrated association in the entire MANIA2, EDN1, SFMBT2, and PPP2R5E genes and segments of CSMD2, LINC01317, HIVEPI, HSP90AB1, and TTLL11 genes. Conclusions This WGS study identified multiple predominantly novel understudied genes associated with IVIG response. These data can serve to inform regarding pathogenesis of KD, as well as lay ground work for developing treatment response predictors.
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Affiliation(s)
- Sadeep Shrestha
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Howard W. Wiener
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hidemi Kajimoto
- Division of Cardiology, Seattle Children’s and University of Washington Department of Pediatrics, Seattle, WA, United States
| | - Vinodh Srinivasasainagendra
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Dolena Ledee
- Division of Cardiology, Seattle Children’s and University of Washington Department of Pediatrics, Seattle, WA, United States
| | - Sabrina Chowdhury
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jinhong Cui
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jake Y. Chen
- Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mikayla A Beckley
- Division of Cardiology, Seattle Children’s and University of Washington Department of Pediatrics, Seattle, WA, United States
| | - Luz A. Padilla
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nagib Dahdah
- CHU Ste-Justine, Universite de Montreal, Montreal, QC, Canada
| | - Hemant K. Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Michael A. Portman
- Division of Cardiology, Seattle Children’s and University of Washington Department of Pediatrics, Seattle, WA, United States
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26
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de Vries PS, Conomos MP, Singh K, Nicholson CJ, Jain D, Hasbani NR, Jiang W, Lee S, Lino Cardenas CL, Lutz SM, Wong D, Guo X, Yao J, Young EP, Tcheandjieu C, Hilliard AT, Bis JC, Bielak LF, Brown MR, Musharoff S, Clarke SL, Terry JG, Palmer ND, Yanek LR, Xu H, Heard-Costa N, Wessel J, Selvaraj MS, Li RH, Sun X, Turner AW, Stilp AM, Khan A, Newman AB, Rasheed A, Freedman BI, Kral BG, McHugh CP, Hodonsky C, Saleheen D, Herrington DM, Jacobs DR, Nickerson DA, Boerwinkle E, Wang FF, Heiss G, Jun G, Kinney GL, Sigurslid HH, Doddapaneni H, Hall IM, Bensenor IM, Broome J, Crapo JD, Wilson JG, Smith JA, Blangero J, Vargas JD, Mosquera JV, Smith JD, Viaud-Martinez KA, Ryan KA, Young KA, Taylor KD, Lange LA, Emery LS, Bittencourt MS, Budoff MJ, Montasser ME, Yu M, Mahaney MC, Mahamdeh MS, Fornage M, Franceschini N, Lotufo PA, Natarajan P, Wong Q, Mathias RA, Gibbs RA, Do R, Mehran R, Tracy RP, Kim RW, Nelson SC, Damrauer SM, Kardia SL, Rich SS, Fuster V, Napolioni V, Zhao W, Tian W, Yin X, Min YI, Manning AK, Peloso G, Kelly TN, O’Donnell CJ, Morrison AC, Curran JE, Zapol WM, Bowden DW, Becker LC, Correa A, Mitchell BD, Psaty BM, Carr JJ, Pereira AC, Assimes TL, Stitziel NO, Hokanson JE, Laurie CA, Rotter JI, Vasan RS, Post WS, Peyser PA, Miller CL, Malhotra R. Whole-genome sequencing uncovers two loci for coronary artery calcification and identifies ARSE as a regulator of vascular calcification. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1159-1172. [PMID: 38817323 PMCID: PMC11138106 DOI: 10.1038/s44161-023-00375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/25/2023] [Indexed: 06/01/2024]
Abstract
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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Affiliation(s)
- Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
| | - Matthew P. Conomos
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Kuldeep Singh
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Christopher J. Nicholson
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Deepti Jain
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Natalie R. Hasbani
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
| | - Wanlin Jiang
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Sujin Lee
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Sharon M. Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR)
Center, Department of Population Medicine, Harvard Medical School and Harvard
Pilgrim Health Care Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of
Public Health, Boston, MA, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia
School of Medicine, Charlottesville, VA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population
Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical
Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population
Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical
Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Erica P. Young
- Cardiovascular Division, Department of Internal Medicine,
Washington University School of Medicine, St. Louis, MO, USA
| | - Catherine Tcheandjieu
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of
Medicine, Stanford, CA, USA
| | - Austin T. Hilliard
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Palo Alto Veterans Institute for Research, Palo Alto, CA,
USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle, WA, USA
| | - Lawrence F. Bielak
- School of Public Health, Department of Epidemiology,
University of Michigan, Ann Arbor, MI, USA
| | - Michael R. Brown
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
| | - Shaila Musharoff
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Genetics, Stanford University School of
Medicine, Stanford, CA, USA
| | - Shoa L. Clarke
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of
Medicine, Stanford, CA, USA
| | - James G. Terry
- Department of Radiology, Vanderbilt Translational and
Clinical Cardiovascular Research Center, Vanderbilt University Medical Center,
Nashville, TN, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of
Medicine, Winston-Salem, NC, USA
| | - Lisa R. Yanek
- Division of General Internal Medicine, Department of
Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition,
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD,
USA
| | - Nancy Heard-Costa
- Boston University School of Medicine, Boston, MA,
USA
- Boston University and National Heart, Lung, and Blood
Institute’s Framingham Heart Study, Framingham, MA, USA
| | - Jennifer Wessel
- Department of Epidemiology, Fairbanks School of Public
Health, Indiana University, Indianapolis, IN, USA
- Diabetes Translational Research Center, Indiana
University, Indianapolis, IN, USA
| | - Margaret Sunitha Selvaraj
- Cardiovascular Research Center and Center for Genomic
Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad
Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston,
MA, USA
| | - Rebecca H. Li
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Xiao Sun
- School of Public Health and Tropical Medicine, Department
of Epidemiology, Tulane University, New Orleans, LA, USA
- College of Medicine, Department of Medicine, Division of
Nephrology, University of Illinois Chicago, Chicago, IL, USA
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia
School of Medicine, Charlottesville, VA, USA
| | - Adrienne M. Stilp
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Alyna Khan
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Anne B. Newman
- Department of Epidemiology, Graduate School of Public
Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asif Rasheed
- Center For Non-Communicable Diseases, Karachi,
Pakistan
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine,
Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Brian G. Kral
- Division of Cardiology, Department of Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD, USA
| | - Caitlin P. McHugh
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Chani Hodonsky
- Center for Public Health Genomics, University of Virginia
School of Medicine, Charlottesville, VA, USA
| | - Danish Saleheen
- Center For Non-Communicable Diseases, Karachi,
Pakistan
- Department of Medicine, Columbia University Irving
Medical Center, New York, NY, USA
- Department of Cardiology, Columbia University Irving
Medical Center, New York, NY, USA
| | - David M. Herrington
- Department of Internal Medicine, Section of
Cardiovascular Medicine, Wake Forest School of Medicine, Winston-Salem, NC,
USA
| | - David R. Jacobs
- Division of Epidemiology and Community Health, University
of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington,
Seattle, WA, USA
- Northwest Genomics Center, University of Washington,
Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of
Medicine, Houston, TX, USA
| | - Fei Fei Wang
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Gerardo Heiss
- Department of Epidemiology, Gillings School of Global
Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Goo Jun
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
| | - Greg L. Kinney
- Department of Epidemiology, Colorado School of Public
Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Haakon H. Sigurslid
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | | | - Ira M. Hall
- Yale Center for Genomic Health, Yale School of Medicine,
New Haven, CT, USA
| | - Isabela M. Bensenor
- Center for Clinical and Epidemiological Research,
University Hospital, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Jai Broome
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - James D. Crapo
- Department of Medicine, National Jewish Health, Denver,
CO, USA
| | - James G. Wilson
- Division of Cardiology, Beth Israel Deaconess Medical
Center, Boston, MA, USA
| | - Jennifer A. Smith
- School of Public Health, Department of Epidemiology,
University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research,
