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Khan SU, Saeed S, Alsuhaibani AM, Fatima S, Ur Rehman K, Zaman U, Ullah M, Refati MS, Lu K. Advances and Challenges for GWAS Analysis in Cardiac Diseases: A Focus on Coronary Artery Disease (CAD). Curr Probl Cardiol 2023:101821. [PMID: 37211304 DOI: 10.1016/j.cpcardiol.2023.101821] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
The achievement of genome-wide association studies (GWAS) has rapidly progressed our understanding of the etiology of coronary artery disease (CAD). It unlocks new strategies to strengthen the stalling of CAD drug development. In this review, we highlighted the recent drawbacks, mainly pointing out those involved in identifying causal genes and interpreting the connections between disease pathology and risk variants. We also benchmark the novel insights into the biological mechanism behind the disease primarily based on outcomes of GWAS. Furthermore, we also shed light on the successful discovery of novel treatment targets by introducing various layers of "omics" data and applying systems genetics strategies. Lastly, we discuss in-depth the significance of precision medicine that is helpful to improve through GWAS analysis in cardiovascular research.
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Affiliation(s)
- Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China; Women Medical and Dental College, Khyber Medical University, Peshawar, KPK, Pakistan
| | - Sumbul Saeed
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia
| | - Amnah Mohammed Alsuhaibani
- Department of Physical Sport Science, College of Education, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Sumaya Fatima
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, China
| | - Khalil Ur Rehman
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Umber Zaman
- Institute of Chemical Sciences, Gomal University, Dera Ismail Khan 29050, Pakistan
| | - Muneeb Ullah
- Department of Pharmacy, Kohat University of Science and Technology, 26000, KPK, Pakistan
| | - Moamen S Refati
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China.
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2
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Jia S, Wang R, Zhang D, Guan Z, Ding T, Zhang J, Zhao X. Quercetin modulates the liver metabolic profile in a chronic unpredictable mild stress rat model based on metabolomics technology. Food Funct 2023; 14:1726-1739. [PMID: 36722921 DOI: 10.1039/d2fo03277e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Depression is the most prevalent psychiatric disease, and its pathogenesis is still unclear. Currently, studies on the pathogenesis of depression are mainly focused on the brain. The liver can modulate brain function via the liver-brain axis, indicating that the liver plays an important role in the development of depression. This study aims to explore the protective effect of quercetin against chronic unpredictable mild stress (CUMS)-induced metabolic changes and the corresponding mechanisms in the rat liver based on untargeted metabolomics technology. In this study, 96 male rats were divided into six groups: control, different doses of quercetin (10 mg per kg bw or 50 mg per kg bw), CUMS, and CUMS + different doses of quercetin. After 8 weeks of CUMS modeling, the liver samples were collected for metabolomics analysis. A total of 17 altered metabolites were identified, including D-glutamic acid, S-adenosylmethionine, lithocholylglycine, L-homocystine, prostaglandin PGE2, leukotriene E4, cholic acid, 5-methyltetrahydrofolic acid, taurochenodeoxycholic acid, S-adenosylhomocysteine, deoxycholic acid, folic acid, L-methionine, leukotriene C5, estriol-17-glucuronide, PE, and PC, indicating that methionine metabolism, bile acid metabolism, and phosphatidylcholine biosynthesis are the major pathways involved in CUMS-induced hepatic metabolic disorders. Hepatic methylation damage may play a role in the pathophysiology of depression, as evidenced by the first discovery of the abnormality of hepatic methionine metabolism. Abnormal changes in hepatic bile acids may provide stronger evidence for depression pathogenesis involving the microbiota-gut-brain axis, suggesting that the liver is involved in depression development and may be a treatment target. The quercetin treatment alleviated the CUMS-induced liver metabolism disorder, suggesting that quercetin may protect against depression by regulating liver metabolism.
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Affiliation(s)
- Siqi Jia
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
| | - Ruijuan Wang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
| | - Dongyan Zhang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
| | - Zhiyu Guan
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
| | - Tingting Ding
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
| | - Jingnan Zhang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
| | - Xiujuan Zhao
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, 194 Xuefu Road, Harbin, Heilongjiang 150081, China.
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Wei B, Liu Y, Li H, Peng Y, Luo Z. Effect of 9p21.3 (lncRNA and CDKN2A/2B) variant on lipid profile. Front Cardiovasc Med 2022; 9:946289. [PMID: 36158791 PMCID: PMC9489913 DOI: 10.3389/fcvm.2022.946289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background Several 9p21.3 variants, such as rs1333049, rs4977574, rs10757274, rs10757278, and rs10811661, identified from recent genome-wide association studies (GWASs) are reported to be associated with coronary artery disease (CAD) susceptibility but independent of dyslipidemia. This study investigated whether these 9p21.3 variants influenced lipid profiles. Methods and results By searching the PubMed and Cochrane databases, 101,099 individuals were included in the analysis. The consistent finding for the rs1333049 C allele on lipid profiles increased the triglyceride (TG) levels. Moreover, the rs4977574 G allele and the rs10757274 G allele, respectively, increased low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL-C) levels. However, the rs10811661 C allele largely reduced LDL-C levels. Subgroup analyses indicated that the effects of the rs1333049 C allele, rs4977574 G allele, and rs10757274 G allele on lipid profiles were stronger in Whites compared with Asians. In contrast, the effect of the rs10811661 C allele on lipid profiles was stronger in Asians compared with Whites. Conclusion The rs1333049 C allele, rs4977574 G allele, and rs10757274 G allele of lncRNA, and the rs10811661 G allele of CDKN2A/2B had a significant influence on lipid levels, which may help the understanding of the underlying mechanisms between 9p21.3 variants and CAD.
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Affiliation(s)
- Baozhu Wei
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
- *Correspondence: Baozhu Wei,
| | - Yang Liu
- Department of Endocrinology, China Resources and WISCO General Hospital, Wuhan, China
| | - Hang Li
- Department of Gerontology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yuanyuan Peng
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Zhi Luo
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Zhi Luo,
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Teng EL, Masutani EM, Yeoman B, Fung J, Lian R, Ngo B, Kumar A, Placone JK, Lo Sardo V, Engler AJ. High shear stress enhances endothelial permeability in the presence of the risk haplotype at 9p21.3. APL Bioeng 2021; 5:036102. [PMID: 34327295 PMCID: PMC8315817 DOI: 10.1063/5.0054639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 11/15/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are exceedingly common in non-coding loci, and while they are significantly associated with a myriad of diseases, their specific impact on cellular dysfunction remains unclear. Here, we show that when exposed to external stressors, the presence of risk SNPs in the 9p21.3 coronary artery disease (CAD) risk locus increases endothelial monolayer and microvessel dysfunction. Endothelial cells (ECs) derived from induced pluripotent stem cells of patients carrying the risk haplotype (R/R WT) differentiated similarly to their non-risk and isogenic knockout (R/R KO) counterparts. Monolayers exhibited greater permeability and reactive oxygen species signaling when the risk haplotype was present. Addition of the inflammatory cytokine TNFα further enhanced EC monolayer permeability but independent of risk haplotype; TNFα also did not substantially alter haplotype transcriptomes. Conversely, when wall shear stress was applied to ECs in a microfluidic vessel, R/R WT vessels were more permeable at lower shear stresses than R/R KO vessels. Transcriptomes of sheared cells clustered more by risk haplotype than by patient or clone, resulting in significant differential regulation of EC adhesion and extracellular matrix genes vs static conditions. A subset of previously identified CAD risk genes invert expression patterns in the presence of high shear concomitant with altered cell adhesion genes, vessel permeability, and endothelial erosion in the presence of the risk haplotype, suggesting that shear stress could be a regulator of non-coding loci with a key impact on CAD.
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Affiliation(s)
- Evan L Teng
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Evan M Masutani
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Benjamin Yeoman
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Jessica Fung
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Rachel Lian
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Brenda Ngo
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Aditya Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Jesse K Placone
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Valentina Lo Sardo
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California 92037, USA
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5
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Roberts R, Chang CC, Hadley T. Genetic Risk Stratification: A Paradigm Shift in Prevention of Coronary Artery Disease. ACTA ACUST UNITED AC 2021; 6:287-304. [PMID: 33778213 PMCID: PMC7987546 DOI: 10.1016/j.jacbts.2020.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
CAD is a pandemic that can be prevented. Conventional risk factors are inadequate to detect who is at risk early in the asymptomatic stage. Genetic risk for CAD can be determined at birth, and those at highest genetic risk have been shown to respond to lifestyle changes and statin therapy with a 40% to 50% reduction in cardiac events. Genetic risk stratification for CAD should be brought to the bedside in an attempt to prevent this pandemic disease.
