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da Cunha Agostini L, Almeida TC, da Silva GN. ANRIL, H19 and TUG1: a review about critical long non-coding RNAs in cardiovascular diseases. Mol Biol Rep 2023; 51:31. [PMID: 38155319 DOI: 10.1007/s11033-023-09007-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/30/2023] [Indexed: 12/30/2023]
Abstract
Cardiovascular diseases are the leading cause of death worldwide. They are non-transmissible diseases that affect the cardiovascular system and have different etiologies such as smoking, lipid disorders, diabetes, stress, sedentary lifestyle and genetic factors. To date, lncRNAs have been associated with increased susceptibility to the development of cardiovascular diseases such as hypertension, acute myocardial infarction, stroke, angina and heart failure. In this way, lncRNAs are becoming a very promising point for the prevention and diagnosis of cardiovascular diseases. Therefore, this review highlights the most important and recent discoveries about the mechanisms of action of the lncRNAs ANRIL, H19 and TUG1 and their clinical relevance in these pathologies. This may contribute to early detection of cardiovascular diseases in order to prevent the pathological phenotype from becoming established.
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Affiliation(s)
- Lívia da Cunha Agostini
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Morro do Cruzeiro, s/nº, Ouro Prêto, Minas Gerais, CEP 35402-163, Brazil
| | - Tamires Cunha Almeida
- Escola Superior Instituto Butantan (ESIB), Laboratório de Dor e Sinalização, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Glenda Nicioli da Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas (CiPharma), Escola de Farmácia, Universidade Federal de Ouro Preto, Morro do Cruzeiro, s/nº, Ouro Prêto, Minas Gerais, CEP 35402-163, Brazil.
- Departamento de Análises Clínicas (DEACL), Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Prêto, Brazil.
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Patel NA, Lui A, Trujillo AN, Motawe ZY, Bader D, Schuster J, Burgess A, Alves NG, Jo M, Breslin JW. Female and male obese Zucker rats display differential inflammatory mediator and long non-coding RNA profiles. Life Sci 2023; 335:122285. [PMID: 37995934 PMCID: PMC10760426 DOI: 10.1016/j.lfs.2023.122285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
AIMS The goal of this study was to identify mediators in peri-lymphatic adipose tissue (PLAT) that are altered in obese versus lean Zucker rats, with focus on potential sex differences MAIN METHODS: Mesenteric PLAT was analyzed with protein and lncRNA arrays. Additional RT-PCR confirmation was performed with epididymal/ovarian fat. KEY FINDINGS MCP-1, TCK-1, Galectin-1, Galectin-3, and neuropilin-1 were elevated in PLAT from obese rats of both sexes. However, 11 additional proteins were elevated only in obese males while 24 different proteins were elevated in obese females. Profiling of lncRNAs revealed lean males have elevated levels of NEAT1, MALAT1 and GAS5 compared to lean females. NEAT1, MALAT1, and GAS5 were significantly reduced with obesity in males but not in females. Another lncRNA, HOTAIR, was higher in lean females compared to males, and its levels in females were reduced with obesity. Obese rats of both sexes had similar histologic findings of mesenteric macrophage crown-like structures and hepatocyte fat accumulation. SIGNIFICANCE While obese male and female Zucker rats both have increased inflammation, they have distinct signals. Future studies of the proteome and lncRNA landscape of obese males vs. females in various animal models and in human subjects are warranted to better guide development of therapeutics for obesity-induced inflammation.
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Affiliation(s)
- Niketa A Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States of America; James A. Haley Veteran's Hospital, United States of America
| | - Ashley Lui
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, United States of America; James A. Haley Veteran's Hospital, United States of America
| | - Andrea N Trujillo
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America
| | - Zeinab Y Motawe
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America
| | - Deena Bader
- James A. Haley Veteran's Hospital, United States of America
| | - Jane Schuster
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America
| | - Andrea Burgess
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America
| | - Natascha G Alves
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America
| | - Michiko Jo
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America; Division of Presymptomatic Disease, Institute of Natural Medicine, University of Toyama, Japan
| | - Jerome W Breslin
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, United States of America.