University of Michigan, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio
Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of
Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Jose D. Vargas
- Medstar Heart and Vascular Institute, Medstar Georgetown
University Hospital, Washington, DC, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia
School of Medicine, Charlottesville, VA, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington,
Seattle, WA, USA
- Northwest Genomics Center, University of Washington,
Seattle, WA, USA
| | | | - Kathleen A. Ryan
- Division of Endocrinology, Diabetes and Nutrition,
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD,
USA
| | - Kendra A. Young
- Department of Epidemiology, Colorado School of Public
Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population
Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical
Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Denver,
Anschutz Medical Campus, Aurora, CO, USA
| | - Leslie S. Emery
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Marcio S. Bittencourt
- Center for Clinical and Epidemiological Research,
University Hospital, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Matthew J. Budoff
- Department of Medicine, The Lundquist Institute for
Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - May E. Montasser
- Division of Endocrinology, Diabetes and Nutrition,
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD,
USA
| | - Miao Yu
- School of Public Health, Department of Epidemiology,
University of Michigan, Ann Arbor, MI, USA
| | - Michael C. Mahaney
- Department of Human Genetics, University of Texas Rio
Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of
Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mohammed S Mahamdeh
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
- Institute of Molecular Medicine, McGovern Medical School,
The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global
Public health, University of North Carolina, Chapel Hill, NC, USA
| | - Paulo A. Lotufo
- Center for Clinical and Epidemiological Research,
University Hospital, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic
Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad
Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston,
MA, USA
| | - Quenna Wong
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Rasika A. Mathias
- Division of General Internal Medicine, Department of
Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Allergy and Clinical Immunology, Department
of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of
Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor
College of Medicine, Houston, TX, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine,
Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai, New York, NY, USA
| | - Roxana Mehran
- Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Robert
Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | | | - Sarah C. Nelson
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Scott M. Damrauer
- Corporal Michael J. Crescenz VA Medical Center,
Philadelphia, PA, USA
- Department of Surgery, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon L.R. Kardia
- School of Public Health, Department of Epidemiology,
University of Michigan, Ann Arbor, MI, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia
School of Medicine, Charlottesville, VA, USA
| | - Valentin Fuster
- Centro Nacional de Investigaciones Cardiovasculares
Carlos III, Madrid, Spain
- Mount Sinai Heart Center, New York, NY, USA
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of
Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Wei Zhao
- School of Public Health, Department of Epidemiology,
University of Michigan, Ann Arbor, MI, USA
| | - Wenjie Tian
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical
Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Yuan-I Min
- Jackson Heart Study, Department of Medicine, University
of Mississippi Medical Center, Jackson, MS, USA
| | - Alisa K. Manning
- Clinical and Translation Epidemiology Unit, Department of
Medicine, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical and Population
Genetics, Broad Institute, Cambridge, MA, USA
| | - Gina Peloso
- Department of Biostatistics, Boston University School of
Public Health, Boston, MA, USA
| | - Tanika N. Kelly
- College of Medicine, Department of Medicine, Division of
Nephrology, University of Illinois Chicago, Chicago, IL, USA
| | - Christopher J. O’Donnell
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital,
Boston, MA, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanne E. Curran
- Department of Human Genetics, University of Texas Rio
Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of
Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Warren M. Zapol
- Department of Anesthesia, Critical Care and Pain Medicine
at Massachusetts General Hospital, Boston, MA, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of
Medicine, Winston-Salem, NC, USA
| | - Lewis C. Becker
- Division of Cardiology, Department of Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University
of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of
Mississippi Medical Center, Jackson, MS, USA
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes and Nutrition,
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD,
USA
- Geriatrics Research and Education Clinical Center,
Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of
Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington,
Seattle, WA, USA
- Department of Health Services, University of Washington,
Seattle, WA, USA
| | - John Jeffrey Carr
- Department of Radiology, Vanderbilt Translational and
Clinical Cardiovascular Research Center, Vanderbilt University Medical Center,
Nashville, TN, USA
| | - Alexandre C. Pereira
- Department of Genetics, Harvard Medical School, Boston,
MA, USA
- Laboratory of Genetics and Molecular Cardiology, Heart
Institute, University of São Paulo, São Paulo, Brazil
| | - Themistocles L. Assimes
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Stanford University School of
Medicine, Stanford, CA, USA
| | - Nathan O. Stitziel
- Cardiovascular Division, Department of Internal Medicine,
Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of
Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School
of Medicine, St. Louis, MO, USA
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public
Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Cecelia A. Laurie
- Genetic Analysis Center, Department of Biostatistics,
School of Public Health, University of Washington, Seattle, WA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population
Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical
Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ramachandran S. Vasan
- Boston University and National Heart, Lung, and Blood
Institute’s Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Boston University School of
Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of
Public Health, Boston, MA, USA
| | - Wendy S. Post
- Division of Cardiology, Department of Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD, USA
| | - Patricia A. Peyser
- School of Public Health, Department of Epidemiology,
University of Michigan, Ann Arbor, MI, USA
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia
School of Medicine, Charlottesville, VA, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Division of Cardiology,
Department of Medicine, Massachusetts General Hospital, Harvard Medical School,
Boston, MA, USA
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27
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Katz AE, Ganesh SK. Advancements in the Genetics of Spontaneous Coronary Artery Dissection. Curr Cardiol Rep 2023; 25:1735-1743. [PMID: 37979122 PMCID: PMC10810930 DOI: 10.1007/s11886-023-01989-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
PURPOSE OF REVIEW Spontaneous coronary artery dissection (SCAD) is a significant cause of acute myocardial infarction that is increasingly recognized in young and middle-aged women. The etiology of SCAD is likely multifactorial and may include the interaction of environmental and individual factors. Here, we summarize the current understanding of the genetic factors contributing to the development of SCAD. RECENT FINDINGS The molecular findings underlying SCAD have been demonstrated to include a combination of rare DNA sequence variants with large effects, common variants contributing to a complex genetic architecture, and variants with intermediate impact. The genes associated with SCAD highlight the role of arterial cells and their extracellular matrix in the pathogenesis of the disease and shed light on the relationship between SCAD and other disorders, including fibromuscular dysplasia and connective tissue diseases. While up to 10% of affected individuals may harbor a rare variant with large effect, SCAD most often presents as a complex genetic condition. Analyses of larger and more diverse cohorts will continue to improve our understanding of risk susceptibility loci and will also enable consideration of the clinical utility of genetic testing strategies in the management of SCAD.
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Affiliation(s)
- Alexander E Katz
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, USA
- Department of Human Genetics, University of Michigan, 7220, MSRB III, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0644, USA
| | - Santhi K Ganesh
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, USA.
- Department of Human Genetics, University of Michigan, 7220, MSRB III, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0644, USA.
