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Ruskovska T, Postolov F, Milenkovic D. Integrated Analysis of Genomic and Genome-Wide Association Studies Identified Candidate Genes for Nutrigenetic Studies in Flavonoids and Vascular Health: Path to Precision Nutrition for (Poly)phenols. Nutrients 2024; 16:1362. [PMID: 38732608 PMCID: PMC11085427 DOI: 10.3390/nu16091362] [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: 02/21/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Flavonoids exert vasculoprotective effects in humans, but interindividual variability in their action has also been reported. This study aims to identify genes that are associated with vascular health effects of flavonoids and whose polymorphisms could explain interindividual variability in response to their intake. Applying the predetermined literature search criteria, we identified five human intervention studies reporting positive effects of flavonoids on vascular function together with global genomic changes analyzed using microarray methods. Genes involved in vascular dysfunction were identified from genome-wide association studies (GWAS). By extracting data from the eligible human intervention studies, we obtained 5807 differentially expressed genes (DEGs). The number of identified upstream regulators (URs) varied across the studies, from 227 to 1407. The search of the GWAS Catalog revealed 493 genes associated with vascular dysfunction. An integrative analysis of transcriptomic data with GWAS genes identified 106 candidate DEGs and 42 candidate URs, while subsequent functional analyses and a search of the literature identified 20 top priority candidate genes: ALDH2, APOE, CAPZA1, CYP11B2, GNA13, IL6, IRF5, LDLR, LPL, LSP1, MKNK1, MMP3, MTHFR, MYO6, NCR3, PPARG, SARM1, TCF20, TCF7L2, and TNF. In conclusion, this integrated analysis identifies important genes to design future nutrigenetic studies for development of precision nutrition for polyphenols.
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Affiliation(s)
- Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (F.P.)
| | - Filip Postolov
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia; (T.R.); (F.P.)
| | - Dragan Milenkovic
- Department of Nutrition, University of California, Davis, Davis, CA 95616, USA
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Mechanistic insights into dietary (poly)phenols and vascular dysfunction-related diseases using multi-omics and integrative approaches: Machine learning as a next challenge in nutrition research. Mol Aspects Med 2023; 89:101101. [PMID: 35728999 DOI: 10.1016/j.mam.2022.101101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/09/2022] [Accepted: 06/11/2022] [Indexed: 02/04/2023]
Abstract
Dietary (poly)phenols have been extensively studied for their vasculoprotective effects and consequently their role in preventing or delaying onsets of cardiovascular and metabolic diseases. Even though early studies have ascribed the vasculoprotective properties of (poly)phenols primarily on their putative free radical scavenging properties, recent data indicate that in biological systems, (poly)phenols act primarily through genomic and epigenomic mechanisms. The molecular mechanisms underlying their health properties are still not well identified, mainly due to the use of physiologically non-relevant conditions (native molecules or extracts at high concentrations, rather than circulating metabolites), but also due to the use of targeted genomic approaches aiming to evaluate the effect only on few specific genes, thus preventing to decipher detailed molecular mechanisms involved. The use of state-of-the-art untargeted analytical methods represents a significant breakthrough in nutrigenomics, as these methods enable detailed insights into the effects at each specific omics level. Moreover, the implementation of multi-omics approaches allows integration of different levels of regulation of cellular functions, to obtain a comprehensive picture of the molecular mechanisms of action of (poly)phenols. In combination with bioinformatics and the methods of machine learning, multi-omics has potential to make a huge contribution to the nutrition science. The aim of this review is to provide an overview of the use of the omics, multi-omics, and integrative approaches in studying the vasculoprotective properties of dietary (poly)phenols and address the potentials for use of the machine learning in nutrigenomics.
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Unveiling the Vital Role of Long Non-Coding RNAs in Cardiac Oxidative Stress, Cell Death, and Fibrosis in Diabetic Cardiomyopathy. Antioxidants (Basel) 2022; 11:antiox11122391. [PMID: 36552599 PMCID: PMC9774664 DOI: 10.3390/antiox11122391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
Diabetes mellitus is a burdensome public health problem. Diabetic cardiomyopathy (DCM) is a major cause of mortality and morbidity in diabetes patients. The pathogenesis of DCM is multifactorial and involves metabolic abnormalities, the accumulation of advanced glycation end products, myocardial cell death, oxidative stress, inflammation, microangiopathy, and cardiac fibrosis. Evidence suggests that various types of cardiomyocyte death act simultaneously as terminal pathways in DCM. Long non-coding RNAs (lncRNAs) are a class of RNA transcripts with lengths greater than 200 nucleotides and no apparent coding potential. Emerging studies have shown the critical role of lncRNAs in the pathogenesis of DCM, along with the development of molecular biology technologies. Therefore, we summarize specific lncRNAs that mainly regulate multiple modes of cardiomyopathy death, oxidative stress, and cardiac fibrosis and provide valuable insights into diagnostic and therapeutic biomarkers and strategies for DCM.
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Wahba AS, Ibrahim ME, Mesbah NM, Saleh SM, Abo-Elmatty DM, Mehanna ET. Long non-coding RNA MEG3 and its genetic variant rs941576 are associated with rheumatoid arthritis pathogenesis in Egyptian patients. Arch Physiol Biochem 2022; 128:1571-1578. [PMID: 32608280 DOI: 10.1080/13813455.2020.1784951] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a joint destructive disorder. This study aimed to assess lncRNA MEG3 expression and its variant rs941576 in Egyptian patients with RA. SUBJECTS AND METHODS 100 RA patients and 100 healthy individuals were enrolled in the study. Quantitative PCR was used for expression analysis and allelic discrimination technology for genotyping. RESULTS LncRNA MEG3 was down-regulated in RA patients and negatively associated with RA clinical features and HIF-1α and VEGF serum levels. On the contrary, it was positively associated with BAX serum levels in RA patients. The major A allele of rs941576 variant was associated with RA patients (p = .0003). AA genotype showed a significant decrease in lncRNA MEG3 expression and BAX and increase in HIF-1α and VEGF. CONCLUSIONS Serum lncRNA MEG3 expression showed negative association with increased susceptibility to RA. MEG3 gene rs941576 (A/G) polymorphism was associated with increased severity of RA in the current population.
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Affiliation(s)
- Alaa S Wahba
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Maha E Ibrahim
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Noha M Mesbah
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Samy M Saleh
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Dina M Abo-Elmatty
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Eman T Mehanna
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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Kang J, Oteiza PI, Milenkovic D. (-)-Epicatechin exerts positive effects on anxiety in high fat diet-induced obese mice through multi-genomic modifications in the hippocampus. Food Funct 2022; 13:10623-10641. [PMID: 36168829 DOI: 10.1039/d2fo01897g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Obesity is associated with increased occurrence of cognitive and mood disorders. While consumption of high-fat diets (HFD) and associated obesity could have a detrimental impact on the brain, dietary bioactives may mitigate these harmful effects. We previously observed that (-)-epicatechin (EC) can mitigate HFD-induced anxiety-associated behaviors in mice. The aim of our study is to investigate the molecular mechanisms of EC actions in the hippocampus which underlies its anti-anxiety effects in HFD-fed mice using a multi-genomic approach. Healthy eight-week old male C57BL/6J mice were fed for 24 weeks either: (A) a control diet containing 10% total calories from fat; (B) a HFD containing 45% total calories from fat; or (C) the HFD supplemented with 20 mg EC per kg body weight. Hippocampi were isolated for genomic analysis using Affymetrix arrays, followed by in-depth bioinformatic analyses. Genomic analysis demonstrated that EC induced significant changes in mouse hippocampal global gene expression. We observed changes in the expression of 1001 protein-coding genes, 241 miRNAs, and 167 long non-coding RNAs. Opposite gene expression profiles were observed when the gene expression profile obtained upon EC supplementation was compared to the profile obtained after consumption of the HFD. Functionality analysis revealed that the differentially expressed genes regulate processes involved in neurofunction, inflammation, endothelial function, cell-cell adhesion, and cell signaling. In summary, the capacity of EC to mitigate anxiety-related behaviors in HFD-induced obese mice can be in part explained by its capacity to exert complex genomic modifications in the hippocampus, counteracting changes driven by consumption of the HFD and/or associated obesity.
