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He W, Gu L, Yang J, Zhang R, Long J, Peng W, Liang B, Zhu L, Lv M, Nan A, Su L. Exosomal circCNOT6L Regulates Astrocyte Apoptotic Signals Induced by Hypoxia Exposure Through miR99a-5p/SERPINE1 and Alleviates Ischemic Stroke Injury. Mol Neurobiol 2023; 60:7118-7135. [PMID: 37531026 DOI: 10.1007/s12035-023-03518-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023]
Abstract
Circular RNAs are involved in intervention strategies for treating ischemic stroke (IS). However, circCNOT6L (hsa_circ_0006168) has not yet been reported in IS. Thus, we aimed to explore the potential role of circCNOT6L and its molecular mechanism in IS. In this study, we first found that the expression of both exosomal circCNOT6L (P = 0.0006) and plasma circCNOT6L (P = 0.0054) was down-regulated in IS patients compared with controls. Clinically, a negative correlation was observed between the relative expression level of circCNOT6L and the National Institutes of Health Stroke Scale (NIHSS) score and infarct volume of the brain. Simultaneously, the relative expression level of circCNOT6L was negatively associated with multiple risk factors for IS, such as mean platelet volume (MPV), red cell distribution width (RDW), very low-density lipoprotein (VLDL), and serum potassium, whereas it was positively correlated with high-density lipoprotein (HDL). In vitro, circCNOT6L silencing blocked cell viability and proliferation, while it promoted cell apoptosis of astrocytes undergoing oxygen-glucose deprivation/reperfusion (OGD/R) treatment. Mechanistically, the RNA antisense purification (RAP) assay and luciferase reporter assay revealed that circCNOT6L acts as a miRNA sponge to absorb miR-99a-5p and then regulates the expression of serine proteinase inhibitor (SERPINE1). In the further rescue experiment, overexpressing SERPINE1 could rescue the cell apoptotic signals due to circCNOT6L depletion. In conclusion, CircCNOT6L attenuated the cell apoptotic signal of astrocytes via the miR99a-5p/SERPINE1 axis and then alleviated injury after hypoxia induced by ischemic stroke.
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Affiliation(s)
- Wanting He
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Lian Gu
- First Affiliated Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Jialei Yang
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ruirui Zhang
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Jianxiong Long
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wenyi Peng
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Baoyun Liang
- First Affiliated Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Lulu Zhu
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Miao Lv
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Aruo Nan
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China.
| | - Li Su
- School of Public Health, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, China.
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Moxon JV, Calcino A, Kraeuter AK, Phie J, Anderson G, Standley G, Sealey C, Jones RE, Field MA, Golledge J. A case-control comparison of acute-phase peripheral blood gene expression in participants diagnosed with minor ischaemic stroke or stroke mimics. Hum Genomics 2023; 17:106. [PMID: 38007520 PMCID: PMC10676587 DOI: 10.1186/s40246-023-00551-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/11/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Past studies suggest that there are changes in peripheral blood cell gene expression in response to ischaemic stroke; however, the specific changes which occur during the acute phase are poorly characterised. The current study aimed to identify peripheral blood cell genes specifically associated with the early response to ischaemic stroke using whole blood samples collected from participants diagnosed with ischaemic stroke (n = 29) or stroke mimics (n = 27) following emergency presentation to hospital. Long non-coding RNA (lncRNA), mRNA and micro-RNA (miRNA) abundance was measured by RNA-seq, and the consensusDE package was used to identify genes which were differentially expressed between groups. A sensitivity analysis excluding two participants with metastatic disease was also conducted. RESULTS The mean time from symptom onset to blood collection was 2.6 h. Most strokes were mild (median NIH stroke scale score 2.0). Ten mRNAs (all down-regulated in samples provided by patients experiencing ischaemic stroke) and 30 miRNAs (14 over-expressed and 16 under-expressed in participants with ischaemic stroke) were significantly different between groups in the whole cohort and sensitivity analyses. No significant over-representation of gene ontology categories by the differentially expressed genes was observed. Random forest analysis suggested a panel of differentially expressed genes (ADGRG7 and miRNAs 96, 532, 6766, 6798 and 6804) as potential ischaemic stroke biomarkers, although modelling analyses demonstrated that these genes had poor diagnostic performance. CONCLUSIONS This study provides evidence suggesting that the early response to minor ischaemic stroke is predominantly reflected by changes in the expression of miRNAs in peripheral blood cells. Further work in independent cohorts particularly in patients with more severe stroke is needed to validate these findings and investigate their clinical relevance.
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Affiliation(s)
- Joseph V Moxon
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - Andrew Calcino
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
| | - Ann-Katrin Kraeuter
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- Faculty of Health and Life Sciences, Psychology, Northumbria University, Newcastle Upon Tyne, UK
| | - James Phie
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
| | - Georgina Anderson
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia
| | - Glenys Standley
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia
| | - Cindy Sealey
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia
| | - Rhondda E Jones
- Research Division, James Cook University, Townsville, QLD, 4811, Australia
- Tropical Australian Academic Health Centre, Townsville, QLD, 4811, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- Immunogenomics Laboratory, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- Menzies School of Health Research, Darwin, NT, 0811, Australia
| | - Jonathan Golledge
- Queensland Research Centre for Peripheral Vascular Disease, College of Medicine and Dentistry, James Cook University, Townsville, QLD, 4811, Australia.
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia.
- Department of Vascular and Endovascular Surgery, Townsville University Hospital, Townsville, QLD, 4811, Australia.
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Xie H, Huang Y, Zhan Y. Construction of a novel circRNA-miRNA-ferroptosis related mRNA network in ischemic stroke. Sci Rep 2023; 13:15077. [PMID: 37699956 PMCID: PMC10497552 DOI: 10.1038/s41598-023-41028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Molecule alterations are important to explore the pathological mechanism of ischemic stroke (IS). Ferroptosis, a newly recognized type of regulated cell death, is related to IS. Identification of the interactions between circular RNA (circRNA), microRNA (miRNA) and ferroptosis related mRNA may be useful to understand the molecular mechanism of IS. The circRNA, miRNA and mRNA transcriptome data in IS, downloaded from the Gene Expression Omnibus (GEO) database, was used for differential expression analysis. Ferroptosis related mRNAs were identified from the FerrDb database, followed by construction of circRNA-miRNA-ferroptosis related mRNA network. Enrichment and protein-protein interaction analysis of mRNAs in circRNA-miRNA-mRNA network was performed, followed by expression validation by reverse transcriptase polymerase chain reaction and online dataset. A total of 694, 41 and 104 differentially expressed circRNAs, miRNAs and mRNAs were respectively identified in IS. Among which, dual specificity phosphatase 1 (DUSP1), nuclear receptor coactivator 4 (NCOA4) and solute carrier family 2 member 3 (SLC2A3) were the only three up-regulated ferroptosis related mRNAs. Moreover, DUSP1, NCOA4 and SLC2A3 were significantly up-regulated in IS after 3, 5 and 24 h of the attack. Based on these three ferroptosis related mRNAs, 4 circRNA-miRNA-ferroptosis related mRNA regulatory relationship pairs were identified in IS, including hsa_circ_0071036/hsa_circ_0039365/hsa_circ_0079347/hsa_circ_0008857-hsa-miR-122-5p-DUSP1, hsa_circ_0067717/hsa_circ_0003956/hsa_circ_0013729-hsa-miR-4446-3p-SLC2A3, hsa_circ_0059347/hsa_circ_0001414/hsa_circ_0049637-hsa-miR-885-3p-SLC2A3, and hsa_circ_0005633/hsa_circ_0004479-hsa-miR-4435-NCOA4. In addition, DUSP1 is involved in the signaling pathway of fluid shear stress and atherosclerosis. Relationship of regulatory action between circRNAs, miRNAs and ferroptosis related mRNAs may be associated with the development of IS.