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Zhan C, Tang T, Wu E, Zhang Y, He M, Wu R, Bi C, Wang J, Zhang Y, Shen B. From multi-omics approaches to personalized medicine in myocardial infarction. Front Cardiovasc Med 2023; 10:1250340. [PMID: 37965091 PMCID: PMC10642346 DOI: 10.3389/fcvm.2023.1250340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe complications such as arrhythmia, cardiac rupture, heart failure, and sudden death. Despite being a research hotspot, the etiological mechanism of MI remains unclear. The emergence and widespread use of omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and other omics, have provided new opportunities for exploring the molecular mechanism of MI and identifying a large number of disease biomarkers. However, a single-omics approach has limitations in understanding the complex biological pathways of diseases. The multi-omics approach can reveal the interaction network among molecules at various levels and overcome the limitations of the single-omics approaches. This review focuses on the omics studies of MI, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and other omics. The exploration extended into the domain of multi-omics integrative analysis, accompanied by a compilation of diverse online resources, databases, and tools conducive to these investigations. Additionally, we discussed the role and prospects of multi-omics approaches in personalized medicine, highlighting the potential for improving diagnosis, treatment, and prognosis of MI.
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Affiliation(s)
- Chaoying Zhan
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tong Tang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Erman Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxin Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengqiao He
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Rongrong Wu
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Bi
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- KeyLaboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiao Wang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yingbo Zhang
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bairong Shen
- Department of Cardiology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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Bink DI, Pauli J, Maegdefessel L, Boon RA. Endothelial microRNAs and long noncoding RNAs in cardiovascular ageing. Atherosclerosis 2023; 374:99-106. [PMID: 37059656 DOI: 10.1016/j.atherosclerosis.2023.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023]
Abstract
Atherosclerosis and numerous other cardiovascular diseases develop in an age-dependent manner. The endothelial cells that line the vessel walls play an important role in the development of atherosclerosis. Non-coding RNA like microRNAs and long non-coding RNAs are known to play an important role in endothelial function and are implicated in the disease progression. Here, we summarize several microRNAs and long non-coding RNAs that are known to have an altered expression with endothelial aging and discuss their role in endothelial cell function and senescence. These processes contribute to aging-induced atherosclerosis development and by targeting the non-coding RNAs controlling endothelial cell function and senescence, atherosclerosis can potentially be attenuated.
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Affiliation(s)
- Diewertje I Bink
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany; German Centre for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany; German Centre for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Reinier A Boon
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands; Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany; German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt Am Main, Germany.
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Shkurat TP, Ammar M, Bocharova O, Teplyakova E, Aleksandrova A, Ali R, Lipovich L. The Role of Genetic Variants in the Long Non-Coding RNA Genes MALAT1 and H19 in the Pathogenesis of Childhood Obesity. Noncoding RNA 2023; 9:ncrna9020022. [PMID: 37104004 PMCID: PMC10141382 DOI: 10.3390/ncrna9020022] [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: 01/14/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/28/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in the maintenance of metabolic homeostasis. Recently, many studies have suggested that lncRNAs, such as Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Imprinted Maternally Expressed Transcript (H19), might participate in the pathogenesis of metabolic disorders such as obesity. We conducted a case-control study with 150 Russian children and adolescents aged between 5 and 17 years old in order to assess the statistical association between the single nucleotide polymorphisms (SNPs) rs3200401 in MALAT1 and rs217727 in H19, and the risk of developing obesity in this population. We further explored the possible association of rs3200401 and rs217727 with BMI Z-score and insulin resistance. The MALAT1 rs3200401 and H19 rs217727 SNPs were genotyped using Taqman SNP genotyping assay. The MALAT1 rs3200401 SNP was identified as a risk factor for childhood obesity (p < 0.05) under the dominant and allelic models, and the CT heterozygous genotype was associated with the risk of increased BMI and with insulin resistance. The H19 rs217727 SNP had no significant association with obesity risk (all p > 0.05). Our findings thus suggest that MALAT1 SNP rs3200401 is a potential indicator of obesity susceptibility and pathogenesis in children and adolescents.