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Affiliation(s)
- Jiye Kang
- Department of Nutrition, University of California, Davis, One Shields Avenue, 95616 Davis, California, USA. .,Department of Environmental Toxicology, University of California, Davis, One Shields Avenue, 95616 Davis, California, USA
| | - Patricia I Oteiza
- Department of Nutrition, University of California, Davis, One Shields Avenue, 95616 Davis, California, USA. .,Department of Environmental Toxicology, University of California, Davis, One Shields Avenue, 95616 Davis, California, USA
| | - Dragan Milenkovic
- Department of Nutrition, University of California, Davis, One Shields Avenue, 95616 Davis, California, USA.
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Transcriptome expression profiles associated with diabetic nephropathy development. Mol Cell Biochem 2022; 477:1931-1946. [PMID: 35357607 DOI: 10.1007/s11010-022-04420-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/18/2022] [Indexed: 01/20/2023]
Abstract
The objective of this study was to identify different transcriptome expression profiles involved in the pathogenesis of diabetic nephropathy (DN) and to illustrate the diagnostic and therapeutic potential of mRNAs, long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) in DN progression. The participants were divided into four groups: normoalbuminuria (group DM), microalbuminuria (group A2), macroalbuminuria (group A3) and healthy controls (group N). There were three individuals in each group for sequencing. Transcriptome sequencing analysis was performed on the peripheral blood of all the participants to identify the differential expression of mRNAs, lncRNAs, and circRNAs between intervention groups and controls. The functional enrichment analysis, the short time-series expression miner (STEM) program, and the miRNA-circRNA-mRNA network were further conducted. To verify the reproducibility of transcriptome sequencing, 10 and 30 blood samples were collected from the control and diseased groups, respectively. Four candidate biomarkers were selected from differentially expressed circRNAs (circ_0005379, circ_0002024, and circ_0000567, and circ_0001017) and their concentrations in the blood were measured using quantitative PCR (qPCR). In the comparison of A2 with N, 549 mRNAs, 1259 lncRNAs, and 12 circRNAs were screened. In the comparison of A3 with N, 1217 mRNAs, 1613 lncRNAs, and 24 circRNAs were screened. Moreover, in the comparison of diabetes mellitus (DM) with N, 948 mRNAs, 1495 lncRNAs, and 25 circRNAs were screened. Functional enrichment analysis showed that differentially expressed mRNAs were related to insulin secretion, insulin resistance, and inflammation, while differentially expressed lncRNAs were mainly associated with crossover junction endodeoxyribonuclease activity. In STEM analysis, a total of 481 mRNAs and 152 differential expression circRNAs showed a significant tendency. The key relationships in the miRNA-circRNA-mRNA network were identified, such as hsa-miR-103a-3p-circ_0005379-PTEN, hsa-miR-497-5p-circ_0002024-IGF1R and hsa-miR-1269a-circ_0000567-SOX6. In addition, qPCR showed consistent results with RNA sequencing. We found that differentially expressed mRNAs, lncRNAs, and circRNAs participated in DN development. Circ_0005379, circ_0002024, and circ_0000567 could be adopted as potential biomarkers for DN.
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Sun X, Feinberg MW. Vascular Endothelial Senescence: Pathobiological Insights, Emerging Long Noncoding RNA Targets, Challenges and Therapeutic Opportunities. Front Physiol 2021; 12:693067. [PMID: 34220553 PMCID: PMC8242592 DOI: 10.3389/fphys.2021.693067] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a stable form of cell cycle arrest in response to various stressors. While it serves as an endogenous pro-resolving mechanism, detrimental effects ensue when it is dysregulated. In this review, we introduce recent advances for cellular senescence and inflammaging, the underlying mechanisms for the reduction of nicotinamide adenine dinucleotide in tissues during aging, new knowledge learned from p16 reporter mice, and the development of machine learning algorithms in cellular senescence. We focus on pathobiological insights underlying cellular senescence of the vascular endothelium, a critical interface between blood and all tissues. Common causes and hallmarks of endothelial senescence are highlighted as well as recent advances in endothelial senescence. The regulation of cellular senescence involves multiple mechanistic layers involving chromatin, DNA, RNA, and protein levels. New targets are discussed including the roles of long noncoding RNAs in regulating endothelial cellular senescence. Emerging small molecules are highlighted that have anti-aging or anti-senescence effects in age-related diseases and impact homeostatic control of the vascular endothelium. Lastly, challenges and future directions are discussed including heterogeneity of endothelial cells and endothelial senescence, senescent markers and detection of senescent endothelial cells, evolutionary differences for immune surveillance in mice and humans, and long noncoding RNAs as therapeutic targets in attenuating cellular senescence. Accumulating studies indicate that cellular senescence is reversible. A better understanding of endothelial cellular senescence through lifestyle and pharmacological interventions holds promise to foster a new frontier in the management of cardiovascular disease risk.
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Affiliation(s)
- Xinghui Sun
- Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, United States
- Nebraska Center for the Prevention of Obesity Diseases Through Dietary Molecules, University of Nebraska–Lincoln, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Mark W. Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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Liu L, He J, Lu X, Yuan Y, Jiang D, Xiao H, Lin S, Xu L, Chen Y. Association of Myopia and Genetic Variants of TGFB2-AS1 and TGFBR1 in the TGF-β Signaling Pathway: A Longitudinal Study in Chinese School-Aged Children. Front Cell Dev Biol 2021; 9:628182. [PMID: 33996791 PMCID: PMC8115727 DOI: 10.3389/fcell.2021.628182] [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: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Background Myopia is a complex multifactorial condition which involves several overlapping signaling pathways mediated by distinct genes. This prospective cohort study evaluated the associations of two genetic variants in the TGF-β signaling pathway with the onset and progression of myopia and ocular biometric parameters in Chinese school-aged children. Methods A total of 556 second grade children were examined and followed up for 3.5 years. Non-cycloplegic refraction and ocular biometric parameters were measured annually. Multivariate regression analysis was used to assess the effect of the TGFBR1 rs10760673 and TGFB2-AS1 rs7550232 variants on the occurrence and progression of myopia. A 10,000 permutations test was used to correct for multiple testing. Functional annotation of single nucleotide polymorphisms (SNPs) was performed using RegulomeDB, HaploReg, and rVarBase. Results A total of 448 children were included in the analysis. After adjustments for gender, age, near work time and outdoor time with 10,000 permutations, the results indicated that the C allele and the AC or CC genotypes of rs7550232 adjacent to TGFB2-AS1 were associated with a significantly increased risk of the onset of myopia in two genetic models (additive: P’ = 0.022; dominant: P’ = 0.025). Additionally, the A allele and the AA or AG genotypes of rs10760673 of TGFBR1 were associated with a significant myopic shift (additive: P’ = 0.008; dominant: P’ = 0.028; recessive: P’ = 0.027). Furthermore, rs10760673 was associated with an increase in axial length (AL) (P’ = 0.013, β = 0.03) and a change in the ratio of AL to the corneal radius of curvature (AL/CRC) (P’ = 0.031, β = 0.003). Analysis using RegulomeDB, HaploReg, and rVarBase indicated that rs7550232 is likely to affect transcription factor binding, any motif, DNase footprint, and DNase peak. Conclusion The present study indicated that rs10760673 and rs7550232 may represent susceptibility loci for the progression and onset of myopia, respectively, in school-aged children. Associations of the variants of the TGFBR1 and TGFB2-AS1 genes with myopia may be mediated by the TGF-β signaling pathway; this hypothesis requires validation in functional studies. This trial was registered as ChiCTR1900020584 at www.Chictr.org.cn.