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Affiliation(s)
- Huirong Xie
- Department of Neurology, Lishui Municipal Central Hospital, Lishui Hospital of Zhejiang University, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Clinical Research Center for Neurological Diseases, 289 Kuocang Road, Lishui, 323000, Zhejiang, China.
| | - Yijie Huang
- Department of Neurology, Lishui Municipal Central Hospital, Lishui Hospital of Zhejiang University, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Clinical Research Center for Neurological Diseases, 289 Kuocang Road, Lishui, 323000, Zhejiang, China
| | - Yanli Zhan
- Cerebrovascular Research Laboratory, Lishui Municipal Central Hospital, Lishui Hospital of Zhejiang University, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Clinical Research Center for Neurological Diseases, 289 Kuocang Road, Lishui, 323000, Zhejiang, China
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Zhang X, Wan M, Min X, Chu G, Luo Y, Han Z, Li W, Xu R, Luo J, Li W, Yang Y, Ma Y, Jiao L, Wang T. Circular RNA as biomarkers for acute ischemic stroke: A systematic review and meta-analysis. CNS Neurosci Ther 2023. [PMID: 37186176 DOI: 10.1111/cns.14220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Rapid diagnosis of acute ischemic stroke (AIS) patients is still challenging, and reliable biomarkers are needed. Noncoding RNAs are important for many physiological activities, among which circular RNAs (circRNAs) have been proven to be more tissue-specific and conservative. Many recent studies found the potential of circRNAs as biomarkers for many diseases, including cardiovascular diseases, cancers, and ischemic stroke. This systemic review and meta-analysis aimed to identify circRNAs as potential biomarkers for AIS. METHODS This study has been prospectively registered in PROSPERO (Registration No. 11 CRD42021288033). Published literature comparing circRNA expression profiles between AIS and non-AIS in human and animal models were retrieved from the articles published by January 2023 in major databases. We descriptively summarized the included studies, conducted meta-analysis under a random effects model, and did bioinformatics analysis including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. RESULTS Totally 23 studies were included, reporting 18 distinctive upregulated and 20 distinctive downregulated circRNAs. Diagnostic meta-analysis indicated discriminative ability of the circRNAs. Furthermore, circRNA HECTD1, circRNA DLGAP4, circRNA CDC14A, circRNA SCMH1, and circRNA TLK1 were reported with the same regulation trend in more than one study (animal studies included). GO and KEGG enrichment analyses indicated that the target genes of these five circRNAs were enriched in regulating cell proliferation, apoptosis, and oxidative stress. CONCLUSIONS This study demonstrates that circRNAs (circRNA HECTD1, circRNA DLGAP4, circRNA CDC14A, circRNA SCMH1, and circRNA TLK1) generally are promising as potential biomarkers for AIS. However, due to the limited number of studies, diagnostic value of individual circRNA could not be validated. More in vitro and in vivo functional studies are needed.
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Affiliation(s)
- Xiao Zhang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- China International Neuroscience Institute (China-INI), Beijing, China
| | - Mengyao Wan
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoli Min
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital, Kunming Medical University, Kunming, China
| | - Guanglei Chu
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yumin Luo
- Institute of Cerebrovascular Diseases Research and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ziping Han
- Institute of Cerebrovascular Diseases Research and Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Wei Li
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Liaocheng People's Hospital, Liaocheng, China
| | - Ran Xu
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- China International Neuroscience Institute (China-INI), Beijing, China
| | - Jichang Luo
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- China International Neuroscience Institute (China-INI), Beijing, China
| | - Wenjing Li
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yutong Yang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Yan Ma
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- China International Neuroscience Institute (China-INI), Beijing, China
| | - Liqun Jiao
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- China International Neuroscience Institute (China-INI), Beijing, China
- Department of Interventional Neuroradiology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Tao Wang
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
- China International Neuroscience Institute (China-INI), Beijing, China
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Guan D, Ji Y, Lu X, Feng W, Ma W. Associations of MTHFR gene polymorphism with lipid metabolism and risk of cerebral infarction in the Northwest Han Chinese population. Front Neurol 2023; 14:1152351. [PMID: 37064173 PMCID: PMC10102478 DOI: 10.3389/fneur.2023.1152351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023] Open
Abstract
ObjectiveGenetic variation in the methylenetetrahydrofolate reductase (MTHFR) gene may contribute to the development of cerebral infarction (CI); however, results have been inconsistent across studies with different populations, including studies of the Chinese population. The aim of this study was to analyze the effect of MTHFR gene polymorphism on serum lipid and homocysteine levels among patients with CI in the Northwest Chinese Han population.Patients and methodsA total of 521 CI patients and 524 non-CI controls were enrolled in the study. Polymerase chain reaction and hybridization were utilized to identify MTHFR gene polymorphisms. Multivariate logistic regression analysis was used to assess the associations of MTHFR gene polymorphism with risk of CI.ResultsFrequencies of the TT genotype and the T allele were markedly higher among CI patients than among controls. After stratifying our data by sex and age, we determined that these differences in frequency of the TT genotype and the T allele were statistically significant among participants of two different age brackets and among men, but not among women (i.e., there were no statistically significant differences between female patients and female controls). CI patients and control participants with the CT or TT genotype had significantly higher homocysteine (Hcy) levels than those with the CC genotype. Among CI patients, CT/TT carriers showed significantly lower high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A-I (ApoA-I) levels as compared with CC carriers, but there was no significant difference for control participants. Multivariable logistic regression analysis showed that drinking; smoking; diabetes mellitus; levels of Hcy, direct bilirubin (DB), indirect bilirubin (IB), ApoA-I, and total protein (TP); and TT genotype were significant independent risk factors for CI.ConclusionsThe results suggested that the TT genotype of the MTHFR C677T gene polymorphism, which is associated with hyperhomocysteinemia (HHcy), might be of great clinical significance in the identification of new biomarkers for CI and in the development of individualized preventive and therapeutic strategies.
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Affiliation(s)
- Dong Guan
- Department of Pharmacology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yichun Ji
- Department of Hepatobiliary Surgery, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoyun Lu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Weiyi Feng
- Department of Pharmacology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wenbing Ma
- Department of Pharmacology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- *Correspondence: Wenbing Ma
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Jin H, Yang Z, Luo J, Li C, Chen J, Lim KJ, Wang Z. Comprehensive identification and analysis of circRNAs during hickory ( Carya cathayensis Sarg.) flower bud differentiation. FRONTIERS IN PLANT SCIENCE 2023; 13:1000489. [PMID: 36684801 PMCID: PMC9846342 DOI: 10.3389/fpls.2022.1000489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Flower bud differentiation represents a crucial transition from vegetative growth to reproductive development. Carya cathayensis (hickory) is an important economic species in China, with a long juvenile period that hinders its commercial development. In recent years, circular RNAs (circRNAs) have been widely studied and identified as sponges for miRNA regulation of mRNA expression. However, little is known regarding the role of circRNAs in flower buds. In this study, we sequenced circRNAs at three developmental stages (undifferentiated, differentiating, and fully differentiated) in both female and male buds. A total of 6,931 circRNAs were identified in the three developmental stages and 4,449 and 2,209 circRNAs were differentially expressed in female and male buds, respectively. Gene ontology demonstrated that many circRNA host genes participated in various processes, for example, cellular and intracellular pH regulation. Function annotation identified 46 differentially expressed circRNAs involved in flowering regulation, with 28 circRNAs found only in female buds, 4 found only in male buds, and 11 found in both female and male buds. A circRNA-miRNA-mRNA network was predicted based on 13 flowering-related circRNAs and their seven putative interacting miRNAs to describe the regulatory mechanism. Our preliminary results demonstrated a potential involvement of circRNA in bud differentiation. They provided a preliminary theoretical basis for how circRNA might participate in flower development in hickory, perhaps in woody plants.