Coronary artery disease (CAD) is a pandemic disease that is highly preventable as shown by secondary prevention. Primary prevention is preferred knowing that 50% of the population can expect a cardiac event in their lifetime. Risk stratification for primary prevention using the American Heart Association/American College of Cardiology predicted 10-year risk based on conventional risk factors for CAD is less than optimal. Conventional risk factors such as hypertension, cholesterol, and age are age-dependent and not present until the sixth or seventh decade of life. The genetic risk score (GRS), which is estimated from the recently discovered genetic variants predisposed to CAD, offers a potential solution to this dilemma. The GRS, which is derived from genotyping the population with a microarray containing these genetic risk variants, has indicated that genetic risk stratification based on the GRS is superior to that of conventional risk factors in detecting those at high risk and who would benefit most from statin therapy. Studies performed in >1 million individuals confirmed genetic risk stratification is superior and primarily independent of conventional risk factors. Prospective clinical trials based on risk stratification for CAD using the GRS have shown lifestyle changes, physical activity, and statin therapy are associated with 40% to 50% reduction in cardiac events in the high genetic risk group (20%). Genetic risk stratification has the advantage of being innate to an individual’s DNA, and because DNA does not change in a lifetime, it is independent of age. Genetic risk stratification is inexpensive and can be performed worldwide, providing risk analysis at any age and thus has the potential to revolutionize primary prevention.
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Key Words
- ACC, American College of Cardiology
- AHA, American Heart Association
- ANRIL, antisense non-coding RNA in the INK4 Locust
- CAD, coronary artery disease
- GRS, genetic risk score
- GWAS, genome-wide association study
- LDL-C, low-density lipoprotein cholesterol
- MR, Mendelian randomization
- SNP, single nucleotide polymorphism
- bp, base pair
- cardiovascular genetics
- coronary artery disease
- genetic risk score for CAD
- genome-wide association studies
- prevention of CAD
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Affiliation(s)
- Robert Roberts
- Department of Medicine, Dignity Health at St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
| | - Chih Chao Chang
- Department of Medicine, Dignity Health at St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
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Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease. Am J Hum Genet 2021; 108:411-430. [PMID: 33626337 DOI: 10.1016/j.ajhg.2021.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/04/2021] [Indexed: 02/08/2023] Open
Abstract
Genetic factors underlying coronary artery disease (CAD) have been widely studied using genome-wide association studies (GWASs). However, the functional understanding of the CAD loci has been limited by the fact that a majority of GWAS variants are located within non-coding regions with no functional role. High cholesterol and dysregulation of the liver metabolism such as non-alcoholic fatty liver disease confer an increased risk of CAD. Here, we studied the function of non-coding single-nucleotide polymorphisms in CAD GWAS loci located within liver-specific enhancer elements by identifying their potential target genes using liver cis-eQTL analysis and promoter Capture Hi-C in HepG2 cells. Altogether, 734 target genes were identified of which 121 exhibited correlations to liver-related traits. To identify potentially causal regulatory SNPs, the allele-specific enhancer activity was analyzed by (1) sequence-based computational predictions, (2) quantification of allele-specific transcription factor binding, and (3) STARR-seq massively parallel reporter assay. Altogether, our analysis identified 1,277 unique SNPs that display allele-specific regulatory activity. Among these, susceptibility enhancers near important cholesterol homeostasis genes (APOB, APOC1, APOE, and LIPA) were identified, suggesting that altered gene regulatory activity could represent another way by which genetic variation regulates serum lipoprotein levels. Using CRISPR-based perturbation, we demonstrate how the deletion/activation of a single enhancer leads to changes in the expression of many target genes located in a shared chromatin interaction domain. Our integrative genomics approach represents a comprehensive effort in identifying putative causal regulatory regions and target genes that could predispose to clinical manifestation of CAD by affecting liver function.
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7
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Manjula G, Pranavchand R, Kumuda I, Reddy BS, Reddy BM. The SNP rs7865618 of 9p21.3 locus emerges as the most promising marker of coronary artery disease in the southern Indian population. Sci Rep 2020; 10:21511. [PMID: 33298998 PMCID: PMC7726101 DOI: 10.1038/s41598-020-77080-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/05/2020] [Indexed: 11/09/2022] Open
Abstract
Development of coronary artery disease (CAD) is primarily due to the process of atherosclerosis, however the prognosis of CAD depends on pleiotropic effects of the genes located at 9p21.3 region. Genome wide association studies revealed association of variants in this region with CAD pathology. However, specific marker in predicting CAD development or progression is not yet identified. In the present study, 35 SNPs at 9p21.3 region, located in the cyclin dependent kinase inhibitor (CDKN2A/CDKN2B) genes, were genotyped among 350 CAD cases and 480 controls from the southern Indian population of Hyderabad using fluidigm nanofluidic SNP genotyping system and the data were analyzed using PLINK and R softwares. Of the 35 SNPs analysed, only one SNP, rs7865618, was found to be highly significantly associated with CAD, even after correction for multiple testing (p = 0.008). The AG and GG genotypes of this SNP conferred 3.08 and 1.93 folds increased risk for CAD respectively. In particular, this SNP was significantly associated with severe anatomic (triple vessel disease p = 0.023) and phenotypic (acute coronary syndrome p = 0.007) categories of CAD. Pair wise SNP interaction analysis between the SNPs of 9p21.3 and 11q23.3 regions revealed significantly increased risk of three SNPs of 11q23.3 region that were not associated individually, in conjunction with rs7865618 of 9p21.3.
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Affiliation(s)
- Gorre Manjula
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Irgam Kumuda
- Department of Genetics, Osmania University, Hyderabad, India
| | - B Sriteja Reddy
- Dr Pinnamaneni, Siddhartha Institute of Medical Sciences and Research Foundation, Vijayawada, India
| | - Battini Mohan Reddy
- Department of Genetics, Osmania University, Hyderabad, India. .,Molecular Anthropology Group, Indian Statistical Institute, Hyderabad, India. .,Emeritus Scientist (ICMR), Department of Genetics, Osmania University, Hyderabad, 500007, India.
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8
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Cabrera CP, Ng FL, Nicholls HL, Gupta A, Barnes MR, Munroe PB, Caulfield MJ. Over 1000 genetic loci influencing blood pressure with multiple systems and tissues implicated. Hum Mol Genet 2019; 28:R151-R161. [PMID: 31411675 PMCID: PMC6872427 DOI: 10.1093/hmg/ddz197] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/26/2019] [Accepted: 08/05/2019] [Indexed: 12/12/2022] Open
Abstract
High blood pressure (BP) remains the major heritable and modifiable risk factor for cardiovascular disease. Persistent high BP, or hypertension, is a complex trait with both genetic and environmental interactions. Despite swift advances in genomics, translating new discoveries to further our understanding of the underlying molecular mechanisms remains a challenge. More than 500 loci implicated in the regulation of BP have been revealed by genome-wide association studies (GWAS) in 2018 alone, taking the total number of BP genetic loci to over 1000. Even with the large number of loci now associated to BP, the genetic variance explained by all loci together remains low (~5.7%). These genetic associations have elucidated mechanisms and pathways regulating BP, highlighting potential new therapeutic and drug repurposing targets. A large proportion of the BP loci were discovered and reported simultaneously by multiple research groups, creating a knowledge gap, where the reported loci to date have not been investigated in a harmonious way. Here, we review the BP-associated genetic variants reported across GWAS studies and investigate their potential impact on the biological systems using in silico enrichment analyses for pathways, tissues, gene ontology and genetic pleiotropy.
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Affiliation(s)
- Claudia P Cabrera
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Fu Liang Ng
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Hannah L Nicholls
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ajay Gupta
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Michael R Barnes
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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9
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Teng EL, Engler AJ. Mechanical influences on cardiovascular differentiation and disease modeling. Exp Cell Res 2019; 377:103-108. [PMID: 30794804 DOI: 10.1016/j.yexcr.2019.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 01/06/2023]
Abstract
Tissues are continuously exposed to forces in vivo, whether from fluid pressure in an artery from our blood or compressive forces on joints from our body weight. The forces that cells are exposed to arise almost immediately after conception; it is therefore important to understand how forces shape stem cell differentiation into lineage committed cells, how they help organize cells into tissues, and how forces can cause or exacerbate disease. No tissue is exempt, but cardiovascular tissues in particular are exposed to these forces. While animal models have been used extensively in the past, there is growing recognition of their limitations when modeling disease complexity or human genetics. In this mini review, we summarize current understanding of the mechanical influences on the differentiation of cardiovascular progeny, how the transduction of forces influence the onset of disease, and how engineering approaches applied to this problem have yielded systems that create mature-like human tissues in vitro in which to assess the impact of disease on cell function.