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28
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Xu J, Jiang X, Xu S. Aprocitentan, a dual endothelin-1 (ET-1) antagonist for treating resistant hypertension: Mechanism of action and therapeutic potential. Drug Discov Today 2023; 28:103788. [PMID: 37742911 DOI: 10.1016/j.drudis.2023.103788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Hypertension is reaching epidemic proportions worldwide and is a significant public health concern. However, ∼15% of patients with hypertension continue to experience elevated blood pressure, even after taking antihypertensive medications [such as angiotensin II receptor blockers (ARBs), angiotensin-converting enzyme inhibitors (ACEIs), dihydropyridine calcium channel blockers (CCBs) and thiazide diuretics], a condition referred to as resistant hypertension (RH). Within the complex realm of blood pressure regulation and vascular function, endothelin-1 (ET-1), a potent vasoconstrictor, plays a pivotal role. Recent research, particularly a Phase III clinical trial (NCT03541174), has shed light on the potential of aprocitentan, a dual ET-1 receptor antagonist, in significantly lowering blood pressure in individuals with RH. In this review, we summarize the mechanism of action and therapeutic potential of aprocitentan as an innovative approach for treating RH.
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Affiliation(s)
- Jingjing Xu
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Xiaohua Jiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China.
| | - Suowen Xu
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China.
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29
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Jeoffrey SMH, Kalyanasundaram A, Zafar MA, Ziganshin BA, Elefteriades JA. Genetic Overlap of Spontaneous Dissection of Either the Thoracic Aorta or the Coronary Arteries. Am J Cardiol 2023; 205:69-74. [PMID: 37591066 DOI: 10.1016/j.amjcard.2023.07.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/07/2023] [Indexed: 08/19/2023]
Abstract
Ascending thoracic aortic dissection (ATAD) is a well-known vascular cause of sudden death. Spontaneous coronary artery dissections (SCAD) are emerging as an important cause of early-onset myocardial infarction and sudden death. Genetic variants in multiple connective tissue genes have been recognized to underlie ATAD; other genetic variants have similarly been recognized to underlie SCAD. Little data are available regarding any genetic commonality between ATAD and SCAD. Our objective is to determine and characterize any genetic overlap between genes coding for ATAD and SCAD. We identified and reviewed 17 retrospective and prospective genetic studies of thoracic aortic dissection and SCAD published between 2016 and 2022 identified through PubMed and Orbis. Articles highlighting the significant plausible triggers for ATAD or SCAD individually were analyzed. No previous study reviewed both ATAD and SCAD genetics together. Separate lists of causative genes were constructed for ATAD and SCAD-and then commonalities were sought. A Venn diagram was constructed to display the genetic overlap and common physiologic pathways involved. We identified a definite, meaningful overlap of 15 independent genes based on a genome-wide association study or other genetic methods. The associated genetic pathways involved various biologic processes including elastin degradation, smooth muscle cell function, and the TGFβ-pathway. The overlapping genes included the following: COL3A1, TGFB2, SMAD3, MYLK, TGFBR2, TGFBR1, LOX, FBN1, NOTCH1, ELN, COL5A1, COL5A2, COL1A2, MYH11, and TLN1. The corresponding molecular pathways were investigated and correlated for both diseases. We are not aware of other studies searching for genetic commonalities between ATAD and SCAD. We have successfully identified overlapping genes-and their corresponding molecular pathways-for ATAD and SCAD. We hope that these insights will lead to further clinical and scientific understanding of each disease through study of their fundamental commonalities.
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Affiliation(s)
| | - Asanish Kalyanasundaram
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut
| | - Mohammad A Zafar
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut
| | - Bulat A Ziganshin
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut
| | - John A Elefteriades
- Aortic Institute at Yale-New Haven Hospital, Yale University School of Medicine, New Haven, Connecticut.
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30
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Le Grand Q, Ecker Ferreira L, Metso TM, Schilling S, Tatlisumak T, Grond-Ginsbach C, Engelter ST, Lyrer P, Majersik JJ, Worrall BB, Southerland AM, Markus HS, Lathrop M, Thijs V, Leys D, Amouyel P, Dallongeville J, Dichgans M, Pezzini A, Bersano A, Sargurupremraj M, Debette S. Genetic Insights on the Relation of Vascular Risk Factors and Cervical Artery Dissection. J Am Coll Cardiol 2023; 82:1411-1423. [PMID: 37758436 DOI: 10.1016/j.jacc.2023.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/16/2023] [Accepted: 07/24/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND The association between vascular risk factors and cervical artery dissections (CeADs), a leading cause of ischemic stroke (IS) in the young, remains controversial. OBJECTIVES This study aimed to explore the causal relation of vascular risk factors with CeAD risk and recurrence and compare it to their relation with non-CeAD IS. METHODS This study used 2-sample Mendelian randomization analyses to explore the association of blood pressure (BP), lipid levels, type 2 diabetes, waist-to-hip ratio, smoking, and body mass index with CeAD and non-CeAD IS. To simulate effects of the most frequently used BP-lowering drugs, this study constructed genetic proxies and tested their association with CeAD and non-CeAD IS. In analyses among patients with CeAD, the investigators studied the association between weighted genetic risk scores of vascular risk factors and the risk of multiple or early recurrent dissections. RESULTS Genetically determined higher systolic BP (OR: 1.51; 95% CI: 1.32-1.72) and diastolic BP (OR: 2.40; 95% CI: 1.92-3.00) increased the risk of CeAD (P < 0.0001). Genetically determined higher body mass index was inconsistently associated with a lower risk of CeAD. Genetic proxies for β-blocker effects were associated with a lower risk of CeAD (OR: 0.65; 95% CI: 0.50-0.85), whereas calcium-channel blockers were associated with a lower risk of non-CeAD IS (OR: 0.75; 95% CI: 0.63-0.90). Weighted genetic risk scores for systolic BP and diastolic BP were associated with an increased risk of multiple or early recurrent CeAD. CONCLUSIONS These results are supportive of a causal association between higher BP and increased CeAD risk and recurrence and provide genetic evidence for lower CeAD risk under β-blockers. This may inform secondary prevention strategies and trial design for CeAD.
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Affiliation(s)
- Quentin Le Grand
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Center (BPH), Unité Mixte de Recherche (U) 1219, Bordeaux, France
| | - Leslie Ecker Ferreira
- Department of Medicine and Joinville Stroke Biobank, University of Region of Joinville, Joinville, Brazil
| | - Tiina M Metso
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Sabrina Schilling
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Center (BPH), Unité Mixte de Recherche (U) 1219, Bordeaux, France
| | - Turgut Tatlisumak
- Department of Clinical Neurosciences/Neurology, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Caspar Grond-Ginsbach
- Department of Vascular and Endovascular Surgery, University of Heidelberg, Heidelberg, Germany
| | - Stefan T Engelter
- Neurology and Neurorehabilitation, University Department of Geriatric Medicine Felix Platter, University of Basel, Basel, Switzerland; Department of Neurology and Stroke Center, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Philippe Lyrer
- Department of Neurology and Stroke Center, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Bradford B Worrall
- Department of Neurology, University of Virginia, Charlottesville, Virginia, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Andrew M Southerland
- Department of Neurology, University of Virginia, Charlottesville, Virginia, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Quebec, Canada
| | - Vincent Thijs
- Stroke Division, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology, Austin Health, Melbourne, Victoria, Australia
| | - Didier Leys
- INSERM U1172, Lille Neuroscience and Cognition, University of Lille, Lille, France
| | - Philippe Amouyel
- Laboratory of Excellence Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease (LabEx DISTALZ), University of Lille, Lille, France; INSERM U1167 (Risk Factors and Molecular Determinants of Aging-Related Diseases - RID-AGE), Lille, France; Centre Hospitalier Universitaire Lille, Lille, France; Institut Pasteur de Lille, Lille, France
| | - Jean Dallongeville
- Laboratory of Excellence Development of Innovative Strategies for a Transdisciplinary Approach to Alzheimer's Disease (LabEx DISTALZ), University of Lille, Lille, France; INSERM U1167 (Risk Factors and Molecular Determinants of Aging-Related Diseases - RID-AGE), Lille, France; Centre Hospitalier Universitaire Lille, Lille, France; Institut Pasteur de Lille, Lille, France
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany; Munich Cluster for Systems Neurology, Munich, Germany; German Center for Neurodegenerative Diseases, Munich, Germany
| | - Alessandro Pezzini
- Department of Clinical and Experimental Sciences, Neurology Unit, University of Brescia, Brescia, Italy
| | - Anna Bersano
- Cerebrovascular Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Neurologico Carlo Besta, Milan, Italy
| | - Muralidharan Sargurupremraj
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Center (BPH), Unité Mixte de Recherche (U) 1219, Bordeaux, France; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, Texas
| | - Stéphanie Debette
- University of Bordeaux, Institut National de la Santé et de la Recherche Médicale (INSERM), Bordeaux Population Health Center (BPH), Unité Mixte de Recherche (U) 1219, Bordeaux, France; Department of Neurology, Institute of Neurodegenerative Diseases, Bordeaux University Hospital, Bordeaux, France.