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Cheng L, Liu Z, Xia J. New insights into circRNA and its mechanisms in angiogenesis regulation in ischemic stroke: a biomarker and therapeutic target. Mol Biol Rep 2023; 50:829-840. [PMID: 36331748 DOI: 10.1007/s11033-022-07949-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
Abstract
Ischemic stroke accounts for about 71% of strokes worldwide. Due to limited recommended therapeutics for ischemic stroke, more attention is focused on angiogenesis in ischemic stroke. Not long after ischemic stroke, angiogenesis arises and is vital for the prognosis. Various pro-angiogenic, anti-angiogenic factors and their downstream pathways engage in angiogenesis regulation. CircRNAs are differentially expressed after ischemic stroke. Up to now, circRNAs have been found to exert many functions in regulating apoptosis, autophagy, proliferation, and differentiation of neurons and neural stem cells mainly as miRNAs sponges or proteins decoy. Thus, many circRNAs are considered promising biomarkers or therapeutic targets for ischemic stroke. Besides, circRNAs participate in the modulation of endothelial-mesenchymal transition and blood-brain barrier maintenance. Moreover, circRNAs play significant roles in endothelial dysfunction concerning inflammation responses, apoptosis, proliferation, and migration. They correlate with many angiogenesis-related signaling pathways and genes via the circRNA/miRNA/mRNA network. Novel insights into circRNAs significance in angiogenesis regulation in ischemic stroke could be provided for further researches on the clinical application of circRNAs in ischemic stroke.
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Affiliation(s)
- Liuyang Cheng
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, P.R. China
| | - Zeyu Liu
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, P.R. China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, P.R. China.
- Clinical Research Center for Cerebrovascular Disease of Hunan Province, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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Bai C, Hao X, Zhou L, Sun Y, Song L, Wang F, Yang L, Liu J, Chen J. Machine learning-based identification of the novel circRNAs circERBB2 and circCHST12 as potential biomarkers of intracerebral hemorrhage. Front Neurosci 2022; 16:1002590. [PMID: 36523430 PMCID: PMC9745062 DOI: 10.3389/fnins.2022.1002590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/14/2022] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND The roles and potential diagnostic value of circRNAs in intracerebral hemorrhage (ICH) remain elusive. METHODS This study aims to investigate the expression profiles of circRNAs by RNA sequencing and RT-PCR in a discovery cohort and an independent validation cohort. Bioinformatics analysis was performed to identify the potential functions of circRNA host genes. Machine learning classification models were used to assess circRNAs as potential biomarkers of ICH. RESULTS A total of 125 and 284 differentially expressed circRNAs (fold change > 1.5 and FDR < 0.05) were found between ICH patients and healthy controls in the discovery and validation cohorts, respectively. Nine circRNAs were consistently altered in ICH patients compared to healthy controls. The combination of the novel circERBB2 and circCHST12 in ICH patients and healthy controls showed an area under the curve of 0.917 (95% CI: 0.869-0.965), with a sensitivity of 87.5% and a specificity of 82%. In combination with ICH risk factors, circRNAs improved the performance in discriminating ICH patients from healthy controls. Together with hsa_circ_0005505, two novel circRNAs for differentiating between patients with ICH and healthy controls showed an AUC of 0.946 (95% CI: 0.910-0.982), with a sensitivity of 89.1% and a specificity of 86%. CONCLUSION We provided a transcriptome-wide overview of aberrantly expressed circRNAs in ICH patients and identified hsa_circ_0005505 and novel circERBB2 and circCHST12 as potential biomarkers for diagnosing ICH.
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Affiliation(s)
- Congxia Bai
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Xiaoyan Hao
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Lei Zhou
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yingying Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengjuan Wang
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Liu Yang
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jiayun Liu
- Department of Clinical Laboratory Medicine, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jingzhou Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
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Zheng J, Luo S, Long Y. Bioinformatic analysis and clinical diagnostic value of hsa_circ_0004099 in acute ischemic stroke. PLoS One 2022; 17:e0277832. [PMID: 36399471 PMCID: PMC9674149 DOI: 10.1371/journal.pone.0277832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
This study investigates the expression and effect of hsa_circ_0004099 in acute ischemic stroke (AIS). We conducted a case-controlled study that included 40 patients with AIS within 24 hours and 40 healthy subjects during the same period as a control group. Differentially expressed circular RNAs (circRNAs) were obtained using GEO2R, and the expression of hsa_circ_0004099 was verified using RT-PCR. Correlation analysis of the National Institutes of Health Stroke Scale (NIHSS) disease severity score and ischemic time with hsa_circ_0004099 expression levels was also performed. The receiver operating characteristic (ROC) curve of hsa_circ_0004099 was constructed, and bioinformatic analysis of hsa_circ_0004099 was performed. NIHSS scores negatively correlated with hsa_circ_0004099 levels (P<0.001, r = -0.7053), whereas infarct time was negatively correlated with hsa_circ_0004099 levels (P<0.001, r = -0.5130); hsa_circ_0004099 could benefit clinical diagnosis (area under the curve [AUC]: 0.923 [95% confidence interval [CI]: 0.8680-0.9904]). Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that hsa_circ_0004099 was enriched in several cancer pathways, which were collectively enriched in four genes namely TCF7L2, NRAS, CTNNB1, and KRAS. Eight core proteins were screened using a protein-protein interaction (PPI) network namely SMAD4, HIF1A, CTNNB1, CDKN1B, CDK6, FOXO3, KRAS, and NRAS. hsa_circ_0004099 is a potential clinical diagnostic marker. In addition, the possible role of hsa_circ_0004099 in the pathogenesis of AIS was analyzed using bioinformatics, which provided a new potential molecular target for AIS treatment.
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Affiliation(s)
- Jiqing Zheng
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shuiming Luo
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yaobin Long
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Yang K, Zeng L, Ge A, Wang S, Zeng J, Yuan X, Mei Z, Wang G, Ge J. A systematic review of the research progress of non-coding RNA in neuroinflammation and immune regulation in cerebral infarction/ischemia-reperfusion injury. Front Immunol 2022; 13:930171. [PMID: 36275741 PMCID: PMC9585453 DOI: 10.3389/fimmu.2022.930171] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/08/2022] [Indexed: 11/15/2022] Open
Abstract
Cerebral infarction/ischemia-reperfusion injury is currently the disease with the highest mortality and disability rate of cardiovascular disease. Current studies have shown that nerve cells die of ischemia several hours after ischemic stroke, which activates the innate immune response in the brain, promotes the production of neurotoxic substances such as inflammatory cytokines, chemokines, reactive oxygen species and − nitrogen oxide, and mediates the destruction of blood-brain barrier and the occurrence of a series of inflammatory cascade reactions. Meanwhile, the expression of adhesion molecules in cerebral vascular endothelial cells increased, and immune inflammatory cells such as polymorphonuclear neutrophils, lymphocytes and mononuclear macrophages passed through vascular endothelial cells and entered the brain tissue. These cells recognize antigens exposed by the central nervous system in the brain, activate adaptive immune responses, and further mediate secondary neuronal damage, aggravating neurological deficits. In order to reduce the above-mentioned damage, the body induces peripheral immunosuppressive responses through negative feedback, which increases the incidence of post-stroke infection. This process is accompanied by changes in the immune status of the ischemic brain tissue in local and systemic systems. A growing number of studies implicate noncoding RNAs (ncRNAs) as novel epigenetic regulatory elements in the dysfunction of various cell subsets in the neurovascular unit after cerebral infarction/ischemia-reperfusion injury. In particular, recent studies have revealed advances in ncRNA biology that greatly expand the understanding of epigenetic regulation of immune responses and inflammation after cerebral infarction/ischemia-reperfusion injury. Identification of aberrant expression patterns and associated biological effects of ncRNAs in patients revealed their potential as novel biomarkers and therapeutic targets for cerebral infarction/ischemia-reperfusion injury. Therefore, this review systematically presents recent studies on the involvement of ncRNAs in cerebral infarction/ischemia-reperfusion injury and neuroimmune inflammatory cascades, and elucidates the functions and mechanisms of cerebral infarction/ischemia-reperfusion-related ncRNAs, providing new opportunities for the discovery of disease biomarkers and targeted therapy. Furthermore, this review introduces clustered regularly interspaced short palindromic repeats (CRISPR)-Display as a possible transformative tool for studying lncRNAs. In the future, ncRNA is expected to be used as a target for diagnosing cerebral infarction/ischemia-reperfusion injury, judging its prognosis and treatment, thereby significantly improving the prognosis of patients.