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Affiliation(s)
- Tatiana Pavlovna Shkurat
- Academy of Biology and Biotechnology named after D I Ivanovsky, Southern Federal University, Rostov on Don 344090, Russia
| | - Manar Ammar
- Academy of Biology and Biotechnology named after D I Ivanovsky, Southern Federal University, Rostov on Don 344090, Russia
| | - Olga Bocharova
- Department of Children's Diseases No. 3, Rostov State Medical University, Rostov on Don 344022, Russia
| | - Elena Teplyakova
- Department of Children's Diseases No. 3, Rostov State Medical University, Rostov on Don 344022, Russia
| | - Anzhela Aleksandrova
- Academy of Biology and Biotechnology named after D I Ivanovsky, Southern Federal University, Rostov on Don 344090, Russia
| | - Ruba Ali
- Academy of Biology and Biotechnology named after D I Ivanovsky, Southern Federal University, Rostov on Don 344090, Russia
| | - Leonard Lipovich
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
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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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Zhang T, Luo JY, Liu F, Zhang XH, Luo F, Yang YN, Li XM. Long noncoding RNA MALAT1 polymorphism predicts MACCEs in patients with myocardial infarction. BMC Cardiovasc Disord 2022; 22:152. [PMID: 35392816 PMCID: PMC8991554 DOI: 10.1186/s12872-022-02590-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Background Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) participates in the occurrence and development of cardiovascular and cerebrovascular diseases such as stroke and coronary heart disease by regulating inflammatory reactions, programmed cell death, and other pathological processes. Previous studies revealed that the MALAT1 gene polymorphism was associated with cardiac and cerebrovascular diseases. However, the prognostic role of the MALAT1 polymorphism in major adverse cardiac and cerebrovascular events (MACCEs) remains unknown. Therefore, this study intends to explore the association between the MALAT1 rs3200401 polymorphism and MACCEs. Method We enrolled 617 myocardial infarction (MI) patients and 1125 control participants who attended the First Affiliated Hospital of Xinjiang Medical University from January 2010 to 2018. SNPscan™ typing assays were used to detect the MALAT1 rs3200401 genotype. During the follow-up, MACCEs were recorded. Kaplan–Meier curves and univariate and multivariate Cox survival analyses were used to explore the correlation between MALAT1 gene polymorphisms and the occurrence of MACCEs. Results Among the total participants and MI patients, the frequencies of the T allele (total Participants 19.5% vs. 15.3%, P = 0.047, MI patients 20.7% vs. 14.1%, P = 0.014) and CT + TT genotypes (total Participants 37.4% vs. 28.1%, P = 0.013, MI patients 39.5% vs. 25.8%, P = 0.003) were significantly higher in subjects with MACCEs than in subjects without MACCEs. However, in control participants, the frequencies of the T allele (16.6% vs. 16.0%, P = 0.860) and CT + TT genotypes (31.4% vs. 29.3%, P = 0.760) were not higher in subjects with MACCEs than in subjects without MACCEs. In addition, among the total participants and MI patients, the Kaplan–Meier curve analysis indicated that the subjects with rs3200401 CT + TT genotypes had a higher incidence of MACCEs than CC genotype carriers (P = 0.015, P = 0.001). Nevertheless, similar results were not observed in the control participants (P = 0.790). Multivariate Cox regression indicated that compared with patients with the CC genotype, patients with CT + TT genotypes had a 1.554-fold increase in MACCE risk (hazard ratio: 1.554, 95% confidence interval: 1.060–2.277, P = 0.024). Conclusions The MALAT1 rs3200401 CT + TT genotypes could be a risk factor for MACCEs in MI patients, suggesting that the MALAT1 gene may become a biomarker for poor prognosis in MI patients.
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Affiliation(s)
- Tong Zhang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Jun-Yi Luo
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Fen Liu
- Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, Xinjiang, China
| | - Xue-He Zhang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Fan Luo
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China
| | - Yi-Ning Yang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China. .,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, Xinjiang, China. .,People's Hospital of Xinjiang Uygur Autonomous Region, 91 Tianchi Road, Urumqi, 830054, Xinjiang, China.
| | - Xiao-Mei Li
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, 137 Liyushan South Road, Urumqi, 830054, Xinjiang, China. .,Xinjiang Key Laboratory of Cardiovascular Disease Research, Urumqi, 830054, Xinjiang, China.