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Affiliation(s)
- Linjie Liu
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Juan He
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Lu
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Yimin Yuan
- Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Dandan Jiang
- Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Haishao Xiao
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Shudan Lin
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Liangde Xu
- School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yanyan Chen
- Eye Hospital, Wenzhou Medical University, Wenzhou, China
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Huang J, Li M, Li J, Liang B, Chen Z, Yang J, Guo X, Huang S, Gu L, Su L. LncRNA H19 rs4929984 Variant is Associated with Coronary Artery Disease Susceptibility in Han Chinese Female Population. Biochem Genet 2021; 59:1359-1380. [PMID: 33826032 DOI: 10.1007/s10528-021-10055-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/24/2021] [Indexed: 11/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been reported to play an important role in cardiovascular diseases. The present study aimed to investigate the levels of lncRNA H19 in patients with coronary artery disease (CAD) and the genetic association of lncRNA H19 rs217727 and rs4929984 polymorphisms with CAD susceptibility. We detected an upregulated expression of lncRNA H19 in the peripheral blood of CAD patients compared with healthy controls, and the area under the receiver operating characteristic curve of lncRNA H19 for CAD diagnosis was 0.918. In addition, rs4929984 was associated with the susceptibility of Han Chinese females to CAD, as shown in the additive and dominant models, and the significant association remained after adjusting for age and Bonferroni correction. The A allele carriers of rs4929984 were correlated with females' susceptibility to CAD compared with the C allele, and the A-G haplotype of rs4929984-rs217727 was associated with females' susceptibility to CAD. Furthermore, rs217727 and rs4929984 were associated with the levels of clinicopathological parameters of CAD cases. We suggest that lncRNA H19 has a potential to be a diagnostic biomarker for CAD; rs4929984 polymorphism is associated with females' susceptibility to CAD in the Han Chinese population, and lncRNA H19 variants may influence lipid metabolism, inflammation, and coagulation function of CAD patients.
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Affiliation(s)
- Jiao Huang
- School of Public Health of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Minhua Li
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Jinhong Li
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Baoyun Liang
- Department of Internal Neurology, First Affiliated Hospital, Guangxi University of Chinese Medicine, 89-9 Dongge Road, Nanning, 530023, Guangxi, China
| | - Zhaoxia Chen
- School of Public Health of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Jialei Yang
- School of Public Health of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Xiaojing Guo
- School of Public Health of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Siyun Huang
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Lian Gu
- Department of Internal Neurology, First Affiliated Hospital, Guangxi University of Chinese Medicine, 89-9 Dongge Road, Nanning, 530023, Guangxi, China.
| | - Li Su
- School of Public Health of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China.
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Ghasemi M, Heidari Nia M, Hashemi M, Keikha N, Fazeli K, Taji O, Naghavi A. An association study of polymorphisms in the H19 imprinted gene in an Iranian population with the risk of polycystic ovary syndrome. Biol Reprod 2020; 103:978-985. [PMID: 32720692 DOI: 10.1093/biolre/ioaa131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/12/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common endocrinopathies that causes problems in female fertility at the reproductive age. PCOS is a multifactorial disease, with genetic factors playing a crucial role in its development. H19 is a long non-coding RNA (lncRNA) expressed from the maternal chromosome, which is correlated with PCOS. In this study, 115 women suffering from PCOS and 130 healthy women with regular menstrual cycles were recruited as case and control groups, respectively. After the extraction of genomic DNA, the restriction fragment length polymorphism polymerase chain reaction was employed for genotyping of rs2067051G>A and rs3741219T>C. Statistical analysis was done using SPSS package V.22 for Windows. In silico analysis was recruited to determine the effects of SNPs on the secondary structure of gene transcript as well as miRNA binding sites. The obtained data showed that the A allele of rs2067051G>A was associated with the high risk of PCOS (OR = 2.00, 95%CI = 1.38-2.91, P = 0.00). AG and AA genotypes led to a 3.64- and (about) a five-fold increase in the risk of PCOS, respectively (95%CI = 2.02-6.54, P = 0.00, and 95%CI = 1.51-16.52, P = 0.00, respectively). These variants caused a significant increase in the risk of this disorder in all genotype models except in the recessive model. However, no association was found between rs3741219T>C and the increased risk of PCOS, either in the allele or in the genotype models. According to the findings, rs2067051G>A is associated with an increased risk of PCOS in the Iranian population.
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Affiliation(s)
- Marzieh Ghasemi
- Department of Obstetrics and Gynecology, Pregnancy Health Research Center, Zahedan, Iran.,Moloud Infertility Center, Ali-ibn-Abitaleb Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Narjes Keikha
- Moloud Infertility Center, Ali-ibn-Abitaleb Hospital, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Kimia Fazeli
- School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Omid Taji
- Medical Genetic Reference Laboratory, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Anoosh Naghavi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Genetics, Zahedan University of Medical Sciences, Zahedan, Iran
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Miramontes-González JP, Usategui-Martín R, Martín-Vallejo J, Ziegler M, de Isla LL, O Connor D, González-Sarmiento R. VAV3 rs7528153 and VAV3-AS1 rs1185222 polymorphisms are associated with an increased risk of developing hypertension. Eur J Intern Med 2020; 80:60-65. [PMID: 32540412 DOI: 10.1016/j.ejim.2020.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 01/04/2023]
Abstract
The aetiology of essential hypertension is complex and involves both environmental and genetic factors. Approximately 30% of the inter-individual variability in blood pressure is genetically determined. It has been shown that numerous vasoconstrictors stimulate RhoA in local populations of vascular SMCs that, in turn, promote localised constriction of arterial blood vessels and elevations in blood pressure. The VAV3 gene encodes for VAV3 protein, a Rho GEF factor. VAV3-AS1 gene, a lncRNA, may regulate VAV3 expression. We performed an observational prospective case-control study, including patients attending in the Vascular Risk Unit from the University Hospital Salamanca for 6 months. A replication study was performed with data from The Kaiser Permanent database of the University of California. The results suggest that T allele of the VAV3 rs7528153 and G allele of the VAV3-AS1 rs11185222 polymorphisms are associated with an increased risk of developing hypertension. We hypothesise that these polymorphisms could modify blood pressure, likely through a modification in the Rho/Rac pathway. Our results suggest that those polymorphisms could be useful genetic markers of susceptibility to suffering hypertension.
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Affiliation(s)
- José Pablo Miramontes-González
- Department of Internal Medicine, Hospital Universitario de Salamanca, Valladolid, Spain; Molecular Medicine Unit, Department of Medicine, Universidad de Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain; Department of Medicine. University of California at San Diego, La Jolla, California-UCSD, United States.
| | - Ricardo Usategui-Martín
- Molecular Medicine Unit, Department of Medicine, Universidad de Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Javier Martín-Vallejo
- Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain; Department of Statistics, Universidad de Salamanca, Salamanca, Spain
| | - Michael Ziegler
- Department of Medicine. University of California at San Diego, La Jolla, California-UCSD, United States
| | - Leopoldo López de Isla
- Cardiac Image Unit. Hospital Clínico San Carlos. Madrid. Facultad de Medicina. Universidad Complutense de Madrid, Madrid, Spain
| | - Daniel O Connor
- Department of Medicine. University of California at San Diego, La Jolla, California-UCSD, United States
| | - Rogelio González-Sarmiento
- Molecular Medicine Unit, Department of Medicine, Universidad de Salamanca, Salamanca, Spain; Institute of Biomedical Research of Salamanca (IBSAL), Hospital Universitario de Salamanca-USAL-CSIC and Institute of Molecular and Cellular Biology of Cancer (IBMCC), Universidad de Salamanca-CSIC, Salamanca, Spain.
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Targeting steroid receptor RNA activator (SRA), a long non-coding RNA, enhances melanogenesis through activation of TRP1 and inhibition of p38 phosphorylation. PLoS One 2020; 15:e0237577. [PMID: 32790741 PMCID: PMC7425936 DOI: 10.1371/journal.pone.0237577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
Abnormal skin melanin homeostasis results in refractory pigmentary diseases. Melanogenesis is influenced by gene regulation, ultraviolet radiation, and host epigenetic responses. Steroid receptor RNA activator (SRA), a long noncoding RNA, is known to regulate steroidogenesis and tumorigenesis. However, how SRA contributes to melanogenesis remains unknown. Using RNA interference against SRA in B16 and A375 melanoma cells, we observed increased pigmentation and increased expression of TRP1 and TRP2 at transcriptional and translational levels only in B16 cells. The constitutive phosphorylation of p38 in B16-shCtrl cells was inhibited in cells with knocked down SRAi. Moreover, the melanin content of control B16 cells was increased by SB202190, a p38 inhibitor. Furthermore, reduced p38 phosphorylation, enhanced TRP1 expression, and hypermelanosis were observed in A375 cells with RNA interference. These results indicate that SRA-p38-TRP1 axis has a regulatory role in melanin homeostasis and that SRA might be a potential therapeutic target for treating pigmentary diseases.