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Affiliation(s)
- Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Liuting Zeng
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Anqi Ge
- The First Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Shanshan Wang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Jinsong Zeng
- The First Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Xiao Yuan
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Zhigang Mei
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Guozuo Wang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
- Hunan Academy of Chinese Medicine, Changsha, China
- *Correspondence: Jinwen Ge,
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Ryšavý P, Kléma J, Merkerová MD. circGPA: circRNA functional annotation based on probability-generating functions. BMC Bioinformatics 2022; 23:392. [PMID: 36167495 PMCID: PMC9513885 DOI: 10.1186/s12859-022-04957-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Recent research has already shown that circular RNAs (circRNAs) are functional in gene expression regulation and potentially related to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. However, the function of most circRNAs remains unknown, and it is expensive and time-consuming to discover it through biological experiments. In this paper, we predict circRNA annotations from the knowledge of their interaction with miRNAs and subsequent miRNA-mRNA interactions. First, we construct an interaction network for a target circRNA and secondly spread the information from the network nodes with the known function to the root circRNA node. This idea itself is not new; our main contribution lies in proposing an efficient and exact deterministic procedure based on the principle of probability-generating functions to calculate the p-value of association test between a circRNA and an annotation term. We show that our publicly available algorithm is both more effective and efficient than the commonly used Monte-Carlo sampling approach that may suffer from difficult quantification of sampling convergence and subsequent sampling inefficiency. We experimentally demonstrate that the new approach is two orders of magnitude faster than the Monte-Carlo sampling, which makes summary annotation of large circRNA files feasible; this includes their reannotation after periodical interaction network updates, for example. We provide a summary annotation of a current circRNA database as one of our outputs. The proposed algorithm could be generalized towards other types of RNA in way that is straightforward.
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Affiliation(s)
- Petr Ryšavý
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Jiří Kléma
- Department of Computer Science, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague, Czech Republic
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Wang H, Shao J, Lu X, Jiang M, Li X, Liu Z, Zhao Y, Zhou J, Lin L, Wang L, Xu Q, Chen Y, Zhang R. Potential of immune-related genes as promising biomarkers for premature coronary heart disease through high throughput sequencing and integrated bioinformatics analysis. Front Cardiovasc Med 2022; 9:893502. [PMID: 36093144 PMCID: PMC9458892 DOI: 10.3389/fcvm.2022.893502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background Coronary heart disease (CHD) is the most common progressive disease that is difficult to diagnose and predict in the young asymptomatic period. Our study explored a mechanistic understanding of the genetic effects of premature CHD (PCHD) and provided potential biomarkers and treatment targets for further research through high throughput sequencing and integrated bioinformatics analysis. Methods High throughput sequencing was performed among recruited patients with PCHD and young healthy individuals, and CHD-related microarray datasets were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified by using R software. Enrichment analysis and CIBERSORT were performed to explore the enriched pathways of DEGs and the characteristics of infiltrating immune cells. Hub genes identified by protein–protein interaction (PPI) networks were used to construct the competitive endogenous RNA (ceRNA) networks. Potential drugs were predicted by using the Drug Gene Interaction Database (DGIdb). Results A total of 35 DEGs were identified from the sequencing dataset and GEO database by the Venn Diagram. Enrichment analysis indicated that DEGs are mostly enriched in excessive immune activation pathways and signal transduction. CIBERSORT exhibited that resting memory CD4 T cells and neutrophils were more abundant, and M2 macrophages, CD8 T cells, and naïve CD4 T cells were relatively scarce in patients with PCHD. After the identification of 10 hub gens, three ceRNA networks of CD83, CXCL8, and NR4A2 were constructed by data retrieval and validation. In addition, CXCL8 might interact most with multiple chemical compounds mainly consisting of anti-inflammatory drugs. Conclusions The immune dysfunction mainly contributes to the pathogenesis of PCHD, and three ceRNA networks of CD83, CXCL8, and NR4A2 may be potential candidate biomarkers for early diagnosis and treatment targets of PCHD.
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Affiliation(s)
- Haiming Wang
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Junjie Shao
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Xuechun Lu
- Department of Hematology, The Second Medical Center of Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Min Jiang
- Department of Respiratory and Critical Care, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Xin Li
- Department of Health Services, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Zifan Liu
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Yunzhang Zhao
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Jingjing Zhou
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Lejian Lin
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Lin Wang
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Qiang Xu
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
| | - Yundai Chen
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
- Yundai Chen
| | - Ran Zhang
- Department of Cardiovascular Medicine, Chinese PLA General Hospital and Chinese People's Liberation Army (PLA) Medical School, Beijing, China
- *Correspondence: Ran Zhang
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Differential expression of non-coding RNAs and association with cerebral ischemic vascular disorders; diagnostic and therapeutic opportunities. Genes Genomics 2022:10.1007/s13258-022-01281-6. [PMID: 35802344 DOI: 10.1007/s13258-022-01281-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 06/24/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Over the last few decades, research associated with the coding genome, primarily DNA and transcriptome (mRNA, rRNA, and tRNA), has changed our understanding in several aspects, including physiology, diagnostics, and therapeutics. A large proportion of the human genome that encodes proteins is essential for physiology. However, the human genome represents a significantly large proportion of non-translational, i.e., non-coding (nc) RNAs like microRNAs, siRNAs, piRNAs, lncRNAs, and circRNAs. These ncRNAs do not translate into functional proteins but are associated with several events, such as the regulation of gene expression via several mechanisms. Our understanding of ncRNAs has advanced in the last decade, such as microRNAs and siRNAs, but still, several other ncRNAs remain unexplored. The study comprehended the association of ncRNAs in cerebral ischemia. METHODS In this study searches utilizing multiple databases, PubMed, EMBASE, and Google Scholar were made. The literature survey was done on ncRNA including short and lncRNA associated with the onset, and progression of cerebral ischemia. The literature search was also made for the studies associated with the diagnostic and therapeutic role of ncRNAs for cerebral ischemia. RESULTS AND DISCUSSION Reports suggested that both short and long ncRNAs are critical players of gene expression and are hence associated with the pathophysiology of cerebral ischemia. The reports demonstrate ncRNAs precisely lncRNAs and microRNAs are not only associated with cerebral ischemia progression but also potential diagnostic and therapeutic candidates. IN CONCLUSION This review is certainly helpful to understand the interplay of ncRNAs in understanding gene expression profile and pathophysiology of cerebral ischemia. These ncRNAs molecules show potential for diagnostic and therapeutic development.