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Affiliation(s)
- Evan L Teng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, United States; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, United States
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, United States; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, United States.
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10
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Kumar A, Thomas SK, Wong KC, Lo Sardo V, Cheah DS, Hou YH, Placone JK, Tenerelli KP, Ferguson WC, Torkamani A, Topol EJ, Baldwin KK, Engler AJ. Mechanical activation of noncoding-RNA-mediated regulation of disease-associated phenotypes in human cardiomyocytes. Nat Biomed Eng 2019; 3:137-146. [PMID: 30911429 PMCID: PMC6430136 DOI: 10.1038/s41551-018-0344-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/07/2018] [Indexed: 12/24/2022]
Abstract
How common polymorphisms in noncoding genome regions can regulate cellular function remains largely unknown. Here we show that cardiac fibrosis, mimicked using a hydrogel with controllable stiffness, affects the regulation of the phenotypes of human cardiomyocytes by a portion of the long noncoding RNA ANRIL, the gene of which is located in the disease-associated 9p21 locus. In a physiological environment, cultured cardiomyocytes derived from induced pluripotent stem cells obtained from patients who are homozygous for cardiovascular-risk alleles (R/R cardiomyocytes) or from healthy individuals who are homozygous for nonrisk alleles contracted synchronously, independently of genotype. After hydrogel stiffening to mimic fibrosis, only the R/R cardiomyocytes exhibited asynchronous contractions. These effects were associated with increased expression of the short ANRIL isoform in R/R cardiomyocytes, which induced a c-Jun N-terminal kinase (JNK) phosphorylation-based mechanism that impaired gap junctions (particularly, loss of connexin-43 expression) following stiffening. Deletion of the risk locus or treatment with a JNK antagonist was sufficient to maintain gap junctions and prevent asynchronous contraction of cardiomyocytes. Our findings suggest that mechanical changes in the microenvironment of cardiomyocytes can activate the regulation of their function by noncoding loci.
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Affiliation(s)
- Aditya Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie K Thomas
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kirsten C Wong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Valentina Lo Sardo
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel S Cheah
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Yang-Hsun Hou
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jesse K Placone
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kevin P Tenerelli
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - William C Ferguson
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA, USA
| | - Eric J Topol
- Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristin K Baldwin
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
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11
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Holdt LM, Teupser D. Long Noncoding RNA ANRIL: Lnc-ing Genetic Variation at the Chromosome 9p21 Locus to Molecular Mechanisms of Atherosclerosis. Front Cardiovasc Med 2018; 5:145. [PMID: 30460243 PMCID: PMC6232298 DOI: 10.3389/fcvm.2018.00145] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022] Open
Abstract
Ever since the first genome-wide association studies (GWAS) on coronary artery disease (CAD), the Chr9p21 risk locus has emerged as a top signal in GWAS of atherosclerotic cardiovascular disease, including stroke and peripheral artery disease. The CAD risk SNPs on Chr9p21 lie within a stretch of 58 kilobases of non-protein-coding DNA, containing the gene body of the long noncoding RNA (lncRNA) antisense non coding RNA in the INK4 locus (ANRIL). How risk is affected by the Chr9p21 locus in molecular detail is a matter of ongoing research. Here we will review recent advances in the understanding that ANRIL serves as a key risk effector molecule of atherogenesis at the locus. One focus of this review is the shift in understanding that genetic variation at Chr9p21 not only affects the abundance of ANRIL, and in some cases expression of the adjacent CDKN2A/B tumor suppressors, but also impacts ANRIL splicing, such that 3′-5′-linked circular noncoding ANRIL RNA species are produced. We describe how the balance of linear and circular ANRIL RNA, determined by the Chr9p21 genotype, regulates molecular pathways and cellular functions involved in atherogenesis. We end with an outlook on how manipulating circular ANRIL abundance may be exploited for therapeutic purposes.
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Affiliation(s)
- Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
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12
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Shu L, Blencowe M, Yang X. Translating GWAS Findings to Novel Therapeutic Targets for Coronary Artery Disease. Front Cardiovasc Med 2018; 5:56. [PMID: 29900175 PMCID: PMC5989327 DOI: 10.3389/fcvm.2018.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/11/2018] [Indexed: 12/21/2022] Open
Abstract
The success of genome-wide association studies (GWAS) has significantly advanced our understanding of the etiology of coronary artery disease (CAD) and opens new opportunities to reinvigorate the stalling CAD drug development. However, there exists remarkable disconnection between the CAD GWAS findings and commercialized drugs. While this could implicate major untapped translational and therapeutic potentials in CAD GWAS, it also brings forward extensive technical challenges. In this review we summarize the motivation to leverage GWAS for drug discovery, outline the critical bottlenecks in the field, and highlight several promising strategies such as functional genomics and network-based approaches to enhance the translational value of CAD GWAS findings in driving novel therapeutics
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Affiliation(s)
- Le Shu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, United States
| | - Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, United States.,Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, United States.,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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13
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The rs10757278 Polymorphism of the 9p21.3 Locus in Children with Arterial Ischemic Stroke: A Family-Based and Case-Control Study. J Stroke Cerebrovasc Dis 2017; 26:2763-2768. [DOI: 10.1016/j.jstrokecerebrovasdis.2017.06.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/03/2017] [Accepted: 06/29/2017] [Indexed: 12/23/2022] Open
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Abstract
Coronary artery disease (or coronary heart disease), is the leading cause of mortality in many of the developing as well as the developed countries of the world. Cholesterol-enriched plaques in the heart's blood vessels combined with inflammation lead to the lesion expansion, narrowing of blood vessels, reduced blood flow, and may subsequently cause lesion rupture and a heart attack. Even though several environmental risk factors have been established, such as high LDL-cholesterol, diabetes, and high blood pressure, the underlying genetic composition may substantially modify the disease risk; hence, genome composition and gene-environment interactions may be critical for disease progression. Ongoing scientific efforts have seen substantial advancements related to the fields of genetics and genomics, with the major breakthroughs yet to come. As genomics is the most rapidly advancing field in the life sciences, it is important to present a comprehensive overview of current efforts. Here, we present a summary of various genetic and genomics assays and approaches applied to coronary artery disease research.
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Affiliation(s)
- Milos Pjanic
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Clint L Miller
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Robert Wirka
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Juyong B Kim
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Daniel M DiRenzo
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5233, USA.
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15
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Wang W, Oh S, Koester M, Abramowicz S, Wang N, Tall AR, Welch CL. Enhanced Megakaryopoiesis and Platelet Activity in Hypercholesterolemic, B6-Ldlr-/-, Cdkn2a-Deficient Mice. ACTA ACUST UNITED AC 2016; 9:213-22. [PMID: 27098250 DOI: 10.1161/circgenetics.115.001294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 04/13/2016] [Indexed: 01/17/2023]
Abstract
BACKGROUND Genome-wide association studies for coronary artery disease/myocardial infarction revealed a 58 kb risk locus on 9p21.3. Refined genetic analyses revealed unique haplotype blocks conferring susceptibility to atherosclerosis per se versus risk for acute complications in the presence of underlying coronary artery disease. The cell proliferation inhibitor locus, CDKN2A, maps just upstream of the myocardial infarction risk block, is at least partly regulated by the noncoding RNA, ANRIL, overlapping the risk block, and has been associated with platelet counts in humans. Thus, we tested the hypothesis that CDKN2A deficiency predisposes to increased platelet production, leading to increased platelet activation in the setting of hypercholesterolemia. METHODS AND RESULTS Platelet production and activation were measured in B6-Ldlr(-/-)Cdkn2a(+/-) mice and a congenic strain carrying the region of homology with the human 9p21.3/CDKN2A locus. The strains exhibit decreased expression of CDKN2A (both p16(INK4a) and p19(ARF)) but not CDKN2B (p15(INK4b)). Compared with B6-Ldlr(-/-) controls, both Cdkn2a-deficient strains exhibited increased platelet counts and bone marrow megakaryopoiesis. The platelet overproduction phenotype was reversed by treatment with cyclin-dependent kinase 4/6 inhibitor, PD0332991/palbociclib, that mimics the endogenous effect of p16(INK4a). Western diet feeding resulted in increased platelet activation, increased thrombin/antithrombin complex, and decreased bleeding times in Cdkn2a-deficient mice compared with controls. CONCLUSIONS Together, the data suggest that one or more Cdkn2a transcripts modulate platelet production and activity in the setting of hypercholesterolemia, amenable to pharmaceutical intervention. Enhanced platelet production and activation may predispose to arterial thrombosis, suggesting an explanation, at least in part, for the association of 9p21.3 and myocardial infarction.