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Manning AK, Goustin AS, Kleinbrink EL, Thepsuwan P, Cai J, Ju D, Leong A, Udler MS, Brown JB, Goodarzi MO, Rotter JI, Sladek R, Meigs JB, Lipovich L. A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1- PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus. Front Genet 2020; 11:615. [PMID: 32754192 PMCID: PMC7367044 DOI: 10.3389/fgene.2020.00615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/20/2020] [Indexed: 01/08/2023] Open
Abstract
AIMS Causal transcripts at genomic loci associated with type 2 diabetes (T2D) are mostly unknown. The chr8p23.1 variant rs4841132, associated with an insulin-resistant diabetes risk phenotype, lies in the second exon of a long non-coding RNA (lncRNA) gene, LOC157273, located 175 kilobases from PPP1R3B, which encodes a key protein regulating insulin-mediated hepatic glycogen storage in humans. We hypothesized that LOC157273 regulates expression of PPP1R3B in human hepatocytes. METHODS We tested our hypothesis using Stellaris fluorescent in situ hybridization to assess subcellular localization of LOC157273; small interfering RNA (siRNA) knockdown of LOC157273, followed by RT-PCR to quantify LOC157273 and PPP1R3B expression; RNA-seq to quantify the whole-transcriptome gene expression response to LOC157273 knockdown; and an insulin-stimulated assay to measure hepatocyte glycogen deposition before and after knockdown. RESULTS We found that siRNA knockdown decreased LOC157273 transcript levels by approximately 80%, increased PPP1R3B mRNA levels by 1.7-fold, and increased glycogen deposition by >50% in primary human hepatocytes. An A/G heterozygous carrier (vs. three G/G carriers) had reduced LOC157273 abundance due to reduced transcription of the A allele and increased PPP1R3B expression and glycogen deposition. CONCLUSION We show that the lncRNA LOC157273 is a negative regulator of PPP1R3B expression and glycogen deposition in human hepatocytes and a causal transcript at an insulin-resistant T2D risk locus.
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Affiliation(s)
- Alisa K. Manning
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Anton Scott Goustin
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Erica L. Kleinbrink
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Pattaraporn Thepsuwan
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Juan Cai
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
| | - Donghong Ju
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute at Wayne State University, Detroit, MI, United States
| | - Aaron Leong
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Miriam S. Udler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, United States
| | - James Bentley Brown
- Department of Statistics, University of California, Berkeley, Berkeley, CA, United States
- Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
- Computational Biosciences Group, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Medicine, McGill University, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - James B. Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Leonard Lipovich
- Center for Molecular Medicine & Genetics, Wayne State University, Detroit, MI, United States
- Department of Neurology, School of Medicine, Wayne State University, Detroit, MI, United States
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14
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Håkansson KEJ, Goossens EAC, Trompet S, van Ingen E, de Vries MR, van der Kwast RVCT, Ripa RS, Kastrup J, Hohensinner PJ, Kaun C, Wojta J, Böhringer S, Le Cessie S, Jukema JW, Quax PHA, Nossent AY. Genetic associations and regulation of expression indicate an independent role for 14q32 snoRNAs in human cardiovascular disease. Cardiovasc Res 2020; 115:1519-1532. [PMID: 30544252 DOI: 10.1093/cvr/cvy309] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/11/2018] [Indexed: 01/12/2023] Open
Abstract
AIMS We have shown that 14q32 microRNAs are highly involved in vascular remodelling and cardiovascular disease. However, the 14q32 locus also encodes 41 'orphan' small nucleolar RNAs (snoRNAs). We aimed to gather evidence for an independent role for 14q32 snoRNAs in human cardiovascular disease. METHODS AND RESULTS We performed a lookup of the 14q32 region within the dataset of a genome wide association scan in 5244 participants of the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER). Single nucleotide polymorphisms (SNPs) in the snoRNA-cluster were significantly associated with heart failure. These snoRNA-cluster SNPs were not linked to SNPs in the microRNA-cluster or in MEG3, indicating that snoRNAs modify the risk of cardiovascular disease independently. We looked at expression of 14q32 snoRNAs throughout the human cardio-vasculature. Expression profiles of the 14q32 snoRNAs appeared highly vessel specific. When we compared expression levels of 14q32 snoRNAs in human vena saphena magna (VSM) with those in failed VSM-coronary bypasses, we found that 14q32 snoRNAs were up-regulated. SNORD113.2, which showed a 17-fold up-regulation in failed bypasses, was also up-regulated two-fold in plasma samples drawn from patients with ST-elevation myocardial infarction directly after hospitalization compared with 30 days after start of treatment. However, fitting with the genomic associations, 14q32 snoRNA expression was highest in failing human hearts. In vitro studies show that the 14q32 snoRNAs bind predominantly to methyl-transferase Fibrillarin, indicating that they act through canonical mechanisms, but on non-canonical RNA targets. The canonical C/D-box snoRNA seed sequences were highly conserved between humans and mice. CONCLUSION 14q32 snoRNAs appear to play an independent role in cardiovascular pathology. 14q32 snoRNAs are specifically regulated throughout the human vasculature and their expression is up-regulated during cardiovascular disease. Our data demonstrate that snoRNAs merit increased effort and attention in future basic and clinical cardiovascular research.
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Affiliation(s)
- Kjell E J Håkansson
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Reginald V C T van der Kwast
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Rasmus S Ripa
- Department of Cardiology, Rigshospitalet University of Copenhagen, Copenhagen, Denmark
| | - Jens Kastrup
- Department of Cardiology, Rigshospitalet University of Copenhagen, Copenhagen, Denmark
| | | | - Christoph Kaun
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Johann Wojta
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Stefan Böhringer
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Saskia Le Cessie
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Ludwig Boltzmann Cluster for Cardiovascular Research, Vienna, Austria
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15
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Zhuo LA, Wen YT, Wang Y, Liang ZF, Wu G, Nong MD, Miao L. LncRNA SNHG8 is identified as a key regulator of acute myocardial infarction by RNA-seq analysis. Lipids Health Dis 2019; 18:201. [PMID: 31739782 PMCID: PMC6862811 DOI: 10.1186/s12944-019-1142-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/27/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are involved in numerous physiological functions. However, their mechanisms in acute myocardial infarction (AMI) are not well understood. METHODS We performed an RNA-seq analysis to explore the molecular mechanism of AMI by constructing a lncRNA-miRNA-mRNA axis based on the ceRNA hypothesis. The target microRNA data were used to design a global AMI triple network. Thereafter, a functional enrichment analysis and clustering topological analyses were conducted by using the triple network. The expression of lncRNA SNHG8, SOCS3 and ICAM1 was measured by qRT-PCR. The prognostic values of lncRNA SNHG8, SOCS3 and ICAM1 were evaluated using a receiver operating characteristic (ROC) curve. RESULTS An AMI lncRNA-miRNA-mRNA network was constructed that included two mRNAs, one miRNA and one lncRNA. After RT-PCR validation of lncRNA SNHG8, SOCS3 and ICAM1 between the AMI and normal samples, only lncRNA SNHG8 had significant diagnostic value for further analysis. The ROC curve showed that SNHG8 presented an AUC of 0.850, while the AUC of SOCS3 was 0.633 and that of ICAM1 was 0.594. After a pairwise comparison, we found that SNHG8 was statistically significant (P SNHG8-ICAM1 = 0.002; P SNHG8-SOCS3 = 0.031). The results of a functional enrichment analysis of the interacting genes and microRNAs showed that the shared lncRNA SNHG8 may be a new factor in AMI. CONCLUSIONS Our investigation of the lncRNA-miRNA-mRNA regulatory networks in AMI revealed a novel lncRNA, lncRNA SNHG8, as a risk factor for AMI and expanded our understanding of the mechanisms involved in the pathogenesis of AMI.