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Investigating the AC079305/DUSP1 Axis as Oxidative Stress-Related Signatures and Immune Infiltration Characteristics in Ischemic Stroke. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8432352. [PMID: 35746962 PMCID: PMC9213160 DOI: 10.1155/2022/8432352] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 12/14/2022]
Abstract
Background Oxidative stress (OS) and immune inflammation play complex intersections in the pathophysiology of ischemic stroke (IS). However, a competing endogenous RNA- (ceRNA-) based mechanism linked to the intersections in IS has not been explored. We aimed to identify potential OS-related signatures and analyze immune infiltration characteristics in IS. Methods Three datasets (GSE22255, GSE110993, and GSE140275) from the GEO database were extracted. Differentially expressed long noncoding RNAs, microRNAs, and messenger RNAs (DElncRNAs, DEmiRNAs, and DEmRNAs) between IS patients and controls were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were explored. Moreover, a triple ceRNA network was constructed to reveal transcriptional regulation mechanisms. A comprehensive strategy among least absolute shrinkage and selection operator (LASSO) regression, DEmRNAs, uprelated DEmRNAs, and OS-related genes was adopted to select the best signature. Then, we evaluated and verified the discriminant ability of the signature via receiver operating characteristic (ROC) analysis. Immune infiltration characteristics were explored via the CIBERSORT algorithm. Moreover, the best signature was verified via qPCR and western blot methods in rat brain tissues and PC12 cells. Results 11 DEmRNAs were identified totally. Enrichment analysis showed that the DEmRNAs were primarily concentrated in MAPK-associated biological processes and immune or inflammation-involved pathways. DUSP1 was identified as the best signature with an area under the ROC curve of 73.5% (95%CI = 57.02-89.98, sensitivity = 95%, and specificity = 60%) in GSE22255 and 100.0% (95%CI = 100.00-100.00, sensitivity = 100%, and specificity = 100%) in GSE140275. Importantly, we also identified the AC079305/DUSP1 axis in the ceRNA network. Immune infiltration showed that resting mast cells infiltrate less in IS patients compared with controls. And DUSP1 was negatively correlated with resting mast cells (r = −0.703, P < 0.01), whereas it was positively correlated with neutrophils (r = 0.339, P < 0.05). Both in vivo and in vitro models confirmed the upregulated expression of DUSP1 and the downregulated expression of miR-429. Conclusion This study identified the ceRNA-based AC079305/DUSP1 axis as a promising OS-related signature for IS. Immune infiltrating cells, especially mast cells, may exert a pivotal role in IS progression. Pharmacological agents targeting signatures, their receptors, or mast cells may shed a novel light on therapeutic targets for IS.
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Cao S, Zeng Y, Chen M, Ouyang W. Integrated Analysis of Immune-Related circRNA-miRNA-mRNA Regulatory Network in Ischemic Stroke. Front Neurol 2022; 13:889855. [PMID: 35785353 PMCID: PMC9240315 DOI: 10.3389/fneur.2022.889855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundStroke is the leading cause of death and disability worldwide, with ischemic stroke (IS) being the most prevalent type. Circular RNAs (circRNAs) are involved in the pathological process of IS and are promising biomarkers for the diagnosis of IS. However, studies focusing on circRNAs acting as microRNAs (miRNAs) sponges in regulating mRNA expression are currently scarce.MethodsIn this study, expression profiles of circRNAs (GSE195442), miRNAs (GSE117064), and mRNAs (GSE58294) from the Gene Expression Omnibus (GEO) database were analyzed. Differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) were identified by R software. The target miRNAs and target genes were predicted by several bioinformatics methods. Then, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEmRNAs. Subsequently, the protein-protein interaction (PPI) network and the competing endogenous RNA (ceRNA) regulatory network were visualized by Cytoscape software. Finally, we further constructed an immune-related circRNA-miRNA-mRNA regulatory sub-network in IS.ResultsA total of 35 DEcircRNAs, 141 DEmiRNAs, and 356 DEmRNAs were identified. By comprehensive analysis of bioinformatics methods, we constructed a circRNA-miRNA-mRNA regulatory network, including 15 DEcircRNAs, eight DEmiRNAs, and 39 DEmRNAs. FGF9 was identified as an immune-related hub gene. Immune cell analysis indicated a significantly higher level of neutrophils in IS, and the expression of FGF9 was significantly negatively correlated with the level of neutrophils. Eventually, miR-767-5p was predicted as the upstream molecules of FGF9, and circ_0127785 and circ_0075008 were predicted as the upstream circRNAs of miR-767-5p.ConclusionOur study provides novel insights into the molecular mechanisms governing the progression of IS from the perspective of immune-related ceRNA networks.
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Liu M, Liu X, Zhou M, Guo S, Sun K. Impact of CircRNAs on Ischemic Stroke. Aging Dis 2022; 13:329-339. [PMID: 35371609 PMCID: PMC8947829 DOI: 10.14336/ad.2021.1113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/13/2021] [Indexed: 12/15/2022] Open
Abstract
Circular RNA (circRNA) is a recently discovered class of endogenous non-coding RNA that is generated by cyclization, driven by intron pairing, and regulated by related regulators. An important biological function of CircRNA is acting as a molecular sponge to significantly alter miRNA levels over a short period. Several studies have shown that circRNA is closely related to stroke. Therefore, a better understanding of CircRNA function and regulatory mechanism in ischemic brain will help us for the early detection, early diagnosis, and early treatment of stroke. Here, we summary the biological characteristics, expression of circRNA, and its effect on outcome after ischemic stroke.
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Affiliation(s)
- Miaomiao Liu
- 1Department of Radiology, The Third People's Hospital of Long Gang District, Shenzhen, China.,2Graduate School of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China.,3Department of Radiology, Baotou Central Hospital, Baotou, Inner Mongolia, China
| | - Xiaolin Liu
- 3Department of Radiology, Baotou Central Hospital, Baotou, Inner Mongolia, China
| | - Maorong Zhou
- 3Department of Radiology, Baotou Central Hospital, Baotou, Inner Mongolia, China
| | - Shao Guo
- 1Department of Radiology, The Third People's Hospital of Long Gang District, Shenzhen, China
| | - Kai Sun
- 1Department of Radiology, The Third People's Hospital of Long Gang District, Shenzhen, China
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Yang M, Zheng H, Su Y, Xu K, Yuan Q, Aihaiti Y, Cai Y, Xu P. Bioinformatics Analysis Identified the Hub Genes, mRNA–miRNA–lncRNA Axis, and Signaling Pathways Involved in Rheumatoid Arthritis Pathogenesis. Int J Gen Med 2022; 15:3879-3893. [PMID: 35422654 PMCID: PMC9005080 DOI: 10.2147/ijgm.s353487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/28/2022] [Indexed: 12/22/2022] Open
Abstract
Objective Rheumatoid arthritis (RA) is a nonspecific, chronic, systemic autoimmune disease characterized by symmetric polyarticular synovitis. Bioinformatics analysis of potential biomarkers, mRNA–miRNA–lncRNA axes, and signaling pathways in the pathogenesis of RA provides potential targets and theoretical basis for further research on RA. Methods The GSE1919 and GSE77298 datasets were downloaded from the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo). Perl was used to perform data merging, and R was used to perform batch correction. The “limma” package of R was used to screen differentially expressed genes, and the “clusterProfiler” package was used to perform enrichment analysis of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Search Tool for the Retrieval of Interacting Genes/Proteins was used to construct the protein–protein interaction network, Cytoscape was used for module analysis, and R was used to screen for hub genes. GraphPad Prism was used to plot the receiver operating characteristic curve of the hub genes. Gene set enrichment analysis and competitive endogenous RNA network analysis were performed on hub genes with the greatest diagnostic values. The hub gene with the greatest diagnostic value was verified using immunohistochemical staining. Results We obtained nine hub genes (ITGB2, VAMP8, HLA-A, PTAFR, SYK, FCER1G, HLA-DPB1, LCP2, and ACTR2) and four mRNA–miRNA–lncRNA axes (ITGB2-hsa-miR-486-3p-SNHG3, ITGB2-hsa-miR-338-5p-XIST, ITGB2-hsa-miR-5581-3p-XIST, and ITGB2-hsa-miR-1226-5p-XIST) related to the pathogenesis of RA. The nine hub genes were highly expressed, and ITGB2 had the highest diagnostic value for RA. We also identified signaling pathways related to the pathogenesis of RA: Fc epsilon Rl and chemokine signaling pathways. The immunohistochemical results showed that ITGB2 expression was significantly upregulated in RA. Conclusion The hub genes, mRNA–miRNA–lncRNA axes, and signaling pathways related to RA pathogenesis identified in this study provide a new research direction for the mechanism, diagnosis, and treatment of RA.