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31
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Malfait J, Wan J, Spicuglia S. Epromoters are new players in the regulatory landscape with potential pleiotropic roles. Bioessays 2023; 45:e2300012. [PMID: 37246247 DOI: 10.1002/bies.202300012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/30/2023]
Abstract
Precise spatiotemporal control of gene expression during normal development and cell differentiation is achieved by the combined action of proximal (promoters) and distal (enhancers) cis-regulatory elements. Recent studies have reported that a subset of promoters, termed Epromoters, works also as enhancers to regulate distal genes. This new paradigm opened novel questions regarding the complexity of our genome and raises the possibility that genetic variation within Epromoters has pleiotropic effects on various physiological and pathological traits by differentially impacting multiple proximal and distal genes. Here, we discuss the different observations pointing to an important role of Epromoters in the regulatory landscape and summarize the evidence supporting a pleiotropic impact of these elements in disease. We further hypothesize that Epromoter might represent a major contributor to phenotypic variation and disease.
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Affiliation(s)
- Juliette Malfait
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Jing Wan
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, LIGUE, Marseille, France
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32
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West CE, Karim M, Falaguera MJ, Speidel L, Green CJ, Logie L, Schwartzentruber J, Ochoa D, Lord JM, Ferguson MAJ, Bountra C, Wilkinson GF, Vaughan B, Leach AR, Dunham I, Marsden BD. Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity. Sci Data 2023; 10:655. [PMID: 37749083 PMCID: PMC10520009 DOI: 10.1038/s41597-023-02513-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023] Open
Abstract
Advancing age is the greatest risk factor for developing multiple age-related diseases. Therapeutic approaches targeting the underlying pathways of ageing, rather than individual diseases, may be an effective way to treat and prevent age-related morbidity while reducing the burden of polypharmacy. We harness the Open Targets Genetics Portal to perform a systematic analysis of nearly 1,400 genome-wide association studies (GWAS) mapped to 34 age-related diseases and traits, identifying genetic signals that are shared between two or more of these traits. Using locus-to-gene (L2G) mapping, we identify 995 targets with shared genetic links to age-related diseases and traits, which are enriched in mechanisms of ageing and include known ageing and longevity-related genes. Of these 995 genes, 128 are the target of an approved or investigational drug, 526 have experimental evidence of binding pockets or are predicted to be tractable, and 341 have no existing tractability evidence, representing underexplored genes which may reveal novel biological insights and therapeutic opportunities. We present these candidate targets for exploration and prioritisation in a web application.
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Affiliation(s)
- Clare E West
- Centre for Medicines Discovery, University of Oxford, Oxford, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, UK.
| | - Mohd Karim
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Maria J Falaguera
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Leo Speidel
- Francis Crick Institute, London, UK
- Genetics Institute, University College London, London, UK
| | | | - Lisa Logie
- Drug Discovery Unit, University of Dundee, Dundee, UK
- Medicines Discovery Catapult, 35 Mereside Alderley Park, Macclesfield, Cheshire, UK
| | - Jeremy Schwartzentruber
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Janet M Lord
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | - Chas Bountra
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Graeme F Wilkinson
- Medicines Discovery Catapult, 35 Mereside Alderley Park, Macclesfield, Cheshire, UK
| | - Beverley Vaughan
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Andrew R Leach
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
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Wass SY, Smith JD, Chung MK. Connecting the Dots From GWAS to Function in Atrial Fibrillation for ZFHX3. Circ Res 2023; 133:330-332. [PMID: 37535755 PMCID: PMC10403289 DOI: 10.1161/circresaha.123.323281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Affiliation(s)
- Sojin Y Wass
- The Department of Cardiovascular Medicine, Heart, Vascular & Thoracic Institute, and the Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, OH
| | - Jonathan D Smith
- The Department of Cardiovascular Medicine, Heart, Vascular & Thoracic Institute, and the Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, OH
| | - Mina K Chung
- The Department of Cardiovascular Medicine, Heart, Vascular & Thoracic Institute, and the Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, OH
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Jiang D, Liu H, Zhu G, Li X, Fan L, Zhao F, Xu C, Wang S, Rose Y, Rhen J, Yu Z, Yin Y, Gu Y, Xu X, Fisher EA, Ge J, Xu Y, Pang J. Endothelial PHACTR1 Promotes Endothelial Activation and Atherosclerosis by Repressing PPARγ Activity Under Disturbed Flow in Mice. Arterioscler Thromb Vasc Biol 2023; 43:e303-e322. [PMID: 37199156 PMCID: PMC10524336 DOI: 10.1161/atvbaha.122.318173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/02/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Numerous genome-wide association studies revealed that SNPs (single nucleotide polymorphisms) at the PHACTR1 (phosphatase and actin regulator 1) locus strongly correlate with coronary artery disease. However, the biological function of PHACTR1 remains poorly understood. Here, we identified the proatherosclerotic effect of endothelial PHACTR1, contrary to macrophage PHACTR1. METHODS We generated global (Phactr1-/-) and endothelial cell (EC)-specific (Phactr1ECKO) Phactr1 KO (knockout) mice and crossed these mice with apolipoprotein E-deficient (Apoe-/-) mice. Atherosclerosis was induced by feeding the high-fat/high-cholesterol diet for 12 weeks or partially ligating carotid arteries combined with a 2-week high-fat/high-cholesterol diet. PHACTR1 localization was identified by immunostaining of overexpressed PHACTR1 in human umbilical vein ECs exposed to different types of flow. The molecular function of endothelial PHACTR1 was explored by RNA sequencing using EC-enriched mRNA from global or EC-specific Phactr1 KO mice. Endothelial activation was evaluated in human umbilical vein ECs transfected with siRNA targeting PHACTR1 and in Phactr1ECKO mice after partial carotid ligation. RESULTS Global or EC-specific Phactr1 deficiency significantly inhibited atherosclerosis in regions of disturbed flow. PHACTR1 was enriched in ECs and located in the nucleus of disturbed flow areas but shuttled to cytoplasm under laminar flow in vitro. RNA sequencing showed that endothelial Phactr1 depletion affected vascular function, and PPARγ (peroxisome proliferator-activated receptor gamma) was the top transcription factor regulating differentially expressed genes. PHACTR1 functioned as a PPARγ transcriptional corepressor by binding to PPARγ through the corepressor motifs. PPARγ activation protects against atherosclerosis by inhibiting endothelial activation. Consistently, PHACTR1 deficiency remarkably reduced endothelial activation induced by disturbed flow in vivo and in vitro. PPARγ antagonist GW9662 abolished the protective effects of Phactr1 KO on EC activation and atherosclerosis in vivo. CONCLUSIONS Our results identified endothelial PHACTR1 as a novel PPARγ corepressor to promote atherosclerosis in disturbed flow regions. Endothelial PHACTR1 is a potential therapeutic target for atherosclerosis treatment.