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Affiliation(s)
- Liu-An Zhuo
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China
| | - Yi-Tao Wen
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China
| | - Yong Wang
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China
| | - Zhi-Fang Liang
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China
| | - Gang Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China
| | - Mei-Dan Nong
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China
| | - Liu Miao
- Department of Cardiology, Institute of Cardiovascular Diseases, the Liu Zhou People's Hospital, 8 Wenchang Road, Liuzhou, 545006, Guangxi, China.
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16
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Miao L, Yin RX, Zhang QH, Hu XJ, Huang F, Chen WX, Cao XL, Wu JZ. A novel lncRNA-miRNA-mRNA triple network identifies lncRNA TWF1 as an important regulator of miRNA and gene expression in coronary artery disease. Nutr Metab (Lond) 2019; 16:39. [PMID: 31182968 PMCID: PMC6555741 DOI: 10.1186/s12986-019-0366-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/21/2019] [Indexed: 02/07/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in numerous physiological functions. Yet, their mechanisms in coronary artery disease (CAD) are not well understood. Methods The expression profile of genes associated to CAD was reannotated into the lncRNA-mRNA biphasic profile. The target microRNA data were used to design a global CAD triple network. Thereafter, we conducted a functional enrichment analysis and clustering using the triple network from the level of topology analyses. The expression of four non-coding RNAs (ncRNAs) was measured by qRT-PCR and the risk of CAD was calculated by nomogram. The prognostic value of three ncRNAs was evaluated using receiver operating characteristic (ROC) curve. Results A CAD lncRNA-miRNA-mRNA network was constructed which included 15 mRNAs, 3 miRNAs, 19 edges and one lncRNA. Nomogram showed that four ncRNAs were the risk of CAD. After RT-PCR validation in four ncRNAs between CAD and non-CAD samples, only three ncRNAs had significant meaning for further analysis. ROC curve showed that TWF1 presented an area under curve (AUC) of 0.862, the AUC of hsa -miR-142-3p was 0.856 and hsa -miR126-5p was 0.822. After the pairwise comparison, we found that TWF1 had significant statistical significance (P TWF1-142 < 0.05 and P TWF1-126 < 0.01). The results of functional enrichment analysis of interacting gene and microRNA showed that the shared lncRNA TWF1 may be a new factor for CAD. Conclusions This investigation on the regulatory networks of lncRNA-miRNA-mRNA in CAD suggests that a novel lncRNA, lncRNA TWF1 is a risk factor for CAD, and expands our understanding into the mechanisms involved in the pathogenesis of CAD.
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Affiliation(s)
- Liu Miao
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Rui-Xing Yin
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Qing-Hui Zhang
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Xi-Jiang Hu
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Feng Huang
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China.,Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Wu-Xian Chen
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Xiao-Li Cao
- Guangxi Key Laboratory Base of Precision Medicine in Cardio-cerebrovascular Disease Control and Prevention, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China.,4Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
| | - Jin-Zhen Wu
- 1Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People's Republic of China
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17
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Che D, Huang W, Fang Z, Li L, Wu H, Pi L, Zhou H, Xu Y, Fu L, Tan Y, Lu Z, Li Q, Gu X. The lncRNA CCAT2 rs6983267 G allele is associated with decreased susceptibility to recurrent miscarriage. J Cell Physiol 2019; 234:20577-20583. [PMID: 30982978 DOI: 10.1002/jcp.28661] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/13/2022]
Abstract
Genetics might play various roles in susceptibility to recurrent miscarriage, and previous studies suggest that some gene polymorphisms might be associated with abortion and breast cancer onset. Colon cancer-associated transcript 2 (CCAT2) is a novel long noncoding RNA (lncRNA) transcript that might be correlated with susceptibility to multiple cancers, including breast cancer. However, whether lncRNA CCAT2 polymorphisms are related to susceptibility to recurrent miscarriage is unclear. We genotyped two lncRNA CCAT2 polymorphisms (rs6983267 and rs3843549) in 248 patients with recurrent miscarriage and 392 controls through a TaqMan real-time polymerase chain reaction assay, and the strength of each association was evaluated via 95% confidence intervals (CIs) and odds ratios (ORs). Our results showed that the rs6983267 G allele in lncRNA CCAT2 was associated with decreased susceptibility to recurrent miscarriage (TG vs. TT: adjusted OR = 0.603; 95% CI = 0.420-0.866; p = 0.0062; GG/TG vs. TT: adjusted OR = 0.620; 95% CI = 0.441-0.873; p = 0.0061). The combined analysis of the two protective polymorphisms (rs3843549 AA and rs6983267 TG/GG) revealed that individuals with two unfavorable alleles exhibited a lower risk of recurrent miscarriage than those with no or only one unfavorable allele (adjusted OR = 0.531; 95% CI = 0.382-0.739). Moreover, the decreased risk associated with the two protective alleles was most obvious in women aged less than 35 years (OR = 0.551; 95% CI = 0.378-0.8803; p = 0.0019) and in women with two to three miscarriages (adjusted OR = 0.466; 95% CI = 0.318-0.683; p < 0.0001). In conclusion, our study indicates that the rs6983267G allele might contribute to a decreased risk of recurrent miscarriage in the South Chinese population.
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Affiliation(s)
- Di Che
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wendong Huang
- Department of Pharmacy, Maoming People's Hospital, Maoming, China
| | - Zhenzhen Fang
- Program of Molecular Medicine, Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Li Li
- Department of Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Haiying Wu
- Department of Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lei Pi
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huazhong Zhou
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yufen Xu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - LanYan Fu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yaqian Tan
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhaoliang Lu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qingfeng Li
- Department of Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaoqiong Gu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Blood Transfusion, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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18
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Kahl KG, Stapel B, Frieling H. Link between depression and cardiovascular diseases due to epigenomics and proteomics: Focus on energy metabolism. Prog Neuropsychopharmacol Biol Psychiatry 2019; 89:146-157. [PMID: 30194950 DOI: 10.1016/j.pnpbp.2018.09.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/13/2018] [Accepted: 09/05/2018] [Indexed: 12/11/2022]
Abstract
Major depression is the most common mental disorder and a leading cause of years lived with disability. In addition to the burden attributed to depressive symptoms and reduced daily life functioning, people with major depression are at increased risk of premature mortality, particularly due to cardiovascular diseases. Several studies point to a bi-directional relation between major depression and cardiovascular diseases, thereby indicating that both diseases may share common pathophysiological pathways. These include lifestyle factors (e.g. physical activity, smoking behavior), dysfunctions of endocrine systems (e.g. hypothalamus-pituitary adrenal axis), and a dysbalance of pro- and anti-inflammatory factors. Furthermore, recent research point to the role of epigenomic and proteomic factors, that are reviewed here with a particular focus on the mitochondrial energy metabolism.
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Affiliation(s)
- Kai G Kahl
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany.
| | - Britta Stapel
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany
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19
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Jia J, Chen Q, Gui L, Jin J, Li Y, Ru Q, Hou S. Association of polymorphisms in bone morphogenetic protein receptor-1B gene exon-9 with litter size in Dorset, Mongolian, and Small Tail Han ewes. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:949-955. [PMID: 30744327 PMCID: PMC6601060 DOI: 10.5713/ajas.18.0541] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/16/2019] [Indexed: 01/14/2023]
Abstract
OBJECTIVE The present study was to investigate the association of polymorphisms in exon-9 of the bone morphogenetic protein receptor-1B (BMPR-1B) gene (C864T) with litter size in 240 Dorset, 232 Mongolian, and 124 Small Tail Han ewes. METHODS Blood samples were collected from 596 ewes and genomic DNA was extracted using the phenol: chloroform extraction method. The 304-bp amplified polymerase chain reaction product was analyzed for polymorphism by single-strand conformation polymorphism method. The genotypic frequency and allele frequency of BMPR-1B gene exon-9 were computed after sequence alignment. The χ2 independence test was used to analyze the association of genotypic frequency and litter size traits with in each ewe breed, where the phenotype was directly treated as category. RESULTS The results indicated two different banding patterns AA and AB for this fragment, with the most frequent genotype and allele of AA and A. Calculated Chi-square test for BMPR-1B gene exon-9 was found to be more than that of p value at the 5% level of significance, indicating that the population under study was in Hardy-Weinberg equilibrium for all ewes. The χ2 independence test analyses indicated litter size differences between genotypes was not the same for each breed. The 304-bp nucleotide sequence was subjected to BLAST analysis, and the C864T mutation significantly affected litter size in singletons, twins and multiples. The heterozygosity in exon-9 of BMPR-1B gene could increase litter size for all the studied ewes. CONCLUSION Consequently, it appears that the polymorphism BMPR-1B gene exon-9 detected in this study may have potential use in marker assisted selection for litter size in Dorset, Mongolian, and Small Tail Han ewes.