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Affiliation(s)
- Wei Wang
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY
| | - Seon Oh
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY
| | - Mark Koester
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY
| | - Sandra Abramowicz
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY
| | - Nan Wang
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY
| | - Alan R Tall
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY
| | - Carrie L Welch
- From the Department of Medicine, Division of Molecular Medicine, Columbia University, New York, NY.
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Abstract
More than 60 genomic loci have been implicated by genome-wide association studies (GWAS) and exome-wide association studies as conferring an increased risk of myocardial infarction and coronary artery disease (CAD). However, the causal gene and variant is often unclear. Using the functional analysis of genetic variants in experimental animal models, we anticipate understanding which candidate gene at a specific locus is associated with atherosclerosis and revealing the underlying molecular and cellular mechanisms, ultimately leading to the identification of causal pathways in atherosclerosis and may provide novel therapeutic targets for the treatment of atherosclerotic cardiovascular disease.
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Affiliation(s)
- Yanhong Guo
- Cardiovascular Center, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | | | - Laiyuan Wang
- Cardiovascular Center, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Y Eugene Chen
- Cardiovascular Center, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA.
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17
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Goncharova IA, Makeeva OA, Golubenko MV, Markov AV, Tarasenko NV, Sleptsov AA, Puzyrev VP. Genes for fibrogenesis in the determination of susceptibility to myocardial infarction. Mol Biol 2016. [DOI: 10.1134/s0026893315060096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Bennett BJ, Davis RC, Civelek M, Orozco L, Wu J, Qi H, Pan C, Packard RRS, Eskin E, Yan M, Kirchgessner T, Wang Z, Li X, Gregory JC, Hazen SL, Gargalovic PS, Lusis AJ. Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains. PLoS Genet 2015; 11:e1005711. [PMID: 26694027 PMCID: PMC4687930 DOI: 10.1371/journal.pgen.1005711] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/06/2015] [Indexed: 12/15/2022] Open
Abstract
Common forms of atherosclerosis involve multiple genetic and environmental factors. While human genome-wide association studies have identified numerous loci contributing to coronary artery disease and its risk factors, these studies are unable to control environmental factors or examine detailed molecular traits in relevant tissues. We now report a study of natural variations contributing to atherosclerosis and related traits in over 100 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP). The mice were made hyperlipidemic by transgenic expression of human apolipoprotein E-Leiden (APOE-Leiden) and human cholesteryl ester transfer protein (CETP). The mice were examined for lesion size and morphology as well as plasma lipid, insulin and glucose levels, and blood cell profiles. A subset of mice was studied for plasma levels of metabolites and cytokines. We also measured global transcript levels in aorta and liver. Finally, the uptake of acetylated LDL by macrophages from HMDP mice was quantitatively examined. Loci contributing to the traits were mapped using association analysis, and relationships among traits were examined using correlation and statistical modeling. A number of conclusions emerged. First, relationships among atherosclerosis and the risk factors in mice resemble those found in humans. Second, a number of trait-loci were identified, including some overlapping with previous human and mouse studies. Third, gene expression data enabled enrichment analysis of pathways contributing to atherosclerosis and prioritization of candidate genes at associated loci in both mice and humans. Fourth, the data provided a number of mechanistic inferences; for example, we detected no association between macrophage uptake of acetylated LDL and atherosclerosis. Fifth, broad sense heritability for atherosclerosis was much larger than narrow sense heritability, indicating an important role for gene-by-gene interactions. Sixth, stepwise linear regression showed that the combined variations in plasma metabolites, including LDL/VLDL-cholesterol, trimethylamine N-oxide (TMAO), arginine, glucose and insulin, account for approximately 30 to 40% of the variation in atherosclerotic lesion area. Overall, our data provide a rich resource for studies of complex interactions underlying atherosclerosis. While recent genetic association studies in human populations have succeeded in identifying genetic loci that contribute to coronary artery disease (CAD) and related phenotypes, these loci explain only a small fraction of the genetic variation in CAD and associated traits. Here, we present a complementary approach using association analysis of atherosclerotic traits among inbred strains of mice. A strength of this approach is that it enables in-depth phenotypic characterization including gene expression and metabolic profiling across a variety of tissues, and integration of these molecular phenotypes with coronary artery disease itself. A striking finding was the large fraction of atherosclerosis that was explained by genetic interactions. Association analysis allowed us to identify genetic loci for atherosclerotic lesion area as well as transcript, cytokine and metabolite levels, and relationships among the traits were examined by correlation and network modeling. The plasma metabolites associated with atherosclerosis in mice, namely, LDL/VLDL-cholesterol, TMAO, arginine, glucose and insulin, overlapped with those observed in humans and accounted for approximately 30 to 40% of the observed variation in atherosclerotic lesion area. In summary, our data provide a detailed overview of the genetic architecture of atherosclerosis in mice and a rich resource for studies of the complex genetic and metabolic interactions that underlie the disease.
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Affiliation(s)
- Brian J. Bennett
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Richard C. Davis
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Mete Civelek
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Luz Orozco
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Judy Wu
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Hannah Qi
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Calvin Pan
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - René R. Sevag Packard
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Mujing Yan
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, New Jersey, United States of America
| | - Todd Kirchgessner
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, New Jersey, United States of America
| | - Zeneng Wang
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Xinmin Li
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Jill C. Gregory
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Stanley L. Hazen
- Department of Cellular and Molecular Medicine (NC10), Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Peter S. Gargalovic
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Princeton, New Jersey, United States of America
| | - Aldons J. Lusis
- Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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Rader DJ. Human genetics of atherothrombotic disease and its risk factors. Arterioscler Thromb Vasc Biol 2015; 35:741-7. [PMID: 25810293 DOI: 10.1161/atvbaha.115.305492] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Daniel J Rader
- From the Departments of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia.
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20
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Hannou SA, Wouters K, Paumelle R, Staels B. Functional genomics of the CDKN2A/B locus in cardiovascular and metabolic disease: what have we learned from GWASs? Trends Endocrinol Metab 2015; 26:176-84. [PMID: 25744911 DOI: 10.1016/j.tem.2015.01.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/27/2015] [Accepted: 01/27/2015] [Indexed: 01/07/2023]
Abstract
Genome-wide association studies (GWASs) provide an unprecedented opportunity to examine, on a large scale, the association of common genetic variants with complex diseases like type 2 diabetes (T2D) and cardiovascular disease (CVD), thus allowing the identification of new potential disease loci. Using this approach, numerous studies have associated SNPs on chromosome 9p21.3 situated near the cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) locus with the risk for coronary artery disease (CAD) and T2D. However, identifying the function of the nearby gene products (CDKN2A/B and ANRIL) in the pathophysiology of these conditions requires functional genomic studies. We review the current knowledge, from studies using human and mouse models, describing the function of CDKN2A/B gene products, which may mechanistically link the 9p21.3 risk locus with CVD and diabetes.
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Affiliation(s)
- Sarah Anissa Hannou
- University of Lille, F-59000, Lille, France; Inserm, U1011, F-59000, Lille, France; European Genomic Institute for Diabetes (EGID), FR3508, Lille, France; Institut Pasteur de Lille, F-59019, Lille, France; Centre National de la Recherche Scientifique (CNRS), UMR 8199, Lille, France
| | - Kristiaan Wouters
- Cardiovascular Research Institute Maastricht (CARIM), Department of Internal Medicine, Maastricht University Medical Center (MUMC), Maastricht, The Netherlands
| | - Réjane Paumelle
- University of Lille, F-59000, Lille, France; Inserm, U1011, F-59000, Lille, France; European Genomic Institute for Diabetes (EGID), FR3508, Lille, France; Institut Pasteur de Lille, F-59019, Lille, France
| | - Bart Staels
- University of Lille, F-59000, Lille, France; Inserm, U1011, F-59000, Lille, France; European Genomic Institute for Diabetes (EGID), FR3508, Lille, France; Institut Pasteur de Lille, F-59019, Lille, France.