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Affiliation(s)
- Dongyang Jiang
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Hao Liu
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Guofu Zhu
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Xiankai Li
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Linlin Fan
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Faxue Zhao
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Chong Xu
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Shumin Wang
- Aab Cardiovascular Research Institute, Department of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA (S. W., Y. R., J. R., X. X., J. P.)
| | - Yara Rose
- Aab Cardiovascular Research Institute, Department of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA (S. W., Y. R., J. R., X. X., J. P.)
| | - Jordan Rhen
- Aab Cardiovascular Research Institute, Department of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA (S. W., Y. R., J. R., X. X., J. P.)
| | - Ze Yu
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Yiheng Yin
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Yuling Gu
- Shanghai Naturethink Life Science&Technology Co., Itd, Shanghai 201809, China (Y. G.)
| | - Xiangbin Xu
- Aab Cardiovascular Research Institute, Department of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA (S. W., Y. R., J. R., X. X., J. P.)
| | - Edward A. Fisher
- Division of Cardiology, Department of Medicine, New York University School of Medicine, New York, NY 10016, USA (E. A. F.)
| | - Junbo Ge
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Yawei Xu
- Department of Cardiology, Pan-vascular Research Institute, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China (D. J., H. L., G. Z., X. L., L. F., F. Z., C. X., Z. Y., Y. Y., J. G., Y. X.)
| | - Jinjiang Pang
- Aab Cardiovascular Research Institute, Department of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA (S. W., Y. R., J. R., X. X., J. P.)
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McChord J, Pereyra VM, Froebel S, Bekeredjian R, Schwab M, Ong P. Drug repurposing-a promising approach for patients with angina but non-obstructive coronary artery disease (ANOCA). Front Cardiovasc Med 2023; 10:1156456. [PMID: 37396593 PMCID: PMC10313125 DOI: 10.3389/fcvm.2023.1156456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
In today's era of individualized precision medicine drug repurposing represents a promising approach to offer patients fast access to novel treatments. Apart from drug repurposing in cancer treatments, cardiovascular pharmacology is another attractive field for this approach. Patients with angina pectoris without obstructive coronary artery disease (ANOCA) report refractory angina despite standard medications in up to 40% of cases. Drug repurposing also appears to be an auspicious option for this indication. From a pathophysiological point of view ANOCA patients frequently suffer from vasomotor disorders such as coronary spasm and/or impaired microvascular vasodilatation. Consequently, we carefully screened the literature and identified two potential therapeutic targets: the blockade of the endothelin-1 (ET-1) receptor and the stimulation of soluble guanylate cyclase (sGC). Genetically increased endothelin expression results in elevated levels of ET-1, justifying ET-1 receptor blockers as drug candidates to treat coronary spasm. sGC stimulators may be beneficial as they stimulate the NO-sGC-cGMP pathway leading to GMP-mediated vasodilatation.
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Affiliation(s)
- Johanna McChord
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | | | - Sarah Froebel
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Raffi Bekeredjian
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- Departments of Clinical Pharmacology, and Biochemistry and Pharmacy, University Tübingen, Tübingen, Germany
| | - Peter Ong
- Department of Cardiology and Angiology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
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Liu R, Yuan T, Wang R, Gong D, Wang S, Du G, Fang L. Insights into Endothelin Receptors in Pulmonary Hypertension. Int J Mol Sci 2023; 24:10206. [PMID: 37373355 DOI: 10.3390/ijms241210206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Pulmonary hypertension (PH) is a disease which affects the cardiopulmonary system; it is defined as a mean pulmonary artery pressure (mPAP) > 20 mmHg as measured by right heart catheterization at rest, and is caused by complex and diverse mechanisms. In response to stimuli such as hypoxia and ischemia, the expression and synthesis of endothelin (ET) increase, leading to the activation of various signaling pathways downstream of it and producing effects such as the induction of abnormal vascular proliferation during the development of the disease. This paper reviews the regulation of endothelin receptors and their pathways in normal physiological processes and disease processes, and describes the mechanistic roles of ET receptor antagonists that are currently approved and used in clinical studies. Current clinical researches on ET are focused on the development of multi-target combinations and novel delivery methods to improve efficacy and patient compliance while reducing side effects. In this review, future research directions and trends of ET targets are described, including monotherapy and precision medicine.
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Affiliation(s)
- Ruiqi Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Tianyi Yuan
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ranran Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Difei Gong
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shoubao Wang
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Guanhua Du
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Lianhua Fang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Drug Targets Identification and Drug Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Qiu Y, Feng D, Jiang W, Zhang T, Lu Q, Zhao M. 3D genome organization and epigenetic regulation in autoimmune diseases. Front Immunol 2023; 14:1196123. [PMID: 37346038 PMCID: PMC10279977 DOI: 10.3389/fimmu.2023.1196123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the relationships between various regulatory components and gene function also requires the integration of multi-omics data such as genomics, transcriptomics, and epigenomics. 3D genome folding is involved in immune cell differentiation, activation, and dysfunction and participates in a wide range of diseases, including autoimmune diseases. We describe hierarchical 3D chromatin organization in this review and conclude with characteristics of C-techniques and multi-omics applications of the 3D genome. In addition, we describe the relationship between 3D genome structure and the differentiation and maturation of immune cells and address how changes in chromosome folding contribute to autoimmune diseases.
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Affiliation(s)
- Yueqi Qiu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Delong Feng
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Wenjuan Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Tingting Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ming Zhao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
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Fabo T, Khavari P. Functional characterization of human genomic variation linked to polygenic diseases. Trends Genet 2023; 39:462-490. [PMID: 36997428 PMCID: PMC11025698 DOI: 10.1016/j.tig.2023.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023]
Abstract
The burden of human disease lies predominantly in polygenic diseases. Since the early 2000s, genome-wide association studies (GWAS) have identified genetic variants and loci associated with complex traits. These have ranged from variants in coding sequences to mutations in regulatory regions, such as promoters and enhancers, as well as mutations affecting mediators of mRNA stability and other downstream regulators, such as 5' and 3'-untranslated regions (UTRs), long noncoding RNA (lncRNA), and miRNA. Recent research advances in genetics have utilized a combination of computational techniques, high-throughput in vitro and in vivo screening modalities, and precise genome editing to impute the function of diverse classes of genetic variants identified through GWAS. In this review, we highlight the vastness of genomic variants associated with polygenic disease risk and address recent advances in how genetic tools can be used to functionally characterize them.