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Affiliation(s)
- Jianlei Jia
- Key of laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, China.,Department of Animal Science, College of agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, China
| | - Qian Chen
- Department of Animal Science, College of agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, China
| | - Linsheng Gui
- Key of laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai 810016, China.,Department of Animal Science, College of agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, China
| | - Jipeng Jin
- Department of Animal Science, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou Gansu, 730070, China
| | - Yongyuan Li
- Animal Husbandry and Veterinary Station, Haidong, Qinghai 810700, China
| | - Qiaohong Ru
- Animal Husbandry and Veterinary Station, Haidong, Qinghai 810700, China
| | - Shengzhen Hou
- Department of Animal Science, College of agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai 810016, China
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21
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Giral H, Landmesser U, Kratzer A. Into the Wild: GWAS Exploration of Non-coding RNAs. Front Cardiovasc Med 2018; 5:181. [PMID: 30619888 PMCID: PMC6304420 DOI: 10.3389/fcvm.2018.00181] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/03/2018] [Indexed: 01/16/2023] Open
Abstract
Genome-wide association studies (GWAS) have proven a fundamental tool to identify common variants associated to complex traits, thus contributing to unveil the genetic components of human disease. Besides, the advent of GWAS contributed to expose unexpected findings that urged to redefine the framework of population genetics. First, loci identified by GWAS had small effect sizes and could only explain a fraction of the predicted heritability of the traits under study. Second, the majority of GWAS hits mapped within non-coding regions (such as intergenic or intronic regions) where new functional RNA species (such as lncRNAs or circRNAs) have started to emerge. Bigger cohorts, meta-analysis and technical improvements in genotyping allowed identification of an increased number of genetic variants associated to coronary artery disease (CAD) and cardiometabolic traits. The challenge remains to infer causal mechanisms by which these variants influence cardiovascular disease development. A tendency to assign potential causal variants preferentially to coding genes close to lead variants contributed to disregard the role of non-coding elements. In recent years, in parallel to an increased knowledge of the non-coding genome, new studies started to characterize disease-associated variants located within non-coding RNA regions. The upcoming of databases integrating single-nucleotide polymorphisms (SNPs) and non-coding RNAs together with novel technologies will hopefully facilitate the discovery of causal non-coding variants associated to disease. This review attempts to summarize the current knowledge of genetic variation within non-coding regions with a focus on long non-coding RNAs that have widespread impact in cardiometabolic diseases.
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Affiliation(s)
- Hector Giral
- Department of Cardiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Ulf Landmesser
- Department of Cardiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Adelheid Kratzer
- Department of Cardiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
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22
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The Role of Long Noncoding RNAs in Diabetic Alzheimer's Disease. J Clin Med 2018; 7:jcm7110461. [PMID: 30469430 PMCID: PMC6262561 DOI: 10.3390/jcm7110461] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in diverse physiological and pathological processes by modulating gene expression. They have been found to be dysregulated in the brain and cerebrospinal fluid of patients with neurodegenerative diseases, and are considered promising therapeutic targets for treatment. Among the various neurodegenerative diseases, diabetic Alzheimer's disease (AD) has been recently emerging as an important issue due to several unexpected reports suggesting that metabolic issues in the brain, such as insulin resistance and glucose dysregulation, could be important risk factors for AD. To facilitate understanding of the role of lncRNAs in this field, here we review recent studies on lncRNAs in AD and diabetes, and summarize them with different categories associated with the pathogenesis of the diseases including neurogenesis, synaptic dysfunction, amyloid beta accumulation, neuroinflammation, insulin resistance, and glucose dysregulation. It is essential to understand the role of lncRNAs in the pathogenesis of diabetic AD from various perspectives for therapeutic utilization of lncRNAs in the near future.
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23
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Xi LC, Li HY, Yin D. Long Non-coding RNA-2271 Promotes Osteogenic Differentiation in Human Bone Marrow Stem Cells. Open Life Sci 2018; 13:404-412. [PMID: 33817109 PMCID: PMC7874714 DOI: 10.1515/biol-2018-0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/18/2018] [Indexed: 11/26/2022] Open
Abstract
Background Human bone marrow mesenchymal stem cells (BMSCs) are of great significance for bone regeneration and bone formation. Long non-coding RNAs (lncRNAs) may be involved in modulating cell differentiation. This study aimed to investigate the role of lncR-2271 in promoting osteogenic differentiation in human BMSCs. Methods Human BMSCs were infected using lncR-2271 overexpression (group A) with lentiviral system or transfected with lncR-2271 siRNA (group B). Cells transfected with scrambled plasmids were used as a negative control (group C). Osteogenesis markers were evaluated using alkaline phosphatase (ALP) activity, RUNX2 and osterix (OSX) at protein levels and calcification by Alizarin Red staining. Results BMSCs from group A showed significantly higher ALP activity compared to BMSCs in group B and control group (group C) at both days 7 and 14 following osteogenic induction; ALP activity was significantly lower in the group B compared to the group C. RUNX2 and OSX protein expressions were significantly higher in group A and significantly lower in group B, compared to those in group C, respectively. At day 21, calcification in human BMSCs in group A was significantly higher compared to groups B and C as shown by Alizarin Red staining; calcification was significantly lower in group B compared to group C. Conclusion Our data suggested lncR-2271 played a role in promoting osteogenic differentiation in human BMSCs. This study is the first to illustrate the important role of lncR-2271 in bone formation.
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Affiliation(s)
- Li-Cheng Xi
- Department of Orthopedics, The People's Hospital of Guangxi Zhuang Autonomous Region, No 6, Taoyuan Road, Qingxiu District, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Hong-Yu Li
- Department of Orthopedics, The People's Hospital of Guangxi Zhuang Autonomous Region, No 6, Taoyuan Road, Qingxiu District, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Dong Yin
- Department of Orthopedics, The People's Hospital of Guangxi Zhuang Autonomous Region, No 6, Taoyuan Road, Qingxiu District, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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24
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Zhang X, Li DY, Reilly MP. Long intergenic noncoding RNAs in cardiovascular diseases: Challenges and strategies for physiological studies and translation. Atherosclerosis 2018; 281:180-188. [PMID: 30316538 DOI: 10.1016/j.atherosclerosis.2018.09.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/25/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as important mediators of many biological processes relevant to human pathophysiologies, including cardiovascular diseases. In vitro studies have provided important knowledge of cellular functions and mechanisms for an increasing number of lincRNAs. Dysregulated lncRNAs have been associated with cell fate programming and development, vascular diseases, atherosclerosis, dyslipidemia and metabolic syndrome, and cardiac pathological hypertrophy. However, functional interrogation of individual lincRNAs in physiological and disease states is largely limited. The complex nature of lincRNA actions and poor species conservation of human lincRNAs pose substantial challenges to physiological studies in animal model systems and in clinical translation. This review summarizes recent findings of specific lincRNA physiological studies, including MALAT1, MeXis, Lnc-DC and others, in the context of cardiovascular diseases, examines complex mechanisms of lincRNA actions, reviews in vivo research strategies to delineate lincRNA functions and highlights challenges and approaches for physiological studies of primate-specific lincRNAs.
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Affiliation(s)
- Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Daniel Y Li
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA.