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Elwazir MY, Hussein MH, Toraih EA, Al Ageeli E, Esmaeel SE, Fawzy MS, Faisal S. Association of Angio-LncRNAs MIAT rs1061540/MALAT1 rs3200401 Molecular Variants with Gensini Score in Coronary Artery Disease Patients Undergoing Angiography. Biomolecules 2022; 12:biom12010137. [PMID: 35053285 PMCID: PMC8773982 DOI: 10.3390/biom12010137] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as essential biomolecules with variable diagnostic and/or prognostic utility in several diseases, including coronary artery disease (CAD). We aimed for the first time to investigate the potential association of five angiogenesis-related lncRNAs (PUNISHER, SENCR, MIAT, MALAT1, and GATA6-AS) variants with CAD susceptibility and/or severity. TaqMan Real-Time genotyping for PUNISHER rs12318065A/C, SENCR rs12420823C/T, MIAT rs1061540C/T, MALAT1 rs3200401T/C, and GATA6-AS1 rs73390820A/G were run on the extracted genomic DNA from 100 unrelated patients with stable CAD undergoing diagnostic coronary angiography and from 100 controls. After adjusting covariates, the studied variants showed no association with disease susceptibility; however, MIAT*T/T genotype was associated with a more severe Gensini score. In contrast, MALAT1*T/C heterozygosity was associated with a lower score. The lipid profile, and to a lesser extent smoking status, male sex, weight, hypertension, and MALAT1 (T > C) (negative correlation), explained the variance between patients/control groups via a principal component analysis. Incorporating the principal components into a logistic regression model to predict CAD yielded a 0.92 AUC. In conclusion: MIAT rs1061540 and MALAT1 rs3200401 variants were associated with CAD severity and Gensini score in the present sample of the Egyptian population. Further large multi-center and functional analyses are needed to confirm the results and identify the underlying molecular mechanisms.
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Affiliation(s)
- Mohamed Y. Elwazir
- Department of Cardiology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Mohammad H. Hussein
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Eman A. Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA;
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (E.A.T.); (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +20-1008584720 (M.S.F.)
| | - Essam Al Ageeli
- Department of Clinical Biochemistry (Medical Genetics), Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia;
| | - Safya E. Esmaeel
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
- Correspondence: (E.A.T.); (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +20-1008584720 (M.S.F.)
| | - Salwa Faisal
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
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LncRNA functional annotation with improved false discovery rate achieved by disease associations. Comput Struct Biotechnol J 2022; 20:322-332. [PMID: 35035785 PMCID: PMC8724965 DOI: 10.1016/j.csbj.2021.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 12/11/2022] Open
Abstract
The long non‐coding RNAs (lncRNAs) play critical roles in various biological processes and are associated with many diseases. Functional annotation of lncRNAs in diseases attracts great attention in understanding their etiology. However, the traditional co-expression-based analysis usually produces a significant number of false positive function assignments. It is thus crucial to develop a new approach to obtain lower false discovery rate for functional annotation of lncRNAs. Here, a novel strategy termed DAnet which combining disease associations with cis-regulatory network between lncRNAs and neighboring protein-coding genes was developed, and the performance of DAnet was systematically compared with that of the traditional differential expression-based approach. Based on a gold standard analysis of the experimentally validated lncRNAs, the proposed strategy was found to perform better in identifying the experimentally validated lncRNAs compared with the other method. Moreover, the majority of biological pathways (40%∼100%) identified by DAnet were reported to be associated with the studied diseases. In sum, the DAnet is expected to be used to identify the function of specific lncRNAs in a particular disease or multiple diseases.
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Huang SF, Peng XF, Jiang L, Hu CY, Ye WC. LncRNAs as Therapeutic Targets and Potential Biomarkers for Lipid-Related Diseases. Front Pharmacol 2021; 12:729745. [PMID: 34421622 PMCID: PMC8371450 DOI: 10.3389/fphar.2021.729745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
Lipid metabolism is an essential biological process involved in nutrient adjustment, hormone regulation, and lipid homeostasis. An irregular lifestyle and long-term nutrient overload can cause lipid-related diseases, including atherosclerosis, myocardial infarction (MI), obesity, and fatty liver diseases. Thus, novel tools for efficient diagnosis and treatment of dysfunctional lipid metabolism are urgently required. Furthermore, it is known that lncRNAs based regulation like sponging microRNAs (miRNAs) or serving as a reservoir for microRNAs play an essential role in the progression of lipid-related diseases. Accordingly, a better understanding of the regulatory roles of lncRNAs in lipid-related diseases would provide the basis for identifying potential biomarkers and therapeutic targets for lipid-related diseases. This review highlighted the latest advances on the potential biomarkers of lncRNAs in lipid-related diseases and summarised current knowledge on dysregulated lncRNAs and their potential molecular mechanisms. We have also provided novel insights into the underlying mechanisms of lncRNAs which might serve as potential biomarkers and therapeutic targets for lipid-related diseases. The information presented here may be useful for designing future studies and advancing investigations of lncRNAs as biomarkers for diagnosis, prognosis, and therapy of lipid-related diseases.