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Affiliation(s)
- Mingyi Yang
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
| | - Haishi Zheng
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
| | - Yani Su
- Yan'an University Affiliated Hospital, Yan’an, Shanxi, 716000, People’s Republic of China
| | - Ke Xu
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
| | - Qiling Yuan
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
| | - Yirixiati Aihaiti
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
| | - Yongsong Cai
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
| | - Peng Xu
- Department of Joint Surgery, HongHui Hospital, Xi’an Jiaotong University, Xi’an, Shanxi, 710054, People’s Republic of China
- Correspondence: Peng Xu, HongHui Hospital, Xi’an Jiaotong University, No. 555, Youyi East Road, Beilin District, Xi’an City, Shaanxi Province, 710054, People’s Republic of China, Tel +86 13772090019, Email
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Yang J, Hao J, Lin Y, Guo Y, Liao K, Yang M, Cheng H, Yang M, Chen K. Profile and Functional Prediction of Plasma Exosome-Derived CircRNAs From Acute Ischemic Stroke Patients. Front Genet 2022; 13:810974. [PMID: 35360855 PMCID: PMC8963851 DOI: 10.3389/fgene.2022.810974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Stroke is one of the major causes of death and long-term disability, of which acute ischemic stroke (AIS) is the most common type. Although circular RNA (circRNA) expression profiles of AIS patients have been reported to be significantly altered in blood and peripheral blood mononuclear cells, the role of exosome-containing circRNAs after AIS is still unknown. Plasma exosomes from 10 AIS patients and 10 controls were isolated, and through microarray and bioinformatics analysis, the profile and putative function of circRNAs in the plasma exosomes were studied. A total of 198 circRNAs were differentially quantified (|log2 fold change| ≥ 1.00, p < 0.05) between AIS patients and controls. The levels of 12 candidate circRNAs were verified by qRT-PCR, and the quantities of 10 of these circRNAs were consistent with the data of microarray. The functions of host genes of differentially quantified circRNAs, including RNA and protein process, focal adhesion, and leukocyte transendothelial migration, were associated with the development of AIS. As a miRNA sponge, differentially quantified circRNAs had the potential to regulate pathways related to AIS, like PI3K-Akt, AMPK, and chemokine pathways. Of 198 differentially quantified circRNAs, 96 circRNAs possessing a strong translational ability could affect cellular structure and activity, like focal adhesion, tight junction, and endocytosis. Most differentially quantified circRNAs were predicted to bind to EIF4A3 and AGO2—two RNA-binding proteins (RBPs)—and to play a role in AIS. Moreover, four of ten circRNAs with verified levels by qRT-PCR (hsa_circ_0112036, hsa_circ_0066867, hsa_circ_0093708, and hsa_circ_0041685) were predicted to participate in processes of AIS, including PI3K-Akt, AMPK, and chemokine pathways as well as endocytosis, and to be potentially useful as diagnostic biomarkers for AIS. In conclusion, plasma exosome-derived circRNAs were significantly differentially quantified between AIS patients and controls and participated in the occurrence and progression of AIS by sponging miRNA/RBPs or translating into proteins, indicating that circRNAs from plasma exosomes could be crucial molecules in the pathogenesis of AIS and promising candidates as diagnostic biomarkers and therapeutic targets for the condition.
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Affiliation(s)
- Jie Yang
- Department of Neurology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Department of Neurology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Junli Hao
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Yapeng Lin
- Department of Neurology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yijia Guo
- International Clinical Research Center, Chengdu Medical College, Chengdu, China
| | - Ke Liao
- International Clinical Research Center, Chengdu Medical College, Chengdu, China
| | - Min Yang
- Department of Neurology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Hang Cheng
- Department of Neurology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Ming Yang
- Department of Neurology, Clinical Medical College, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Kejie Chen
- School of Public Health, Chengdu Medical College, Chengdu, China
- *Correspondence: Kejie Chen,
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Liu J, Zhang H, Di K, Hou L, Yu S. Circular noncoding RNA circ_0007865, serves as a competing endogenous RNA, targeting the miR-214-3p/FKBP5 axis to regulate oxygen-glucose deprivation-induced injury in brain microvascular endothelial cells. Neuroreport 2022; 33:163-172. [PMID: 35143446 DOI: 10.1097/wnr.0000000000001751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Ischemic stroke (IS) is a major cause of permanent morbidity and lifelong disability worldwide. Circular RNA (circRNA) circ_0007865 has been reported to be upregulated in acute ischemic stroke (AIS) patients. Also, AIS patients exhibited increased death of human brain microvascular endothelial cells (HBMECs). This study is designed to explore the role and mechanism of circ_0007865 in the oxygen-glucose deprivation (OGD)-induced cell damage in AIS. METHODS Circ_0007865, microRNA-214-3p (miR-214-3p), and FK506-binding protein 5 (FKBP5) levels were detected by real-time quantitative PCR. Cell proliferative angiogenesis, migration, and apoptosis were assessed by Cell Counting Kit-8, 5-ethynyl-2'-deoxyuridine, colony formation, tube formation, wound healing, transwell, and flow cytometry assays. B-cell lymphoma-2 (Bcl-2), Bcl-2-related X protein (Bax), cleaved caspase-3, and FKBP5 protein levels were determined by western blot assay. The binding relationship between miR-214-3p and circ_0007865 or FKBP5 was predicted by StarBase, and verified by a dual-luciferase reporter, RNA pull-down assay. RESULTS Circ_0007865 and FKBP5 were increased, and miR-214-3p was decreased in OGD-treated HBMECs. Furthermore, the silencing of circ_0007865 could promote cell proliferative angiogenesis, migration, and inhibit apoptosis in OGD-triggered HBMECs in vitro. Mechanically, circ_0007865 acted as a sponge of miR-214-3p to regulate FKBP5. CONCLUSION According to these results, circ_0007865 deficiency could attenuate OGD-induced HBMEC damage by modulating the miR-214-3p/FKBP5 axis, hinting at a promising therapeutic target for future acute IS therapy.