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Affiliation(s)
- Tania Fabo
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Khavari
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Graduate Program in Genetics, Stanford University, Stanford, CA, USA; Stanford University School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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Pelzer N, de Boer I, van den Maagdenberg AMJM, Terwindt GM. Neurological and psychiatric comorbidities of migraine: Concepts and future perspectives. Cephalalgia 2023; 43:3331024231180564. [PMID: 37293935 DOI: 10.1177/03331024231180564] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BACKGROUND This narrative review aims to discuss several common neurological and psychiatric disorders that show comorbidity with migraine. Not only can we gain pathophysiological insights by studying these disorders, comorbidities also have important implications for treating migraine patients in clinical practice. METHODS A literature search on PubMed and Embase was conducted with the keywords "comorbidity", "migraine disorders", "migraine with aura", "migraine without aura", "depression", "depressive disorders", "epilepsy", "stroke", "patent foramen ovale", "sleep wake disorders", "restless legs syndrome", "genetics", "therapeutics". RESULTS Several common neurological and psychiatric disorders show comorbidity with migraine. Major depression and migraine show bidirectional causality and have shared genetic factors. Dysregulation of both hypothalamic and thalamic pathways have been implicated as a possibly cause. The increased risk of ischaemic stroke in migraine likely involves spreading depolarizations. Epilepsy is not only bidirectionally related to migraine, but is also co-occurring in monogenic migraine syndromes. Neuronal hyperexcitability is an important overlapping mechanism between these conditions. Hypothalamic dysfunction is suggested as the underlying mechanism for comorbidity between sleep disorders and migraine and might explain altered circadian timing in migraine. CONCLUSION These comorbid conditions in migraine with distinct pathophysiological mechanisms have important implications for best treatment choices and may provide clues for future approaches.
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Affiliation(s)
- Nadine Pelzer
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Irene de Boer
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arn M J M van den Maagdenberg
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
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López Rodríguez M, Arasu UT, Kaikkonen MU. Exploring the genetic basis of coronary artery disease using functional genomics. Atherosclerosis 2023; 374:87-98. [PMID: 36801133 DOI: 10.1016/j.atherosclerosis.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Genome-wide Association Studies (GWAS) have identified more than 300 loci associated with coronary artery disease (CAD), defining the genetic risk map of the disease. However, the translation of the association signals into biological-pathophysiological mechanisms constitute a major challenge. Through a group of examples of studies focused on CAD, we discuss the rationale, basic principles and outcomes of the main methodologies implemented to prioritize and characterize causal variants and their target genes. Additionally, we highlight the strategies as well as the current methods that integrate association and functional genomics data to dissect the cellular specificity underlying the complexity of disease mechanisms. Despite the limitations of existing approaches, the increasing knowledge generated through functional studies helps interpret GWAS maps and opens novel avenues for the clinical usability of association data.
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Affiliation(s)
- Maykel López Rodríguez
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland; Department of Pathology and Laboratory Medicine, University of California, UCLA, Los Angeles, USA.
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland.
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De Beer D, Mels CMC, Schutte AE, Delles C, Mary S, Mullen W, Latosinska A, Mischak H, Kruger R. Identifying a urinary peptidomics profile for hypertension in young adults: The African-PREDICT study: Urinary peptidomics and hypertension: Urinary peptidomics and hypertension. Proteomics 2023; 23:e2200444. [PMID: 36943111 DOI: 10.1002/pmic.202200444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Hypertension is one of the most important and complex risk factors for cardiovascular diseases (CVDs). By using urinary peptidomics analyses, we aimed to identify peptides associated with hypertension, building a framework for future research towards improved prediction and prevention of premature development of CVD. We included 78 hypertensive and 79 normotensive participants from the African-PREDICT study (aged 20-30 years), matched for sex (51% male) and ethnicity (49% black and 51% white). Urinary peptidomics data were acquired using capillary-electrophoresis-time-of-flight-mass-spectrometry. Hypertension-associated peptides were identified and combined into a support vector machine-based multidimensional classifier. When comparing the peptide data between the normotensive and hypertensive groups, 129 peptides were nominally differentially abundant (Wilcoxon p < 0.05). Nonetheless, only three peptides, all derived from collagen alpha-1(III), remained significantly different after rigorous adjustments for multiple comparisons. The 37 most significant peptides (all p ≤ 0.001) served as basis for the development of a classifier, with 20 peptides being combined into a unifying score, resulting in an AUC of 0.85 in the ROC analysis (p < 0.001), with 83% sensitivity at 80% specificity. Our study suggests potential value of urinary peptides in the classification of hypertension, which could enable earlier diagnosis and better understanding of the pathophysiology of hypertension and premature cardiovascular disease development.
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Affiliation(s)
- Dalene De Beer
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Catharina M C Mels
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Aletta E Schutte
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
- School of Population Health, The George Institute for Global Health, University of New South Wales, Sydney, Australia
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sheon Mary
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ruan Kruger
- Hypertension in Africa Research Team (HART), North-West University (Potchefstroom Campus), Potchefstroom, South Africa
- MRC Research Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
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Severino P, D'Amato A, Prosperi S, Myftari V, Colombo L, Tomarelli E, Piccialuti A, Di Pietro G, Birtolo LI, Maestrini V, Badagliacca R, Sardella G, Fedele F, Vizza CD, Mancone M. Myocardial Infarction with Non-Obstructive Coronary Arteries (MINOCA): Focus on Coronary Microvascular Dysfunction and Genetic Susceptibility. J Clin Med 2023; 12:jcm12103586. [PMID: 37240691 DOI: 10.3390/jcm12103586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/14/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Among the most common causes of death worldwide, ischemic heart disease (IHD) is recognized to rank first. Even if atherosclerotic disease of the epicardial arteries is known as the leading cause of IHD, the presence of myocardial infarction with non-obstructive coronary artery disease (MINOCA) is increasingly recognized. Notwithstanding the increasing interest, MINOCA remains a puzzling clinical entity that can be classified by distinguishing different underlying mechanisms, which can be divided into atherosclerotic and non-atherosclerotic. In particular, coronary microvascular dysfunction (CMD), classifiable in non-atherosclerotic mechanisms, is a leading factor for the pathophysiology and prognosis of patients with MINOCA. Genetic susceptibility may have a role in primum movens in CMD. However, few results have been obtained for understanding the genetic mechanisms underlying CMD. Future studies are essential in order to find a deeper understanding of the role of multiple genetic variants in the genesis of microcirculation dysfunction. Progress in research would allow early identification of high-risk patients and the development of pharmacological, patient-tailored strategies. The aim of this review is to revise the pathophysiology and underlying mechanisms of MINOCA, focusing on CMD and actual knowledge about genetic predisposition to it.
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Affiliation(s)
- Paolo Severino
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Andrea D'Amato
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Silvia Prosperi
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Vincenzo Myftari
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Lorenzo Colombo
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Elisa Tomarelli
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Alice Piccialuti
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Gianluca Di Pietro
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Lucia Ilaria Birtolo
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Viviana Maestrini
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Roberto Badagliacca
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Gennaro Sardella
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Francesco Fedele
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Carmine Dario Vizza
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Massimo Mancone
- Department of Clinical, Internal, Anesthesiology and Cardiovascular Sciences, Sapienza University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
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Rada I, Calderón JF, Martínez G, Muñoz Venturelli P. Genetics of spontaneous cervical and coronary artery dissections. Front Glob Womens Health 2023; 4:1007795. [PMID: 37214559 PMCID: PMC10196206 DOI: 10.3389/fgwh.2023.1007795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023] Open
Abstract
Objectives Spontaneous cervical artery dissections (SCeAD) and coronary artery dissections (SCoAD) are major causes of neurovascular and cardiovascular morbidity in young adults. Although multiple aspects of their etiology are still unknown, most consensuses are focused on the presence of constitutional genetic aspects and environmental triggers. Since recent evidence of genetic contribution points to a possible overlap between these conditions, we aimed to describe current information on SCeAD and SCoAD genetics and their potential shared pathological aspects. Materials and methods A narrative review is presented. Publications in English and Spanish were queried using database search. The articles were evaluated by one team member in terms of inclusion criteria. After collecting, the articles were categorized based on scientific content. Results Given that patients with SCeAD and SCoAD rarely present connective tissue disorders, other genetic loci are probably responsible for the increased susceptibility in some individuals. The common variant rs9349379 at PHACTR1 gene is associated with predisposition to pathologies of the arterial wall, likely mediated by variations in Endothelin-1 (ET-1) levels. The risk of arterial dissection may be increased for those who carry the rs9349379(A) allele, associated with lower expression levels of ET-1; however, the local effect of this vasomotor imbalance remains unclear. Sex differences seen in SCeAD and SCoAD support a role for sex hormones that could modulate risk, tilting the delicate balance and forcing vasodilator actions to prevail over vasoconstriction due to a reduction in ET-1 expression. Conclusions New evidence points to a common gene variation that could explain dissection in both the cervical and coronary vasculatures. To further confirm the risk conferred by the rs9349379 variant, genome wide association studies are warranted, hopefully in larger and ethnically diverse populations.