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21
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Fuentes-Antrás J, Picatoste B, Ramírez E, Egido J, Tuñón J, Lorenzo Ó. Targeting metabolic disturbance in the diabetic heart. Cardiovasc Diabetol 2015; 14:17. [PMID: 25856422 PMCID: PMC4328972 DOI: 10.1186/s12933-015-0173-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/02/2015] [Indexed: 02/07/2023] Open
Abstract
Diabetic cardiomyopathy is defined as ventricular dysfunction initiated by alterations in cardiac energy substrates in the absence of coronary artery disease and hypertension. In addition to the demonstrated burden of cardiovascular events associated with diabetes, diabetic cardiomyopathy partly explains why diabetic patients are subject to a greater risk of heart failure and a worse outcome after myocardial ischemia. The raising prevalence and accumulating costs of cardiovascular disease in diabetic patients underscore the deficiencies of tertiary prevention and call for a shift in medical treatment. It is becoming increasingly clearer that the effective prevention and treatment of diabetic cardiomyopathy require measures to regulate the metabolic derangement occurring in the heart rather than merely restoring suitable systemic parameters. Recent research has provided deeper insight into the metabolic etiology of diabetic cardiomyopathy and numerous heart-specific targets that may substitute or reinforce current strategies. From both experimental and translational perspectives, in this review we first discuss the progress made with conventional therapies, and then focus on the need for prospective metabolic targets that may avert myocardial vulnerability and functional decline in next-generation diabetic care.
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Affiliation(s)
- Jesús Fuentes-Antrás
- />Vascular, Renal and Diabetes Laboratory, IIS-Fundación Jiménez Díaz, Autónoma University, Av. Reyes Católicos 2, Madrid, 28040 Spain
| | - Belén Picatoste
- />Vascular, Renal and Diabetes Laboratory, IIS-Fundación Jiménez Díaz, Autónoma University, Av. Reyes Católicos 2, Madrid, 28040 Spain
- />Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) network, Madrid, Spain
| | - Elisa Ramírez
- />Vascular, Renal and Diabetes Laboratory, IIS-Fundación Jiménez Díaz, Autónoma University, Av. Reyes Católicos 2, Madrid, 28040 Spain
- />Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) network, Madrid, Spain
| | - Jesús Egido
- />Vascular, Renal and Diabetes Laboratory, IIS-Fundación Jiménez Díaz, Autónoma University, Av. Reyes Católicos 2, Madrid, 28040 Spain
- />Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) network, Madrid, Spain
| | - José Tuñón
- />Vascular, Renal and Diabetes Laboratory, IIS-Fundación Jiménez Díaz, Autónoma University, Av. Reyes Católicos 2, Madrid, 28040 Spain
| | - Óscar Lorenzo
- />Vascular, Renal and Diabetes Laboratory, IIS-Fundación Jiménez Díaz, Autónoma University, Av. Reyes Católicos 2, Madrid, 28040 Spain
- />Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM) network, Madrid, Spain
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Abstract
The 9p21.3 locus was the first to yield to genome-wide association studies (GWAS) seeking common genetic variants predisposing to increased risk of coronary artery atherosclerotic disease (CAD). The 59 single nucleotide polymorphisms that show highest association with CAD are clustered in a region 100,000 to 150,000 base pairs 5' to the cyclin-dependent kinase inhibitors CDKN2B (coding for p15(ink4b)) and CDKN2A (coding for p16(ink4a) and p14(ARF)). This region also covers the 3' end of a long noncoding RNA transcribed antisense to CDKN2B (CDKN2BAS, aka ANRIL for antisense noncoding RNA at the ink4 locus) whose expression has been linked to chromatin remodeling at the locus. Despite intensive investigation over the past 7 years, the functional significance of the 9p21.3 locus remains elusive. Other variants at this locus have been associated with glaucoma, glioma, and type 2 diabetes mellitus, diseases that implicate tissue-resident macrophages. Here, we review the evidence that genetic variants at 9p21.3 disrupt tissue-specific enhancers and propose new insights to guide future studies.
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Abstract
Genome-wide association studies for coronary artery disease utilizing the case control association study approach has identified 50 genetic risk variants associated with coronary artery disease or myocardial infarction. All of these genetic variants are of genome wide significance and replicated in an independent population. It is of note that 35 of these 50 genetic risk variants act through mechanisms as yet unknown. These findings have great implications for the pathogenesis of atherosclerosis, as well as new targets for the development of novel therapies for the prevention and treatment of CAD. The genetic variant PCSK9 has already led to the development of a monoclonal anti-body which is undergoing assessment in phases I, II, and III clinical trials. This therapy shows very promising results and since it increases removal of LDL-C, it is complementary to current statin therapy. Assessing the beneficial or deleterious effects of a lifelong exposure to a genetic risk variant (Mendelian randomization) will be an important adjunct to clinical trials.
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Affiliation(s)
- Robert Roberts
- From the Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
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25
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Patel RS, Asselbergs FW, Quyyumi AA, Palmer TM, Finan CI, Tragante V, Deanfield J, Hemingway H, Hingorani AD, Holmes MV. Genetic variants at chromosome 9p21 and risk of first versus subsequent coronary heart disease events: a systematic review and meta-analysis. J Am Coll Cardiol 2014; 63:2234-45. [PMID: 24607648 PMCID: PMC4035794 DOI: 10.1016/j.jacc.2014.01.065] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/07/2014] [Accepted: 01/22/2014] [Indexed: 11/30/2022]
Abstract
Objectives The purpose of this analysis was to compare the association between variants at the chromosome 9p21 locus (Ch9p21) and risk of first versus subsequent coronary heart disease (CHD) events through systematic review and meta-analysis. Background Ch9p21 is a recognized risk factor for a first CHD event. However, its association with risk of subsequent events in patients with established CHD is less clear. Methods We searched PubMed and EMBASE for prospective studies reporting association of Ch9p21 with incident CHD events and extracted information on cohort type (individuals without prior CHD or individuals with established CHD) and effect estimates for risk of events. Results We identified 31 cohorts reporting on 193,372 individuals. Among the 16 cohorts of individuals without prior CHD (n = 168,209), there were 15,664 first CHD events. Ch9p21 was associated with a pooled hazard ratio (HR) of a first event of 1.19 (95% confidence interval: 1.17 to 1.22) per risk allele. In individuals with established CHD (n = 25,163), there were 4,436 subsequent events providing >99% and 91% power to detect a per-allele HR of 1.19 or 1.10, respectively. The pooled HR for subsequent events was 1.01 (95% confidence interval: 0.97 to 1.06) per risk allele. There was strong evidence of heterogeneity between the effect estimates for first and subsequent events (p value for heterogeneity = 5.6 × 10−11). We found no evidence for biases to account for these findings. Conclusions Ch9p21 shows differential association with risk of first versus subsequent CHD events. This has implications for genetic risk prediction in patients with established CHD and for mechanistic understanding of how Ch9p21 influences risk of CHD.
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Affiliation(s)
- Riyaz S Patel
- Department of Epidemiology and Public Health, University College London, London, United Kingdom; Department of Cardiology, The Heart Hospital, University College London NHS Trust, London, United Kingdom; Genetic Epidemiology Group, Department of Epidemiology and Public Health, Institute of Cardiovascular Science, University College London, London, United Kingdom.
| | - Folkert W Asselbergs
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, Institute of Cardiovascular Science, University College London, London, United Kingdom; Department of Cardiology, Division of Heart & Lungs, University Medical Center, Utrecht, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, the Netherlands
| | - Arshed A Quyyumi
- Department of Medicine, Emory Clinical Cardiovascular Research Institute, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia
| | - Tom M Palmer
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Chris I Finan
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Vinicius Tragante
- Department of Cardiology, Division of Heart & Lungs, University Medical Center, Utrecht, the Netherlands
| | - John Deanfield
- National Institute for Cardiovascular Outcome Research, University College London, London, United Kingdom
| | - Harry Hemingway
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Aroon D Hingorani
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Michael V Holmes
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, Institute of Cardiovascular Science, University College London, London, United Kingdom; Department of Surgery, Division of Transplantation, and Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Kojima Y, Downing K, Kundu R, Miller C, Dewey F, Lancero H, Raaz U, Perisic L, Hedin U, Schadt E, Maegdefessel L, Quertermous T, Leeper NJ. Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis. J Clin Invest 2014. [PMID: 24531546 DOI: 10.1172/jci7039170391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
Genetic variation at the chromosome 9p21 risk locus promotes cardiovascular disease; however, it is unclear how or which proteins encoded at this locus contribute to disease. We have previously demonstrated that loss of one candidate gene at this locus, cyclin-dependent kinase inhibitor 2B (Cdkn2b), in mice promotes vascular SMC apoptosis and aneurysm progression. Here, we investigated the role of Cdnk2b in atherogenesis and found that in a mouse model of atherosclerosis, deletion of Cdnk2b promoted advanced development of atherosclerotic plaques composed of large necrotic cores. Furthermore, human carriers of the 9p21 risk allele had reduced expression of CDKN2B in atherosclerotic plaques, which was associated with impaired expression of calreticulin, a ligand required for activation of engulfment receptors on phagocytic cells. As a result of decreased calreticulin, CDKN2B-deficient apoptotic bodies were resistant to efferocytosis and not efficiently cleared by neighboring macrophages. These uncleared SMCs elicited a series of proatherogenic juxtacrine responses associated with increased foam cell formation and inflammatory cytokine elaboration. The addition of exogenous calreticulin reversed defects associated with loss of Cdkn2b and normalized engulfment of Cdkn2b-deficient cells. Together, these data suggest that loss of CDKN2B promotes atherosclerosis by increasing the size and complexity of the lipid-laden necrotic core through impaired efferocytosis.