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Affiliation(s)
- Jinghua Liu
- Department of Neurology, The Second People's Hospital of Dongying, Dongying
| | - Hong Zhang
- School of Medicine, Tianjin Tianshi College, Tianjin
| | - Kuiyi Di
- Department of Neurology, The Second People's Hospital of Dongying, Dongying
| | | | - Shanshan Yu
- Department of Pharmacy, The Second People's Hospital of Dongying, Dongying, China
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Fan J, Chen M, Cao S, Yao Q, Zhang X, Du S, Qu H, Cheng Y, Ma S, Zhang M, Huang Y, Zhang N, Shi K, Zhan S. Identification of a ferroptosis-related gene pair biomarker with immune infiltration landscapes in ischemic stroke: a bioinformatics-based comprehensive study. BMC Genomics 2022; 23:59. [PMID: 35033021 PMCID: PMC8761271 DOI: 10.1186/s12864-022-08295-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/29/2021] [Indexed: 12/14/2022] Open
Abstract
Background Ischemic stroke (IS) is a principal contributor to long-term disability in adults. A new cell death mediated by iron is ferroptosis, characterized by lethal aggregation of lipid peroxidation. However, a paucity of ferroptosis-related biomarkers early identify IS until now. This study investigated potential ferroptosis-related gene pair biomarkers in IS and explored their roles in immune infiltration. Results In total, we identified 6 differentially expressed ferroptosis-related genes (DEFRGs) in the metadata cohort. Of these genes, 4 DEFRGs were incorporated into the competitive endogenous RNA (ceRNA) network, including 78 lncRNA-miRNA and 16 miRNA-mRNA interactions. Based on relative expression values of DEFRGs, we constructed gene pairs. An integrated scheme consisting of machine learning algorithms, ceRNA network, and gene pair was proposed to screen the key DEFRG biomarkers. The receiver operating characteristic (ROC) curve witnessed that the diagnostic performance of DEFRG pair CDKN1A/JUN was superior to that of single gene. Moreover, the CIBERSORT algorithm exhibited immune infiltration landscapes: plasma cells, resting NK cells, and resting mast cells infiltrated less in IS samples than controls. Spearman correlation analysis confirmed a significant correlation between plasma cells and CDKN1A/JUN (CDKN1A: r = − 0.503, P < 0.001, JUN: r = − 0.330, P = 0.025). Conclusions Our findings suggested that CDKN1A/JUN could be a robust and promising gene-pair diagnostic biomarker for IS, regulating ferroptosis during IS progression via C9orf106/C9orf139-miR-22-3p-CDKN1A and GAS5-miR-139-5p/miR-429-JUN axes. Meanwhile, plasma cells might exert a vital interplay in IS immune microenvironment, providing an innovative insight for IS therapeutic target. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08295-0.
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Affiliation(s)
- Jiaxin Fan
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Mengying Chen
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Shuai Cao
- Department of Orthopedics, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Qingling Yao
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Xiaodong Zhang
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Shuang Du
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Huiyang Qu
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Yuxuan Cheng
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Shuyin Ma
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Meijuan Zhang
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Yizhou Huang
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Nan Zhang
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Kaili Shi
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China
| | - Shuqin Zhan
- Department of Neurology, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157 West Five Road, Xi'an, 710004, China.
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21
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Chen B, Yi J, Xu Y, Zheng P, Tang R, Liu B. Construction of a circRNA-miRNA-mRNA network revealed the potential mechanism of Buyang Huanwu Decoction in the treatment of cerebral ischemia. Biomed Pharmacother 2021; 145:112445. [PMID: 34844103 DOI: 10.1016/j.biopha.2021.112445] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND AND AIM Buyang Huanwu Decoction (BHD) is a traditional Chinese herbal medicine that is effective for treating cerebral ischemia (CI). However, the molecular mechanisms of BHD in CI have not been fully elucidated. In this study, we integrated the circular RNA (circRNA)-microRNA (miRNA)-messenger RNA (mRNA) network of middle cerebral artery occlusion (MACO) rats treated with BHD. METHODS SD rats were randomly divided into a control group, model group, model+BHD group (2.5, 5, 10 g/kg) and model+butylphthalide (NBP) group (54 mg/kg). The neurological functions of the rats were evaluated by a modified neurological severity scoring (mNSS) system. Pathological lesions were assessed by Nissl staining, and the effects of BHD on neurovascular unit (NVU) associated protein microtubule-associated protein 2 (MAP2), glial fibrillary acidic protein (GFAP) and von Willebrand factor (VWF) were assessed by immunohistochemistry. CeRNA and miRNA microarrays were used to establish the circRNA, miRNA, and mRNA profiles. Finally, a circRNA-miRNA-mRNA ternary transcription network was constructed. RESULTS BHD improved the neurobehavioral test scores (P < 0.01) and the histopathological changes in ischemic brain tissue in MCAO rats. The expression of MAP2 and VWF decreased and the expression of GFAP increased in the ischemic side brain tissue of MCAO rats (P < 0.01), and treatment with BHD reversed the above changes (P < 0.01 or 0.05). We identified seven, three, and 86 significantly dysregulated circRNAs, miRNAs, and mRNAs, respectively, that were associated with the neuroprotective effects of BHD. Furthermore, bioinformatics analysis showed that these targets may exert therapeutic effects through multiple pathways, such as the VEGF and Hippo signaling pathways. Finally, we constructed a circRNA-miRNA-mRNA network. CONCLUSIONS In brief, our study provides novel insights into ceRNA-mediated gene regulation in the progression of NVU after CI and the mechanism of action for BHD.
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Affiliation(s)
- Bowei Chen
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Jian Yi
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Yaqian Xu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Piao Zheng
- The Second Xiangya Hospital, Central South University, Changsha, China
| | - Rongmei Tang
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, China
| | - Baiyan Liu
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, China.
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22
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Circular RNA circPHKA2 Relieves OGD-Induced Human Brain Microvascular Endothelial Cell Injuries through Competitively Binding miR-574-5p to Modulate SOD2. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:3823122. [PMID: 34790286 PMCID: PMC8592726 DOI: 10.1155/2021/3823122] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/28/2021] [Accepted: 08/14/2021] [Indexed: 11/18/2022]
Abstract
Background Circular RNA phosphorylase kinase regulatory subunit alpha 2 (circPHKA2; hsa_circ_0090002) has a significantly, specifically different expression in acute ischemic stroke (AIS) patients' blood. Here, we intended to investigate the role and mechanism of circPHKA2 in oxygen-glucose deprivation- (OGD-) induced stoke model in human brain microvascular endothelial cells (HBMEC). Methods Expression of circPHKA2, microRNA- (miR-) 574-5p, and superoxide dismutase-2 (SOD2) was detected by quantitative PCR and western blotting. Cell injury was measured by detecting cell proliferation (EdU assay and CCK-8 assay), migration (transwell assay), neovascularization (tube formation assay), apoptosis (flow cytometry and western blotting), endoplasmic reticulum stress (western blotting), and oxidative stress (assay kits). Direct intermolecular interaction was determined by bioinformatics algorithms, dual-luciferase reporter assay, biotin-labelled miRNA capture, and argonaute 2 RNA immunoprecipitation. Results circPHKA2 was downregulated in AIS patients' blood in SOD2-correlated manner. Reexpressing circPHKA2 rescued EdU incorporation, cell viability and migration, tube formation, B cell lymphoma-2 (Bcl-2) expression, and SOD activity of OGD-induced HBMEC and alleviate apoptotic rate and levels of Bcl-2-associated protein (Bax), glucose-regulated protein 78 kD (GRP78), C/EBP-homologous protein (CHOP), caspase-12, reactive oxygen species (ROS), and malondialdehyde (MDA). Additionally, blocking SOD2 partially attenuated these roles of circPHKA2 overexpression. Molecularly, circPHKA2 upregulated SOD2 expression via interacting with miR-574-5p, and miR-574-5p could target SOD2. Similarly, allied to neurovascular protection of circPHKA2 was the downregulation of miR-574-5p. Conclusion circPHKA2 could protect HBMEC against OGD-induced cerebral stroke model via the miR-574-5p/SOD2 axis, suggesting circPHKA2 as a novel and promising candidate in ischemic brain injury.