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Affiliation(s)
- Isabel Rada
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Juan Francisco Calderón
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Gonzalo Martínez
- División de Enfermedades Cardiovasculares, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Muñoz Venturelli
- Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Gupta RM, Schnitzler GR, Fang S, Lee-Kim VS, Barry A. Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. Arterioscler Thromb Vasc Biol 2023; 43:600-608. [PMID: 36994731 PMCID: PMC10170398 DOI: 10.1161/atvbaha.123.318328] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/01/2023] [Indexed: 03/31/2023]
Abstract
Endothelial cells (EC) are an important mediator of atherosclerosis and vascular disease. Their exposure to atherogenic risk factors such as hypertension and serum cholesterol leads to endothelial dysfunction and many disease-associated processes. Identifying which of these multiple EC functions is causally related to disease risk has been challenging. There is evidence from in vivo models and human sequencing studies that dysregulation of nitric oxide production directly affects risk of coronary artery disease. Human genetics can help prioritize the other EC functions with causal relationships because germline mutations are acquired at birth and serve as a randomized test of which pathways affect disease risk. Though several coronary artery disease risk variants have been linked to EC function, this process has been slow and laborious. Unbiased analyses of EC dysfunction using multiomic approaches promise to identify the causal genetic mechanisms responsible for vascular disease. Here, we review the data from genomic, epigenomic, and transcriptomic studies that prioritize EC-specific causal pathways. New methods that CRISPR (clustered regularly interspaced short palindromic repeats) perturbation technology with genomic, epigenomic, and transcriptomic analysis promise to speed up the characterization of disease-associated genetic variation. We summarize several recent studies in ECs which use high-throughput genetic perturbation to identify disease-relevant pathways and novel mechanisms of disease. These genetically validated pathways can accelerate the identification of drug targets for the prevention and treatment of atherosclerosis.
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Affiliation(s)
- Rajat M Gupta
- Divisions of Genetics and Cardiology, Department of Medicine, Brigham and Women's Hospital, Boston MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
| | - Gavin R Schnitzler
- Divisions of Genetics and Cardiology, Department of Medicine, Brigham and Women's Hospital, Boston MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
| | - Shi Fang
- Divisions of Genetics and Cardiology, Department of Medicine, Brigham and Women's Hospital, Boston MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
| | - Vivian S Lee-Kim
- Divisions of Genetics and Cardiology, Department of Medicine, Brigham and Women's Hospital, Boston MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
| | - Aurelie Barry
- Divisions of Genetics and Cardiology, Department of Medicine, Brigham and Women's Hospital, Boston MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA (R.M.G., G.R.S., S.F., V.S.L.-K., A.B.)
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Granata A. Functional genomics in stroke: current and future applications of iPSCs and gene editing to dissect the function of risk variants. BMC Cardiovasc Disord 2023; 23:223. [PMID: 37120540 PMCID: PMC10148993 DOI: 10.1186/s12872-023-03227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/04/2023] [Indexed: 05/01/2023] Open
Abstract
Stroke is an important disease with unmet clinical need. To uncover novel paths for treatment, it is of critical importance to develop relevant laboratory models that may help to shed light on the pathophysiological mechanisms of stroke. Induced pluripotent stem cells (iPSCs) technology has enormous potential to advance our knowledge into stroke by creating novel human models for research and therapeutic testing. iPSCs models generated from patients with specific stroke types and specific genetic predisposition in combination with other state of art technologies including genome editing, multi-omics, 3D system, libraries screening, offer the opportunity to investigate disease-related pathways and identify potential novel therapeutic targets that can then be tested in these models. Thus, iPSCs offer an unprecedented opportunity to make rapid progress in the field of stroke and vascular dementia research leading to clinical translation. This review paper summarizes some of the key areas in which patient-derived iPSCs technology has been applied to disease modelling and discusses the ongoing challenges and the future directions for the application of this technology in the field of stroke research.
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Affiliation(s)
- Alessandra Granata
- Department of Clinical Neurosciences, Victor Phillip Dahdaleh Heart & Lung Research Institute, Papworth Road, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0BB, UK.
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Wong D, Auguste G, Cardenas CLL, Turner AW, Chen Y, Song Y, Ma L, Perry RN, Aherrahrou R, Kuppusamy M, Yang C, Mosquera JV, Dube CJ, Khan MD, Palmore M, Kalra JK, Kavousi M, Peyser PA, Matic L, Hedin U, Manichaikul A, Sonkusare SK, Civelek M, Kovacic JC, Björkegren JL, Malhotra R, Miller CL. FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells. Circ Res 2023; 132:1144-1161. [PMID: 37017084 PMCID: PMC10147587 DOI: 10.1161/circresaha.122.321692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/21/2023] [Indexed: 04/06/2023]
Abstract
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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Affiliation(s)
- Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Christian L. Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Yixuan Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Yipei Song
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - R. Noah Perry
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Redouane Aherrahrou
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Maniselvan Kuppusamy
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
| | - Chaojie Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jose Verdezoto Mosquera
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Collin J. Dube
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Jaspreet K. Kalra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, The Netherlands
| | | | - Ljubica Matic
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ani Manichaikul
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Swapnil K. Sonkusare
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mete Civelek
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Jason C. Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St. Vincent’s Clinical School, University of New South Wales, Sydney, Australia
| | - Johan L.M. Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Clint L. Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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Zhang XH, Song YC, Qiu F, Wang ZC, Li N, Zhao FB. Hypoxic glioma cell-secreted exosomal circ101491 promotes the progression of glioma by regulating miR-125b-5p/EDN1. Brain Res Bull 2023; 195:55-65. [PMID: 36796652 DOI: 10.1016/j.brainresbull.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Hypoxia and exosomes play important roles in the occurrence and development of glioma. While circRNAs are involved in biological processes of various tumors, the mechanism underlying exosome-dependent regulatory effects of circRNAs on the progression of glioma under hypoxia is unclear. Results suggested that circ101491 was overexpressed in tumor tissues and plasma exosomes of glioma patients, while the overexpression of circ101491 was closely related to the differentiation degree and TNM staging of the patients. Moreover, circ101491 overexpression promoted viability, invasion and migration of glioma cells both in vivo and in vitro; the above regulatory effects can be reversed by inhibition of circ101491 expression. Mechanistic studies revealed that circ101491 upregulated EDN1 expression through sponging miR-125b-5p, thus facilitating glioma progression. In summary, hypoxia could promote circ101491 overexpression in glioma cell-derived exosomes, and circ101491/miR-125b-5p/EDN1 regulatory axis might be implicated in the malignant progression of glioma.