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Kojima Y, Downing K, Kundu R, Miller C, Dewey F, Lancero H, Raaz U, Perisic L, Hedin U, Schadt E, Maegdefessel L, Quertermous T, Leeper NJ. Cyclin-dependent kinase inhibitor 2B regulates efferocytosis and atherosclerosis. J Clin Invest 2014; 124:1083-97. [PMID: 24531546 DOI: 10.1172/jci70391] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 12/05/2013] [Indexed: 12/14/2022] Open
Abstract
Genetic variation at the chromosome 9p21 risk locus promotes cardiovascular disease; however, it is unclear how or which proteins encoded at this locus contribute to disease. We have previously demonstrated that loss of one candidate gene at this locus, cyclin-dependent kinase inhibitor 2B (Cdkn2b), in mice promotes vascular SMC apoptosis and aneurysm progression. Here, we investigated the role of Cdnk2b in atherogenesis and found that in a mouse model of atherosclerosis, deletion of Cdnk2b promoted advanced development of atherosclerotic plaques composed of large necrotic cores. Furthermore, human carriers of the 9p21 risk allele had reduced expression of CDKN2B in atherosclerotic plaques, which was associated with impaired expression of calreticulin, a ligand required for activation of engulfment receptors on phagocytic cells. As a result of decreased calreticulin, CDKN2B-deficient apoptotic bodies were resistant to efferocytosis and not efficiently cleared by neighboring macrophages. These uncleared SMCs elicited a series of proatherogenic juxtacrine responses associated with increased foam cell formation and inflammatory cytokine elaboration. The addition of exogenous calreticulin reversed defects associated with loss of Cdkn2b and normalized engulfment of Cdkn2b-deficient cells. Together, these data suggest that loss of CDKN2B promotes atherosclerosis by increasing the size and complexity of the lipid-laden necrotic core through impaired efferocytosis.
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Shanker J, Arvind P, Jambunathan S, Nair J, Kakkar V. Genetic analysis of the 9p21.3 CAD risk locus in Asian Indians. Thromb Haemost 2014; 111:960-9. [PMID: 24452806 DOI: 10.1160/th13-08-0706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/16/2013] [Indexed: 12/27/2022]
Abstract
The 9p21.3 locus is the best replicated region to date for coronary artery disease (CAD). We investigated the association of 9p21.3 common variants with CAD, candidate gene expression including ANRIL, a non-coding RNA, followed by in vitro validation. Five variants, rs10757278, rs10757274, rs2383206, rs1333049 and rs4977574 were genotyped in 1,034 cases and 1,034 controls. Gene expression of C9orf5, MTAP1, MTAP 2, p16INK4a, p14ARF, p15INK4b and two ANRIL splice variants, NR_003529 and EU741058, were measured in 100 cases and 100 controls. Human aortic smooth muscle cells (HuAoSMCs) were transfected with siRNA targeting ANRIL exon 19 (siRNA-1) or exon 2 (siRNA-2) and consequent effect determined. rs2383206 showed the highest association with CAD (odds ratio [OR] 2.02, 95% confidence interval [CI] 1.56 -2.62) and an adjusted OR of 2.55, 1.33-2.88 along with rs10757278. Conventional risk factors (conventional RFs), rs2383206 and rs10757278 variants together yielded a higher c index (OR 0.790, 95% CI 0.770 -0.810) as compared to conventional RFs (OR 0.783, 95% CI 0.763-0.803) or genetic variants (OR 0.561, 95% CI 0.536-0.586) alone. GAAAA haplotype showed significant protective association with CAD compared to CGGGG risk haplotype (OR 0.45, 95% CI 0.27-0.77). Expression of p16INK4a, p14ARF and p15INK4b as well as plasma CDKN2A levels were lower in cases than controls. GG genotype was associated with higher EU741058 expression and lower p16INK4a expression. HuAoSMCs transfected with siRNA-1 showed lower NR_003529, p16INK4aand p14ARFexpression. Our study provides further evidence on the significance of 9p21.3 locus for CAD wherein the risk allele regulate the expression of ANRIL and adjacent tumour suppressor genes which in turn alter smooth muscle proliferation, a fundamental process in atherosclerosis.
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Affiliation(s)
- Jayashree Shanker
- Dr. Jayashree Shanker, Mary and Garry Weston Functional Genomics Unit, Thrombosis Research Institute, India, Narayana Hrudayalaya 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore 560099, Karnataka, India, Tel.: +91 80 27835303, Fax: +91 80 27835302, E-mail:
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Abstract
The latest genome-wide association studies (GWAS) have re-energized our effort to understand the genetic basis of atherosclerotic cardiovascular disease. Although the knowledge generated by GWAS has confirmed that mediators of inflammation and perturbed lipid metabolism are major players in cardiovascular disease (CVD) development, much of individual disease heritability remains unexplained by the variants identified through GWAS. Moreover, results from interventions that aim at the pharmaceutical modification of lipid parameters fall short of expectation. These elusive treatment goals based on heritability studies highlight a key supportive, and perhaps even primary, role of nutritional therapy to achieve better health outcomes. Nonetheless, effective and specific interventions for CVD prevention using principles of "personalized" nutrition require a better knowledge of gene-diet interactions, an area that remains poorly explored. Dietary fatty acids such as omega-3 polyunsaturated fatty acids (PUFAs) are an excellent example of a widely studied "environment" that interacts with the genetic makeup in relation to CVD. A thorough exploration of the nutrigenomics and nutrigenetics of omega-3 PUFAs is key to understanding the etiology, and developing effective preventive measures. In this review, we will summarize the current state of knowledge of genetic interactions with omega-3 PUFAs in modulating lipid metabolism and inflammation, and defining health outcomes. Nutrigenetics and nutrigenomics are still in their infancy with respect to CVD prediction and therapy. Integration of the progress in the omics, including metabolomics, lipidomics, transcriptomics, and proteomics, coupled with advances in nutrigenomic and nutrigenetic research will move us towards personalized medicine as the ultimate paradigm of responsible clinical practice.
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Affiliation(s)
- Aksam J Merched
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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Patel A, Schwab R, Liu YT, Bafna V. Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. Genome Res 2013; 24:318-28. [PMID: 24307551 PMCID: PMC3912422 DOI: 10.1101/gr.161497.113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Deletion of tumor-suppressor genes as well as other genomic rearrangements pervade cancer genomes across numerous types of solid tumor and hematologic malignancies. However, even for a specific rearrangement, the breakpoints may vary between individuals, such as the recurrent CDKN2A deletion. Characterizing the exact breakpoints for structural variants (SVs) is useful for designating patient-specific tumor biomarkers. We propose AmBre (Amplification of Breakpoints), a method to target SV breakpoints occurring in samples composed of heterogeneous tumor and germline DNA. Additionally, AmBre validates SVs called by whole-exome/genome sequencing and hybridization arrays. AmBre involves a PCR-based approach to amplify the DNA segment containing an SV's breakpoint and then confirms breakpoints using sequencing by Pacific Biosciences RS. To amplify breakpoints with PCR, primers tiling specified target regions are carefully selected with a simulated annealing algorithm to minimize off-target amplification and maximize efficiency at capturing all possible breakpoints within the target regions. To confirm correct amplification and obtain breakpoints, PCR amplicons are combined without barcoding and simultaneously long-read sequenced using a single SMRT cell. Our algorithm efficiently separates reads based on breakpoints. Each read group supporting the same breakpoint corresponds with an amplicon and a consensus amplicon sequence is called. AmBre was used to discover CDKN2A deletion breakpoints in cancer cell lines: A549, CEM, Detroit562, MOLT4, MCF7, and T98G. Also, we successfully assayed RUNX1–RUNX1T1 reciprocal translocations by finding both breakpoints in the Kasumi-1 cell line. AmBre successfully targets SVs where DNA harboring the breakpoints are present in 1:1000 mixtures.