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25
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Abstract
Long non-coding RNAs (lncRNAs) refer to functional cellular RNAs molecules longer than 200 nucleotides in length. Unlike microRNAs, which have been widely studied, little is known about the enigmatic role of lncRNAs. However, lncRNAs have motivated extensively attention in the past few years and are emerging as potentially important regulators in pathological processes, including in cancer. We now understand that lncRNAs play role in cancer through their interactions with DNA, protein, and RNA in many instances. Moreover, accumulating evidence has recognized that large classes of lncRNAs are functional for ovarian cancer. Nevertheless, the biological phenomena and molecular mechanisms of lncRNAs in ovarian cancer remain to be better identified. In this review, we outline the dysregulated expression of lncRNAs and their potential clinical implications in ovarian cancer, with a particular emphasis on discussing the well characterized mechanisms underlying lncRNAs in ovarian cancer.
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Affiliation(s)
- Lei Zhan
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032 China
| | - Bing Wei
- Department of gynecology and obstetrics, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601 China
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26
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Sonea L, Buse M, Gulei D, Onaciu A, Simon I, Braicu C, Berindan-Neagoe I. Decoding the Emerging Patterns Exhibited in Non-coding RNAs Characteristic of Lung Cancer with Regard to their Clinical Significance. Curr Genomics 2018; 19:258-278. [PMID: 29755289 PMCID: PMC5930448 DOI: 10.2174/1389202918666171005100124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022] Open
Abstract
Lung cancer continues to be the leading topic concerning global mortality rate caused by can-cer; it needs to be further investigated to reduce these dramatic unfavorable statistic data. Non-coding RNAs (ncRNAs) have been shown to be important cellular regulatory factors and the alteration of their expression levels has become correlated to extensive number of pathologies. Specifically, their expres-sion profiles are correlated with development and progression of lung cancer, generating great interest for further investigation. This review focuses on the complex role of non-coding RNAs, namely miR-NAs, piwi-interacting RNAs, small nucleolar RNAs, long non-coding RNAs and circular RNAs in the process of developing novel biomarkers for diagnostic and prognostic factors that can then be utilized for personalized therapies toward this devastating disease. To support the concept of personalized medi-cine, we will focus on the roles of miRNAs in lung cancer tumorigenesis, their use as diagnostic and prognostic biomarkers and their application for patient therapy.
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Affiliation(s)
- Laura Sonea
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihail Buse
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Gulei
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Onaciu
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioan Simon
- Surgery Department IV, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Surgery Department, Romanian Railway (CF) University Hospital, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Functional Genomics and Experimental Pathology, "Prof. Dr. Ion Chiricuta" The Oncology Institute, Republicii Street, No. 34-36, 401015, Cluj-Napoca, Romania
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27
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Leung A, Amaram V, Natarajan R. Linking diabetic vascular complications with LncRNAs. Vascul Pharmacol 2018; 114:139-144. [PMID: 29398367 DOI: 10.1016/j.vph.2018.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 12/26/2022]
Abstract
Diabetes leads to markedly accelerated rates of many associated macrovascular complications like hypertension and atherosclerosis, and microvascular complications like nephropathy and retinopathy. High glucose, the hallmark of diabetes, drives changes in vascular and inflammatory cells that promote the development of these complications. Understanding the molecular processes involved in the development of diabetes and its debilitating complications can lead to much needed newer clinical therapies. Recently, long-noncoding RNAs (lncRNAs) have been shown to be important in the biology of vascular cells and there is growing evidence that lncRNAs are also involved in the cell biology relevant to diabetic vascular complications. In this review, we provide an overview of lncRNAs that function in vascular cells, and those that have been linked to diabetic complications.
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Affiliation(s)
- Amy Leung
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolic Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States
| | - Vishnu Amaram
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolic Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, United States
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolic Research Institute, 1500 East Duarte Road, Duarte, CA 91010, United States; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, United States.
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De Rosa S, Arcidiacono B, Chiefari E, Brunetti A, Indolfi C, Foti DP. Type 2 Diabetes Mellitus and Cardiovascular Disease: Genetic and Epigenetic Links. Front Endocrinol (Lausanne) 2018; 9:2. [PMID: 29387042 PMCID: PMC5776102 DOI: 10.3389/fendo.2018.00002] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/03/2018] [Indexed: 12/14/2022] Open
Abstract
Type 2 diabetes mellitus (DM) is a common metabolic disorder predisposing to diabetic cardiomyopathy and atherosclerotic cardiovascular disease (CVD), which could lead to heart failure through a variety of mechanisms, including myocardial infarction and chronic pressure overload. Pathogenetic mechanisms, mainly linked to hyperglycemia and chronic sustained hyperinsulinemia, include changes in metabolic profiles, intracellular signaling pathways, energy production, redox status, increased susceptibility to ischemia, and extracellular matrix remodeling. The close relationship between type 2 DM and CVD has led to the common soil hypothesis, postulating that both conditions share common genetic and environmental factors influencing this association. However, although the common risk factors of both CVD and type 2 DM, such as obesity, insulin resistance, dyslipidemia, inflammation, and thrombophilia, can be identified in the majority of affected patients, less is known about how these factors influence both conditions, so that efforts are still needed for a more comprehensive understanding of this relationship. The genetic, epigenetic, and environmental backgrounds of both type 2 DM and CVD have been more recently studied and updated. However, the underlying pathogenetic mechanisms have seldom been investigated within the broader shared background, but rather studied in the specific context of type 2 DM or CVD, separately. As the precise pathophysiological links between type 2 DM and CVD are not entirely understood and many aspects still require elucidation, an integrated description of the genetic, epigenetic, and environmental influences involved in the concomitant development of both diseases is of paramount importance to shed new light on the interlinks between type 2 DM and CVD. This review addresses the current knowledge of overlapping genetic and epigenetic aspects in type 2 DM and CVD, including microRNAs and long non-coding RNAs, whose abnormal regulation has been implicated in both disease conditions, either etiologically or as cause for their progression. Understanding the links between these disorders may help to drive future research toward an integrated pathophysiological approach and to provide future directions in the field.
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Affiliation(s)
- Salvatore De Rosa
- Department of Medical and Surgical Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Eusebio Chiefari
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
| | - Antonio Brunetti
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti, ; Ciro Indolfi, ; Daniela P. Foti,
| | - Ciro Indolfi
- Department of Medical and Surgical Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti, ; Ciro Indolfi, ; Daniela P. Foti,
| | - Daniela P. Foti
- Department of Health Sciences, Magna Græcia University of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti, ; Ciro Indolfi, ; Daniela P. Foti,
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29
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Raut SK, Khullar M. The Big Entity of New RNA World: Long Non-Coding RNAs in Microvascular Complications of Diabetes. Front Endocrinol (Lausanne) 2018; 9:300. [PMID: 29915562 PMCID: PMC5994400 DOI: 10.3389/fendo.2018.00300] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 05/18/2018] [Indexed: 12/14/2022] Open
Abstract
A major part of the genome is known to be transcribed into non-protein coding RNAs (ncRNAs), such as microRNA and long non-coding RNA (lncRNA). The importance of ncRNAs is being increasingly recognized in physiological and pathological processes. lncRNAs are a novel class of ncRNAs that do not code for proteins and are important regulators of gene expression. In the past, these molecules were thought to be transcriptional "noise" with low levels of evolutionary conservation. However, recent studies provide strong evidence indicating that lncRNAs are (i) regulated during various cellular processes, (ii) exhibit cell type-specific expression, (iii) localize to specific organelles, and (iv) associated with human diseases. Emerging evidence indicates an aberrant expression of lncRNAs in diabetes and diabetes-related microvascular complications. In the present review, we discuss the current state of knowledge of lncRNAs, their genesis from genome, and the mechanism of action of individual lncRNAs in the pathogenesis of microvascular complications of diabetes and therapeutic approaches.