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Affiliation(s)
- Xiao-Hui Zhang
- Department of Pathology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China.
| | - Yi-Cun Song
- Department of Pathology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Feng Qiu
- Department of Pathology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Zheng-Cai Wang
- Department of Pathology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Nan Li
- Department of Pathology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Fang-Bo Zhao
- College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, PR China
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Wood A, Antonopoulos A, Chuaiphichai S, Kyriakou T, Diaz R, Al Hussaini A, Marsh AM, Sian M, Meisuria M, McCann G, Rashbrook VS, Drydale E, Draycott S, Polkinghorne MD, Akoumianakis I, Antoniades C, Watkins H, Channon KM, Adlam D, Douglas G. PHACTR1 modulates vascular compliance but not endothelial function: a translational study. Cardiovasc Res 2023; 119:599-610. [PMID: 35653516 PMCID: PMC10064844 DOI: 10.1093/cvr/cvac092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/09/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
AIMS The non-coding locus at 6p24 located in Intron 3 of PHACTR1 has consistently been implicated as a risk allele in myocardial infarction and multiple other vascular diseases. Recent murine studies have identified a role for Phactr1 in the development of atherosclerosis. However, the role of PHACTR1 in vascular tone and in vivo vascular remodelling has yet to be established. The aim of this study was to investigate the role of PHACTR1 in vascular function. METHODS AND RESULTS Prospectively recruited coronary artery disease (CAD) patients undergoing bypass surgery and retrospectively recruited spontaneous coronary artery dissection (SCAD) patients and matched healthy volunteers were genotyped at the PHACTR1 rs9349379 locus. We observed a significant association between the PHACTR1 loci and changes in distensibility in both the ascending aorta (AA = 0.0053 ± 0.0004, AG = 0.0041 ± 0.003, GG = 0.0034 ± 0.0009, P < 0.05, n = 58, 54, and 7, respectively) and carotid artery (AA = 12.83 ± 0.51, AG = 11.14 ± 0.38, GG = 11.69 ± 0.66, P < 0.05, n = 70, 65, and 18, respectively). This association was not observed in the descending aorta or in SCAD patients. In contrast, the PHACTR1 locus was not associated with changes in endothelial cell function with no association between the rs9349379 locus and in vivo or ex vivo vascular function observed in CAD patients. This finding was confirmed in our murine model where the loss of Phactr1 on the pro-atherosclerosis ApoE-/- background did not alter ex vivo vascular function. CONCLUSION In conclusion, we have shown a role for PHACTR1 in arterial compliance across multiple vascular beds. Our study suggests that PHACTR1 has a key structural role within the vasculature.
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Affiliation(s)
- Alice Wood
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Alexios Antonopoulos
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Surawee Chuaiphichai
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Theodosios Kyriakou
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Rebeca Diaz
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Abtehale Al Hussaini
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Anna-Marie Marsh
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Manjit Sian
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Mitul Meisuria
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Gerry McCann
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Victoria S Rashbrook
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Edward Drydale
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Sally Draycott
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Murray David Polkinghorne
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Ioannis Akoumianakis
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Charalambos Antoniades
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Hugh Watkins
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Keith M Channon
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - David Adlam
- Department of Cardiovascular Sciences, Glenfield Hospital, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Gillian Douglas
- BHF Centre of Research Excellence, Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
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Venkat V, Abdelhalim H, DeGroat W, Zeeshan S, Ahmed Z. Investigating genes associated with heart failure, atrial fibrillation, and other cardiovascular diseases, and predicting disease using machine learning techniques for translational research and precision medicine. Genomics 2023; 115:110584. [PMID: 36813091 DOI: 10.1016/j.ygeno.2023.110584] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/06/2023] [Accepted: 02/11/2023] [Indexed: 02/22/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality and loss of disability adjusted life years (DALYs) globally. CVDs like Heart Failure (HF) and Atrial Fibrillation (AF) are associated with physical effects on the heart muscles. As a result of the complex nature, progression, inherent genetic makeup, and heterogeneity of CVDs, personalized treatments are believed to be critical. Rightful application of artificial intelligence (AI) and machine learning (ML) approaches can lead to new insights into CVDs for providing better personalized treatments with predictive analysis and deep phenotyping. In this study we focused on implementing AI/ML techniques on RNA-seq driven gene-expression data to investigate genes associated with HF, AF, and other CVDs, and predict disease with high accuracy. The study involved generating RNA-seq data derived from the serum of consented CVD patients. Next, we processed the sequenced data using our RNA-seq pipeline and applied GVViZ for gene-disease data annotation and expression analysis. To achieve our research objectives, we developed a new Findable, Accessible, Intelligent, and Reproducible (FAIR) approach that includes a five-level biostatistical evaluation, primarily based on the Random Forest (RF) algorithm. During our AI/ML analysis, we have fitted, trained, and implemented our model to classify and distinguish high-risk CVD patients based on their age, gender, and race. With the successful execution of our model, we predicted the association of highly significant HF, AF, and other CVDs genes with demographic variables.
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Affiliation(s)
- Vignesh Venkat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - William DeGroat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ, USA
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, 112 Paterson St, New Brunswick, NJ, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, 125 Paterson St, New Brunswick, NJ, USA.
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Tsao CW, Aday AW, Almarzooq ZI, Anderson CAM, Arora P, Avery CL, Baker-Smith CM, Beaton AZ, Boehme AK, Buxton AE, Commodore-Mensah Y, Elkind MSV, Evenson KR, Eze-Nliam C, Fugar S, Generoso G, Heard DG, Hiremath S, Ho JE, Kalani R, Kazi DS, Ko D, Levine DA, Liu J, Ma J, Magnani JW, Michos ED, Mussolino ME, Navaneethan SD, Parikh NI, Poudel R, Rezk-Hanna M, Roth GA, Shah NS, St-Onge MP, Thacker EL, Virani SS, Voeks JH, Wang NY, Wong ND, Wong SS, Yaffe K, Martin SS. Heart Disease and Stroke Statistics-2023 Update: A Report From the American Heart Association. Circulation 2023; 147:e93-e621. [PMID: 36695182 DOI: 10.1161/cir.0000000000001123] [Citation(s) in RCA: 1209] [Impact Index Per Article: 1209.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The American Heart Association, in conjunction with the National Institutes of Health, annually reports the most up-to-date statistics related to heart disease, stroke, and cardiovascular risk factors, including core health behaviors (smoking, physical activity, diet, and weight) and health factors (cholesterol, blood pressure, and glucose control) that contribute to cardiovascular health. The Statistical Update presents the latest data on a range of major clinical heart and circulatory disease conditions (including stroke, congenital heart disease, rhythm disorders, subclinical atherosclerosis, coronary heart disease, heart failure, valvular disease, venous disease, and peripheral artery disease) and the associated outcomes (including quality of care, procedures, and economic costs). METHODS The American Heart Association, through its Epidemiology and Prevention Statistics Committee, continuously monitors and evaluates sources of data on heart disease and stroke in the United States to provide the most current information available in the annual Statistical Update with review of published literature through the year before writing. The 2023 Statistical Update is the product of a full year's worth of effort in 2022 by dedicated volunteer clinicians and scientists, committed government professionals, and American Heart Association staff members. The American Heart Association strives to further understand and help heal health problems inflicted by structural racism, a public health crisis that can significantly damage physical and mental health and perpetuate disparities in access to health care, education, income, housing, and several other factors vital to healthy lives. This year's edition includes additional COVID-19 (coronavirus disease 2019) publications, as well as data on the monitoring and benefits of cardiovascular health in the population, with an enhanced focus on health equity across several key domains. RESULTS Each of the chapters in the Statistical Update focuses on a different topic related to heart disease and stroke statistics. CONCLUSIONS The Statistical Update represents a critical resource for the lay public, policymakers, media professionals, clinicians, health care administrators, researchers, health advocates, and others seeking the best available data on these factors and conditions.
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