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Affiliation(s)
- Anand Patel
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California 92093, USA
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Abstract
At least 468 individual genes have been manipulated by molecular methods to study their effects on the initiation, promotion, and progression of atherosclerosis. Most clinicians and many investigators, even in related disciplines, find many of these genes and the related pathways entirely foreign. Medical schools generally do not attempt to incorporate the relevant molecular biology into their curriculum. A number of key signaling pathways are highly relevant to atherogenesis and are presented to provide a context for the gene manipulations summarized herein. The pathways include the following: the insulin receptor (and other receptor tyrosine kinases); Ras and MAPK activation; TNF-α and related family members leading to activation of NF-κB; effects of reactive oxygen species (ROS) on signaling; endothelial adaptations to flow including G protein-coupled receptor (GPCR) and integrin-related signaling; activation of endothelial and other cells by modified lipoproteins; purinergic signaling; control of leukocyte adhesion to endothelium, migration, and further activation; foam cell formation; and macrophage and vascular smooth muscle cell signaling related to proliferation, efferocytosis, and apoptosis. This review is intended primarily as an introduction to these key signaling pathways. They have become the focus of modern atherosclerosis research and will undoubtedly provide a rich resource for future innovation toward intervention and prevention of the number one cause of death in the modern world.
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Affiliation(s)
- Paul N Hopkins
- Cardiovascular Genetics, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.
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Horswell SD, Fryer LGD, Hutchison CE, Zindrou D, Speedy HE, Town MM, Duncan EJ, Sivapackianathan R, Patel HN, Jones EL, Braithwaite A, Salm MPA, Neuwirth CKY, Potter E, Anderson JR, Taylor KM, Seed M, Betteridge DJ, Crook MA, Wierzbicki AS, Scott J, Naoumova RP, Shoulders CC. CDKN2B expression in adipose tissue of familial combined hyperlipidemia patients. J Lipid Res 2013; 54:3491-505. [PMID: 24103848 DOI: 10.1194/jlr.m041814] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this study was to determine the core biological processes perturbed in the subcutaneous adipose tissue of familial combined hyperlipidemia (FCHL) patients. Annotation of FCHL and control microarray datasets revealed a distinctive FCHL transcriptome, characterized by gene expression changes regulating five overlapping systems: the cytoskeleton, cell adhesion and extracellular matrix; vesicular trafficking; lipid homeostasis; and cell cycle and apoptosis. Expression values for the cell-cycle inhibitor CDKN2B were increased, replicating data from an independent FCHL cohort. In 3T3-L1 cells, CDKN2B knockdown induced C/EBPα expression and lipid accumulation. The minor allele at SNP site rs1063192 (C) was predicted to create a perfect seed for the human miRNA-323b-5p. A miR-323b-5p mimic significantly reduced endogenous CDKN2B protein levels and the activity of a CDKN2B 3'UTR luciferase reporter carrying the rs1063192 C allele. Although the allele displayed suggestive evidence of association with reduced CDKN2B mRNA in the MuTHER adipose tissue dataset, family studies suggest the association between increased CDKN2B expression and FCHL-lipid abnormalities is driven by factors external to this gene locus. In conclusion, from a comparative annotation analysis of two separate FCHL adipose tissue transcriptomes and a subsequent focus on CDKN2B, we propose that dysfunctional adipogenesis forms an integral part of FCHL pathogenesis.
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Affiliation(s)
- Stuart D Horswell
- Medical Research Council, Clinical Sciences Centre, Hammersmith Hospital, London, United Kingdom
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Abstract
PURPOSE OF REVIEW Since 2007, genome-wide association studies (GWAS) have led to the identification of numerous loci of atherosclerotic cardiovascular disease. The majority of these loci harbor genes previously not known to be involved in atherogenesis. In this review, we summarize the recent progress in understanding the pathophysiology of genetic variants in atherosclerosis. RECENT FINDINGS Fifty-eight loci with P < 10⁻⁷ have been identified in GWAS for coronary heart disease and myocardial infarction. Of these, 23 loci (40%) overlap with GWAS loci of classical risk factors such as lipids, blood pressure, and diabetes mellitus, suggesting a potential causal relation. The vast majority of the remaining 35 loci (60%) are at genomic regions where the mechanism in atherogenesis is unclear. Loci most frequently found in independent GWAS were at Chr9p21.3 (ANRIL/CDKN2B-AS1), Chr6p24.1 (PHACTR1), and Chr1p13.3 (CELSR2, PSRC1, MYBPHL, SORT1). Recent work suggests that Chr9p21.3 exerts its effects through epigenetic regulation of target genes, whereas mechanisms at Chr6p24.1 remain obscure, and Chr1p13.3 affects plasma LDL cholesterol. SUMMARY Novel GWAS loci indicate that our understanding of atherosclerosis is limited and implicate a role of hitherto unknown mechanisms, such as epigenetic gene regulation in atherogenesis.
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Affiliation(s)
- Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital Munich-LMU and Ludwig-Maximilians-University Munich, Munich, Germany
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Lv X, Zhang Y, Rao S, Su D, Feng D, Wang M, Li X, Li D, Guo H, Zuo X, Xia M, Ouyang H, Ling W, Qiu J. Association between rs10118757(A/G) in methylthioadenosine phosphorylase gene and coronary artery disease in Chinese Hans. Gene 2013; 526:344-6. [PMID: 23462334 DOI: 10.1016/j.gene.2013.02.013] [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: 08/12/2012] [Revised: 12/28/2012] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Studies focusing on the association of gene methylthioadenosine phosphorylase (MTAP) with the risk of coronary artery disease (CAD) and myocardial infarction (MI) are limited. In this study, we explored the effects of rs10118757 in MTAP gene on CAD and MI by performing association analysis in a Chinese Han population. rs10118757 was genotyped in 1007 CAD patients (including 338 MI patients) and 885 healthy controls. Allelic analysis showed that allele A of rs10118757 was associated with increased risk of CAD, with OR (95%CI)=1.193 (1.035-1.376), and P=0.015. After adjusted for age, BMI, gender, hypertension and smoking, rs10118757 was still significantly associated with CAD under additive and dominant models, with OR (95%CI)=1.252 (1.070-1.465), P=0.005, and OR (95%CI)=1.698 (1.168-2.467), P=0.006, respectively. Compared to additive model, dominant model may be the best-fitting model (P=6.63E-10 vs P=6.70E-10). As reported previously, rs10118757 was not associated with MI in the current study. Our study firstly reported that SNP rs10118757 was associated with CAD risk in a Chinese Han population, indicating that MTAP gene may play a potential role in the pathophysiological process of CAD.
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Affiliation(s)
- Xiaofei Lv
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Nutrition, School of Public Health, Sun Yat-Sen University (Northern Campus), 74 Zhongshan Road 2, Guangzhou, 510080, China.
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Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, Gielen S, Schuler G, Gäbel G, Bergert H, Bechmann I, Stadler PF, Thiery J, Teupser D. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet 2013; 9:e1003588. [PMID: 23861667 PMCID: PMC3701717 DOI: 10.1371/journal.pgen.1003588] [Citation(s) in RCA: 287] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/09/2013] [Indexed: 01/01/2023] Open
Abstract
The chromosome 9p21 (Chr9p21) locus of coronary artery disease has been identified in the first surge of genome-wide association and is the strongest genetic factor of atherosclerosis known today. Chr9p21 encodes the long non-coding RNA (ncRNA) antisense non-coding RNA in the INK4 locus (ANRIL). ANRIL expression is associated with the Chr9p21 genotype and correlated with atherosclerosis severity. Here, we report on the molecular mechanisms through which ANRIL regulates target-genes in trans, leading to increased cell proliferation, increased cell adhesion and decreased apoptosis, which are all essential mechanisms of atherogenesis. Importantly, trans-regulation was dependent on Alu motifs, which marked the promoters of ANRIL target genes and were mirrored in ANRIL RNA transcripts. ANRIL bound Polycomb group proteins that were highly enriched in the proximity of Alu motifs across the genome and were recruited to promoters of target genes upon ANRIL over-expression. The functional relevance of Alu motifs in ANRIL was confirmed by deletion and mutagenesis, reversing trans-regulation and atherogenic cell functions. ANRIL-regulated networks were confirmed in 2280 individuals with and without coronary artery disease and functionally validated in primary cells from patients carrying the Chr9p21 risk allele. Our study provides a molecular mechanism for pro-atherogenic effects of ANRIL at Chr9p21 and suggests a novel role for Alu elements in epigenetic gene regulation by long ncRNAs. Chromosome 9p21 is the strongest genetic factor for coronary artery disease and encodes the long non-coding RNA (ncRNA) ANRIL. Here, we show that increased ANRIL expression mediates atherosclerosis risk through trans-regulation of gene networks leading to pro-atherogenic cellular properties, such as increased proliferation and adhesion. ANRIL may act as a scaffold, guiding effector-proteins to chromatin. These functions depend on an Alu motif present in ANRIL RNA and mirrored several thousand-fold in the genome. Alu elements are a family of primate-specific short interspersed repeat elements (SINEs) and have been linked with genetic disease. Current models propose that either exonisation of Alu elements or changes of cis-regulation of adjacent genes are the underlying disease mechanisms. Our work extends the function of Alu transposons to regulatory components of long ncRNAs with a central role in epigenetic trans-regulation. Furthermore, it implies a pivotal role for Alu elements in genetically determined vascular disease and describes a plausible molecular mechanism for a pro-atherogenic function of ANRIL at chromosome 9p21.