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Affiliation(s)
- Shi-Feng Huang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Xiao-Fei Peng
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lianggui Jiang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Ching Yuan Hu
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Wen-Chu Ye
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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Tsilimigras DI, Bibli SI, Siasos G, Oikonomou E, Perrea DN, Filis K, Tousoulis D, Sigala F. Regulation of Long Non-Coding RNAs by Statins in Atherosclerosis. Biomolecules 2021; 11:biom11050623. [PMID: 33922114 PMCID: PMC8143454 DOI: 10.3390/biom11050623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 01/04/2023] Open
Abstract
Despite increased public health awareness, atherosclerosis remains a leading cause of mortality worldwide. Significant variations in response to statin treatment have been noted among different populations suggesting that the efficacy of statins may be altered by both genetic and environmental factors. The existing literature suggests that certain long noncoding RNAs (lncRNAs) might be up- or downregulated among patients with atherosclerosis. LncRNA may act on multiple levels (cholesterol homeostasis, vascular inflammation, and plaque destabilization) and exert atheroprotective or atherogenic effects. To date, only a few studies have investigated the interplay between statins and lncRNAs known to be implicated in atherosclerosis. The current review characterizes the role of lncRNAs in atherosclerosis and summarizes the available evidence related to the effect of statins in regulating lncRNAs.
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Affiliation(s)
- Diamantis I. Tsilimigras
- First Propaedeutic Department of Surgery, Division of Vascular Surgery, Hippokration Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (K.F.); (F.S.)
- Correspondence: ; Tel.: +30-697-5683-212
| | - Sofia-Iris Bibli
- Centre for Molecular Medicine, Institute for Vascular Signalling, Goethe University, 60323 Frankfurt am Main, Germany;
| | - Gerasimos Siasos
- First Department of Cardiology, Hippokration Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (G.S.); (E.O.); (D.T.)
| | - Evangelos Oikonomou
- First Department of Cardiology, Hippokration Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (G.S.); (E.O.); (D.T.)
| | - Despina N. Perrea
- Laboratory for Experimental Surgery and Surgical Research “N.S. Christeas”, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Konstantinos Filis
- First Propaedeutic Department of Surgery, Division of Vascular Surgery, Hippokration Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (K.F.); (F.S.)
| | - Dimitrios Tousoulis
- First Department of Cardiology, Hippokration Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (G.S.); (E.O.); (D.T.)
| | - Fragiska Sigala
- First Propaedeutic Department of Surgery, Division of Vascular Surgery, Hippokration Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (K.F.); (F.S.)
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Song N, Luo JY, Zhao Q, Zhang JY, Liu F, Li XM, Yang YN. MALAT1 gene rs600231 polymorphism positively associated with acute coronary syndrome in Chinese population: a case-control study. Cardiovasc Diagn Ther 2021; 11:435-446. [PMID: 33968621 DOI: 10.21037/cdt-20-906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been recognized as a major player in the pathogenesis of coronary artery disease (CAD). The aim of the study was to determine the association between polymorphisms of the MALAT1 gene and acute coronary syndrome (ACS) in a Chinese population in Xinjiang. Methods In the case-control study, we genotyped three nucleotide polymorphisms (rs3200401, rs4102217, rs600231) of the MALAT1 gene using SNPscanTM typing assays (1,053 controls and 929 ACS patients). Furthermore, we explored a predictive model using MALAT1 rs600231 and clinical variables to predict the risk of ACS. Finally, the relative expression of long noncoding RNA (lncRNA) MALAT1 was also measured in 92 ACS patients and 92 controls using quantitative real-time polymerase chain reaction (qRT-PCR). Results The prevalence of the GG genotype of rs600231 in ACS group was higher than that in control group (15.7% vs. 14.7%, P=0.048). The dominant model differed (AG + GG vs. AA) and the G allele of rs600231 in ACS group was higher than that in control group (for dominant model: 66.2% vs. 60.9%, P=0.014; for allele: 41.0% vs. 37.8%, P=0.042). Multivariate logistic regression analysis and the predictive nomogram model showed that the dominant model of rs600231 remained an independent risk factor for ACS [odds ratio (OR) =1.32, 95% confidence interval (CI): 1.07-1.63, P=0.009]. The area under the receiver operating characteristic (ROC) curve (AUC) for the nomogram model for the prediction of ACS was 0.738 (95% CI: 0.716-0.761). In addition, in the AG and GG phenotypes, the relative expression of lncRNA MALAT1 was significantly higher in ACS patients than in controls with the same phenotypes (P<0.05). Among ACS group, compared to other genotype carriers, the relative expression level of MALAT1 in GG genotype carriers was higher (P<0.05). Conclusions The present study suggested that the AG and GG genotype of rs600231 in MALAT1 gene was independently associated with ACS, and could be a risk genetic marker of ACS in a Chinese population in Xinjiang.