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30
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Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis. Int J Mol Sci 2017; 18:ijms18122578. [PMID: 29189723 PMCID: PMC5751181 DOI: 10.3390/ijms18122578] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 12/15/2022] Open
Abstract
Single cell organisms can surprisingly exceed the number of human protein-coding genes, which are thus not at the origin of the complexity of an organism. In contrast, the relative amount of non-protein-coding sequences increases consistently with organismal complexity. Moreover, the mammalian transcriptome predominantly comprises non-(protein)-coding RNAs (ncRNA), of which the long ncRNAs (lncRNAs) constitute the most abundant part. lncRNAs are highly species- and tissue-specific with very versatile modes of action in accordance with their binding to a large spectrum of molecules and their diverse localization. lncRNAs are transcriptional regulators adding an additional regulatory layer in biological processes and pathophysiological conditions. Here, we review lncRNAs affecting metabolic organs with a focus on the liver, pancreas, skeletal muscle, cardiac muscle, brain, and adipose organ. In addition, we will discuss the impact of lncRNAs on metabolic diseases such as obesity and diabetes. In contrast to the substantial number of lncRNA loci in the human genome, the functionally characterized lncRNAs are just the tip of the iceberg. So far, our knowledge concerning lncRNAs in energy homeostasis is still in its infancy, meaning that the rest of the iceberg is a treasure chest yet to be discovered.
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31
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Liao B, Chen R, Lin F, Mai A, Chen J, Li H, Xu Z, Dong S. Long noncoding RNA HOTTIP promotes endothelial cell proliferation and migration via activation of the Wnt/β‐catenin pathway. J Cell Biochem 2017; 119:2797-2805. [DOI: 10.1002/jcb.26448] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/17/2017] [Indexed: 01/17/2023]
Affiliation(s)
- Bihong Liao
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Ruimian Chen
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Feng Lin
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Aihuan Mai
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Jie Chen
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Huimin Li
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Zhenglei Xu
- Department of Gastroenterology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
| | - Shaohong Dong
- Department of Cardiology, Shenzhen People's HospitalSecond Clinical Medical College of Jinan UniversityShenzhenGuangdong ProvinceChina
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32
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Li N, Yang M, Shi K, Li W. Long non-coding RNA HOXA11-AS in human cancer: A meta-analysis. Clin Chim Acta 2017; 474:165-170. [PMID: 28942241 DOI: 10.1016/j.cca.2017.09.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/17/2017] [Accepted: 09/20/2017] [Indexed: 12/27/2022]
Abstract
BACKGROUND Homeobox A11 antisense (HOXA11-AS), a newly identified lncRNA, is up-regulated in various carcinomas. We conducted the present meta-analysis to explore the potential of HOXA11-AS as a common predictive biomarker for metastasis and prognosis in malignant tumors. METHODS A systematic literature search on the online electronic databases of PubMed, Web of Science, and Embase was carried out to determine relevant studies (as of July 9, 2017). The pooled hazard ratios (HRs)/odds rates (ORs), and their 95% confidence intervals (CIs) were used to evaluate the relationship. RESULTS A total of 608 patients from seven studies were included in the current meta-analysis. The pooled results indicated that high HOXA11-AS expression was related to poor overall survival (OS) (HR=2.02, 95% CI: 1.48-2.75, P<0.001) and progression-free survival (PFS) (HR=1.91, 95% CI: 1.15-3.17, P=0.012). Further analyses reveal that patients with high HOXA11-AS expression are prone to develop distant metastasis (DM) (OR=6.05, 95% CI: 1.66-22.06, P=0.006). CONCLUSIONS This meta-analysis showed that increased expression of HOXA11-AS is a risk factor for poor clinical outcomes in numerous tumors and may act as a novel biomarker for poor prognosis and metastasis in cancers.
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Affiliation(s)
- Na Li
- Department of Pathology, The First Affiliated Hospital of Hunan University of Medicine, Huaihua, Hunan Province, China
| | - Meilan Yang
- Department of Pathology, The First Affiliated Hospital of Hunan University of Medicine, Huaihua, Hunan Province, China
| | - Ke Shi
- Department of Geriatrics, Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Wei Li
- Department of Geriatrics, Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, Hunan Province, China.
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33
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Sommese L, Zullo A, Mancini FP, Fabbricini R, Soricelli A, Napoli C. Clinical relevance of epigenetics in the onset and management of type 2 diabetes mellitus. Epigenetics 2017; 12:401-415. [PMID: 28059593 DOI: 10.1080/15592294.2016.1278097] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epigenetics is involved in the altered expression of gene networks that underlie insulin resistance and insufficiency. Major genes controlling β-cell differentiation and function, such as PAX4, PDX1, and GLP1 receptor, are epigenetically controlled. Epigenetics can cause insulin resistance through immunomediated pro-inflammatory actions related to several factors, such as NF-kB, osteopontin, and Toll-like receptors. Hereafter, we provide a critical and comprehensive summary on this topic with a particular emphasis on translational and clinical aspects. We discuss the effect of epigenetics on β-cell regeneration for cell replacement therapy, the emerging bioinformatics approaches for analyzing the epigenetic contribution to type 2 diabetes mellitus (T2DM), the epigenetic core of the transgenerational inheritance hypothesis in T2DM, and the epigenetic clinical trials on T2DM. Therefore, prevention or reversion of the epigenetic changes occurring during T2DM development may reduce the individual and societal burden of the disease.
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Affiliation(s)
- Linda Sommese
- a U.O.C. Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology , Department of Internal and Specialty Medicine , Azienda Ospedaliera Universitaria (AOU), Università degli Studi della Campania "Luigi Vanvitelli ," Italy.,b Department of Experimental Medicine , Second University of Naples , Italy
| | - Alberto Zullo
- c Department of Sciences and Technologies , University of Sannio , Benevento , Italy.,d CEINGE-Advanced Biotechnologies , Naples , Italy
| | | | - Rossella Fabbricini
- a U.O.C. Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology , Department of Internal and Specialty Medicine , Azienda Ospedaliera Universitaria (AOU), Università degli Studi della Campania "Luigi Vanvitelli ," Italy
| | - Andrea Soricelli
- e IRCCS Research Institute SDN , Naples , Italy.,f Department of Studies of Institutions and Territorial Systems , University of Naples Parthenope , Naples , Italy
| | - Claudio Napoli
- a U.O.C. Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology, Regional Reference Laboratory of Transplant Immunology , Department of Internal and Specialty Medicine , Azienda Ospedaliera Universitaria (AOU), Università degli Studi della Campania "Luigi Vanvitelli ," Italy.,e IRCCS Research Institute SDN , Naples , Italy.,g Department of Medical, Surgical, Neurological, Metabolic and Geriatric Sciences , Second University of Naples , Italy
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A Long Noncoding RNA ZEB1-AS1 Promotes Tumorigenesis and Predicts Poor Prognosis in Glioma. Int J Mol Sci 2016; 17:ijms17091431. [PMID: 27589728 PMCID: PMC5037710 DOI: 10.3390/ijms17091431] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 12/17/2022] Open
Abstract
Emerging studies show that long noncoding RNAs (lncRNAs) have important roles in carcinogenesis. lncRNA ZEB1 antisense 1 (ZEB1-AS1) is a novel lncRNA, whose clinical significance, biological function, and underlying mechanism remains unclear in glioma. Here, we found that ZEB1-AS1 was highly expressed in glioma tissues, being closely related to clinical stage of glioma. Moreover, patients with high ZEB1-AS1 levels had poor prognoses, with the evidence provided by multivariate Cox regression analysis indicating that ZEB1-AS1 expression could serve as an independent prognostic factor in glioma patients. Functionally, silencing of ZEB1-AS1 could significantly inhibit cell proliferation, migration, and invasion, as well as promote apoptosis. Knockdown of ZEB1-AS1 significantly induced the G0/G1 phase arrest and correspondingly decreased the percentage of S phase cells. Further analysis indicated that ZEB1-AS1 could regulate the cell cycle by inhibiting the expression of G1/S transition key regulators, such as Cyclin D1 and CDK2. Furthermore, ZEB1-AS1 functioned as an important regulator of migration and invasion via activating epithelial to mesenchymal transition (EMT) through up-regulating the expression of ZEB1, MMP2, MMP9, N-cadherin, and Integrin-β1 as well as decreasing E-cadherin levels in the metastatic progression of glioma. Additionally, forced down-regulation of ZEB1-AS1 could dramatically promote apoptosis by increasing the expression level of Bax and reducing Bcl-2 expression in glioma. Taken together, our data suggest that ZEB1-AS1 may serve as a new prognostic biomarker and therapeutic target of glioma.
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