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Affiliation(s)
- Lesca M. Holdt
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Steve Hoffmann
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Transcriptome Bioinformatics Group and Interdisciplinary Centre for Bioinformatics, University Leipzig, Leipzig, Germany
| | - Kristina Sass
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - David Langenberger
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Transcriptome Bioinformatics Group and Interdisciplinary Centre for Bioinformatics, University Leipzig, Leipzig, Germany
| | - Markus Scholz
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University Leipzig, Leipzig, Germany
| | - Knut Krohn
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Interdisciplinary Center for Clinical Research, University Leipzig, Leipzig, Germany
| | - Knut Finstermeier
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Anika Stahringer
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Wolfgang Wilfert
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Frank Beutner
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Department of Internal Medicine/Cardiology, Heart Center, University Leipzig, Leipzig, Germany
| | - Stephan Gielen
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Department of Internal Medicine/Cardiology, Heart Center, University Leipzig, Leipzig, Germany
| | - Gerhard Schuler
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Department of Internal Medicine/Cardiology, Heart Center, University Leipzig, Leipzig, Germany
| | - Gabor Gäbel
- Department of General, Thoracic, and Vascular Surgery, University Dresden, Dresden, Germany
| | - Hendrik Bergert
- Department of General, Thoracic, and Vascular Surgery, University Dresden, Dresden, Germany
| | - Ingo Bechmann
- Institute of Anatomy, University Leipzig, Leipzig, Germany
| | - Peter F. Stadler
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Transcriptome Bioinformatics Group and Interdisciplinary Centre for Bioinformatics, University Leipzig, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Joachim Thiery
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Daniel Teupser
- LIFE – Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
- * E-mail:
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Chan K, Patel RS, Newcombe P, Nelson CP, Qasim A, Epstein SE, Burnett S, Vaccarino VL, Zafari AM, Shah SH, Anderson JL, Carlquist JF, Hartiala J, Allayee H, Hinohara K, Lee BS, Erl A, Ellis KL, Goel A, Schaefer AS, El Mokhtari NE, Goldstein BA, Hlatky MA, Go AS, Shen GQ, Gong Y, Pepine C, Laxton RC, Whittaker JC, Tang WHW, Johnson JA, Wang QK, Assimes TL, Nöthlings U, Farrall M, Watkins H, Richards AM, Cameron VA, Muendlein A, Drexel H, Koch W, Park JE, Kimura A, Shen WF, Simpson IA, Hazen SL, Horne BD, Hauser ER, Quyyumi AA, Reilly MP, Samani NJ, Ye S. Association between the chromosome 9p21 locus and angiographic coronary artery disease burden: a collaborative meta-analysis. J Am Coll Cardiol 2013; 61:957-70. [PMID: 23352782 DOI: 10.1016/j.jacc.2012.10.051] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/30/2012] [Indexed: 01/21/2023]
Abstract
OBJECTIVES This study sought to ascertain the relationship of 9p21 locus with: 1) angiographic coronary artery disease (CAD) burden; and 2) myocardial infarction (MI) in individuals with underlying CAD. BACKGROUND Chromosome 9p21 variants have been robustly associated with coronary heart disease, but questions remain on the mechanism of risk, specifically whether the locus contributes to coronary atheroma burden or plaque instability. METHODS We established a collaboration of 21 studies consisting of 33,673 subjects with information on both CAD (clinical or angiographic) and MI status along with 9p21 genotype. Tabular data are provided for each cohort on the presence and burden of angiographic CAD, MI cases with underlying CAD, and the diabetic status of all subjects. RESULTS We first confirmed an association between 9p21 and CAD with angiographically defined cases and control subjects (pooled odds ratio [OR]: 1.31, 95% confidence interval [CI]: 1.20 to 1.43). Among subjects with angiographic CAD (n = 20,987), random-effects model identified an association with multivessel CAD, compared with those with single-vessel disease (OR: 1.10, 95% CI: 1.04 to 1.17)/copy of risk allele). Genotypic models showed an OR of 1.15, 95% CI: 1.04 to 1.26 for heterozygous carrier and OR: 1.23, 95% CI: 1.08 to 1.39 for homozygous carrier. Finally, there was no significant association between 9p21 and prevalent MI when both cases (n = 17,791) and control subjects (n = 15,882) had underlying CAD (OR: 0.99, 95% CI: 0.95 to 1.03)/risk allele. CONCLUSIONS The 9p21 locus shows convincing association with greater burden of CAD but not with MI in the presence of underlying CAD. This adds further weight to the hypothesis that 9p21 locus primarily mediates an atherosclerotic phenotype.
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Affiliation(s)
- Kenneth Chan
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University London, London, United Kingdom
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ANRIL: molecular mechanisms and implications in human health. Int J Mol Sci 2013; 14:1278-92. [PMID: 23306151 PMCID: PMC3565320 DOI: 10.3390/ijms14011278] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/28/2012] [Accepted: 01/04/2013] [Indexed: 01/19/2023] Open
Abstract
ANRIL is a recently discovered long non-coding RNA encoded in the chromosome 9p21 region. This locus is a hotspot for disease-associated polymorphisms, and it has been consistently associated with cardiovascular disease, and more recently with several cancers, diabetes, glaucoma, endometriosis among other conditions. ANRIL has been shown to regulate its neighbor tumor suppressors CDKN2A/B by epigenetic mechanisms and thereby regulate cell proliferation and senescence. However, the clear role of ANRIL in the pathogenesis of these conditions is yet to be understood. Here, we review the recent findings on ANRIL molecular characterization and function, with a particular focus on its implications in human disease.
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Hamsten A, Eriksson P. Quest for genes and mechanisms linking the human chromosome 9p21.3 locus to cardiovascular disease. Circulation 2012; 126:1815-7. [PMID: 23044606 DOI: 10.1161/circulationaha.112.136556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Leeper NJ, Raiesdana A, Kojima Y, Kundu RK, Cheng H, Maegdefessel L, Toh R, Ahn GO, Ali ZA, Anderson DR, Miller CL, Roberts SC, Spin JM, de Almeida PE, Wu JC, Xu B, Cheng K, Quertermous M, Kundu S, Kortekaas KE, Berzin E, Downing KP, Dalman RL, Tsao PS, Schadt EE, Owens GK, Quertermous T. Loss of CDKN2B promotes p53-dependent smooth muscle cell apoptosis and aneurysm formation. Arterioscler Thromb Vasc Biol 2012; 33:e1-e10. [PMID: 23162013 DOI: 10.1161/atvbaha.112.300399] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Genomewide association studies have implicated allelic variation at 9p21.3 in multiple forms of vascular disease, including atherosclerotic coronary heart disease and abdominal aortic aneurysm. As for other genes at 9p21.3, human expression quantitative trait locus studies have associated expression of the tumor suppressor gene CDKN2B with the risk haplotype, but its potential role in vascular pathobiology remains unclear. METHODS AND RESULTS Here we used vascular injury models and found that Cdkn2b knockout mice displayed the expected increase in proliferation after injury, but developed reduced neointimal lesions and larger aortic aneurysms. In situ and in vitro studies suggested that these effects were attributable to increased smooth muscle cell apoptosis. Adoptive bone marrow transplant studies confirmed that the observed effects of Cdkn2b were mediated through intrinsic vascular cells and were not dependent on bone marrow-derived inflammatory cells. Mechanistic studies suggested that the observed increase in apoptosis was attributable to a reduction in MDM2 and an increase in p53 signaling, possibly due in part to compensation by other genes at the 9p21.3 locus. Dual inhibition of both Cdkn2b and p53 led to a reversal of the vascular phenotype in each model. CONCLUSIONS These results suggest that reduced CDKN2B expression and increased smooth muscle cell apoptosis may be one mechanism underlying the 9p21.3 association with aneurysmal disease.
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Affiliation(s)
- Nicholas J Leeper
- Department of Surgery, Stanford University, 300 Pasteur Dr, Stanford, CA 94305, USA
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