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Affiliation(s)
- Ning Song
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jun-Yi Luo
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Qian Zhao
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Jin-Yu Zhang
- Department of Rehabilitation, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Fen Liu
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Xiao-Mei Li
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yi-Ning Yang
- Department of Cardiology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China.,Xinjiang Key Laboratory of Cardiovascular Disease Research, Clinical Medicine Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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Association of Long Non-Coding RNA Polymorphisms with Gastric Cancer and Atrophic Gastritis. Genes (Basel) 2020; 11:genes11121505. [PMID: 33333725 PMCID: PMC7765138 DOI: 10.3390/genes11121505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNA) play an important role in the carcinogenesis of various tumours, including gastric cancer. This study aimed to assess the associations of lncRNA ANRIL, H19, MALAT1, MEG3, HOTAIR single-nucleotide polymorphisms (SNPs) with gastric cancer and atrophic gastritis. SNPs were analyzed in 613 gastric cancer patients, 118 patients with atrophic gastritis and 476 controls from three tertiary centers in Germany, Lithuania and Latvia. Genomic DNA was extracted from peripheral blood leukocytes. SNPs were genotyped by the real-time polymerase chain reaction. Results showed that carriers of MALAT1 rs3200401 CT genotype had the significantly higher odds of atrophic gastritis than those with CC genotype (OR-1.81; 95% CI 1.17–2.80, p = 0.0066). Higher odds of AG were found in a recessive model (CC vs. TT + CT) for ANRIL rs1333045 (OR-1.88; 95% CI 1.19–2.95, p = 0.0066). Carriers of ANRIL (rs17694493) GG genotype had higher odds of gastric cancer (OR-4.93; 95% CI 1.28–19.00) and atrophic gastritis (OR-5.11; 95% CI 1.10–23.80) compared with the CC genotype, and carriers of HOTAIR rs17840857 TG genotype had higher odds of atrophic gastritis (OR-1.61 95% CI 1.04–2.50) compared with the TT genotype; however, the ORs did not reach the adjusted significance threshold (p < 0.007). In summary, our data provide novel evidence for a possible link between lncRNA SNPs and premalignant condition of gastric cancer, suggesting the involvement of lncRNAs in gastric cancer development.
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Genetic variations associated with long noncoding RNAs. Essays Biochem 2020; 64:867-873. [DOI: 10.1042/ebc20200033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Abstract
Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including the long noncoding RNA (lncRNA) regions. The changes at locus might produce numerous effects in a variety of aspects. Multiple bioinformatics resources and tools were also developed for systematically dealing with genetic variations associated with lncRNAs. Moreover, correlation of the genetic variations in lncRNAs with immune disease, cancers, and other disease as well as development process were all included for discussion. In this essay, we summarized how and in what aspects these changes would affect lncRNA functions.
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Lee KH, Hwang HJ, Cho JY. Long Non-Coding RNA Associated with Cholesterol Homeostasis and Its Involvement in Metabolic Diseases. Int J Mol Sci 2020; 21:E8337. [PMID: 33172104 PMCID: PMC7664438 DOI: 10.3390/ijms21218337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Cholesterol is an essential cell component that functions to create and maintain all kinds of cell membranes and lipoprotein particles. It is crucial to maintain the proper amount of cholesterol at both the cellular and systemic level. Recently, the importance of cholesterol has been reported not only in various cell development processes but also in the development of diseases. Furthermore, the involvement of long non-coding RNAs (lncRNAs), which are regarded as important epigenetic regulators in gene expression, has also been reported in cholesterol homeostasis. It is thus necessary to summarize the research on lncRNAs related to cholesterol with increased interest. This review organized the role of lncRNAs according to the major issues in cholesterol homeostasis: efflux, metabolism and synthesis, and disease process.
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Affiliation(s)
| | | | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (K.-H.L.); (H.-J.H.)
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