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23
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Han Z, Feng W, Hu R, Ge Q, Sun X, Ma W, Zhang W, Xu S, Zhan B, Zhang L, Li Q, Zhou X. CircRNA expression profiling of PBMCs from patients with hepatocellular carcinoma by RNA-sequencing. Exp Ther Med 2021; 22:1467. [PMID: 34737807 PMCID: PMC8561760 DOI: 10.3892/etm.2021.10902] [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: 11/04/2020] [Accepted: 06/22/2021] [Indexed: 11/06/2022] Open
Abstract
Circular RNAs (circRNAs) are differentially expressed in various cancer types. The present study aimed to investigate the expression and clinical implication of circRNAs in hepatocellular carcinoma (HCC) and to evaluate the potential of circRNAs as diagnostic biomarkers for HCC. CircRNA expression was profiled in 19 patients with HCC and 19 normal controls using ribosomal RNA-depleted RNAs. Differentially expressed circRNAs (DE-circRNAs) between HCC and controls were identified using CIRI2 and distinct circRNA expression signatures were screened. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used to predict the potential functions of these DE-circRNAs and the circRNA-miRNA-mRNA regulatory networks were then constructed. Several DE-circRNAs were selected and confirmed by RT-qPCR. A total of 40 DE-circRNAs (27 upregulated and 13 downregulated) were identified between patients with HCC and controls. Functional annotation indicated that these DE-circRNAs were involved in cellular components, molecular functions and cancer-associated pathways related to HCC. These included pathways in cancer, TNF signaling pathway, hepatitis B, hepatitis C and hepatocyte differentiation. The circRNA-miRNA-mRNA regulatory network was generated based on 11 candidate circRNAs. Receiver operating characteristic curve analysis indicated that Homo sapiens (hsa)_circ_0073239, hsa_circ_007090, hsa_circ_0008304, hsa_circ_0017586, hsa_circ_0000369 and hsa_circ_0001181 may serve as potential biomarkers for HCC. Results from Cell Counting Kit-8 assay suggested that small interfering RNA targeting hsa_circ_0001181 reduced the proliferation of HepG2 cells, which implicated it as a potential therapeutic target for HCC. Therefore, in the present study, the differential expression pattern and important role of circRNAs in HCC were determined. The present results highlight the diagnostic potential of circRNAs in HCC and provide novel insight into the development of and treatment approaches for HCC.
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Affiliation(s)
- Zhiyi Han
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Wenxing Feng
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Rui Hu
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, P.R. China
| | - Xinfeng Sun
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Wenfeng Ma
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Wei Zhang
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Shaomin Xu
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Bolin Zhan
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Lai Zhang
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Qun Li
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
| | - Xiaozhou Zhou
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China.,Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong 518033, P.R. China
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Wei D, Chen J, Chen X, Wu S, Chen Z, Huang Y, Shen Z, He W. Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing. BMC Neurol 2021; 21:370. [PMID: 34563140 PMCID: PMC8464123 DOI: 10.1186/s12883-021-02397-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ischemic stroke is a disease with high rate of death and disability worldwide. CircRNAs, as a novel type of non-coding RNAs, lacking 5' caps and 3' poly-A tails, has been associated with ischemic stroke. This study aimed to investigate key circRNAs related to ischemic stroke. METHODS RNA sequencing was performed obtain the circRNA expression profiles from peripheral whole blood of three ischemic stroke patients and three healthy individuals. Through bioinformatic analysis, differentially expressed circRNAs (DEcircRNAs) were identified, and GO and pathway analyses for the host genes of DEcircRNAs were conducted. The expression levels of selected circRNAs were analyzed with qRT-PCR. To further explore the functions of key circRNAs, a DEcircRNA-miRNA interaction network was constructed. RESULTS A total of 736 DEcircRNAs were detected in ischemic stroke. Functional annotation of host genes of DEcircRNAs revealed several significantly enriched pathways, including Fc epsilon RI signaling pathway, B cell receptor signaling pathway, and T cell receptor signaling pathway. The qRT-PCR results were largely in keeping with our RNA-seq data. The ROC curve analyses indicated that hsa_circ_0000745, hsa_circ_0001459, hsa_circ_0003694 and hsa_circ_0007706 with relatively high diagnostic value. A circRNA-miRNA network, including 1544 circRNA-miRNA pairs, 456 circRNAs and 4 miRNAs, was obtained. CONCLUSIONS The results of our study may help to elucidate the specific mechanism underlying ischemic stroke.
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Affiliation(s)
- Duncan Wei
- Department of Pharmacy, The First Affiliated Hospital of Shantou University Medical College, No. 57, Changping Road, Guangdong, 515041, Shantou, China
| | - Jian Chen
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiaopu Chen
- Department of Neurology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Shaoyan Wu
- Department of Neurology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zhaolin Chen
- Shantou University Medical College, Shantou, China
| | - Yinting Huang
- Department of Neurology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zibin Shen
- Department of Neurology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wenzhen He
- Department of Neurology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China.
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25
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Bai C, Liu T, Sun Y, Li H, Xiao N, Zhang M, Feng Y, Xu H, Ge J, Wang X, Song L, Ping J, Chen J. Identification of circular RNA expression profiles and potential biomarkers for intracerebral hemorrhage. Epigenomics 2021; 13:379-395. [PMID: 33507103 DOI: 10.2217/epi-2020-0432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To investigate the expression profiles of circRNAs after intracerebral hemorrhage (ICH). Materials & methods: RNA sequencing and qRT-PCR were used to investigate and validate circRNA expression levels. Bioinformatics analysis was performed to explore potential functions of the circRNAs. Results: Expression levels of 15 circRNAs were consistently altered in patients with ICH compared with their expression levels in hypertension. Three circRNAs, hsa_circ_0001240, hsa_circ_0001947 and hsa_circ_0001386, individually or combined, were confirmed as promising biomarkers for predicting and diagnosing ICH. The circRNAs were involved mainly in lysine degradation and the immune system. Conclusion: This is the first study to report expression profiles of circRNAs after ICH and to propose that three circRNAs are potential biomarkers for ICH.
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Affiliation(s)
- Congxia Bai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Tingting Liu
- General Hospital of Ningxia Medical University, Ningxia 750004, PR China
| | - Yingying Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Hao Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Ning Xiao
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Meijun Zhang
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, PR China
| | - Yanjie Feng
- Annoroad Gene Technology (Beijing) Company Limited, Beijing 100176, PR China
| | - Haochen Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Jing Ge
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Xuliang Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Li Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Jiedan Ping
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China
| | - Jingzhou Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100037, PR China.,National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Fuwai Central-China Hospital, Central-China Branch of National Center for Cardiovascular Diseases, Zhengzhou 451464, PR China
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26
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Xu X, Wu Z, Qiu H, Wu J. Circular RNA circPHC3 Promotes Cell Death and Apoptosis in Human BMECs After Oxygen Glucose Deprivation via miR-455-5p/TRAF3 Axis in vitro. Neuropsychiatr Dis Treat 2021; 17:147-156. [PMID: 33519202 PMCID: PMC7837587 DOI: 10.2147/ndt.s288669] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Brain microvascular endothelial cells (BMECs) are involved in brain vascular dysfunction in ischemic stroke. Abnormal expression of circular RNAs regulate physiological and pathophysiological processes in the central nervous system. The aim of the present study was to investigate profile circRNAs in human BMECs after oxygen glucose deprivation (OGD), which was an in vitro model of ischemic stroke, and find promising biomarkers in ischemic stroke. METHODS RNA sequencing (RNA-seq) technology was conducted to analyze the differential expression of circRNAs between BMECs after OGD and non-OGD treated BMECs. RT-qPCR, cell proliferation, cell apoptosis and dual-luciferase assay, and so on, were used to investigate the functions and molecular mechanisms of hsa_circ_0001360 (named circPHC3 in this study) in ischemic stroke. RESULTS CircPHC3 was highly expressed in human BMECs after OGD. Knockdown of circPHC3 inhibited cell death and apoptosis in human BMECs treated with OGD. Mechanistically, circPHC3 acted as miR-455-5p sponge to activate TRAF3 to promote cell death and apoptosis in human BMECs after OGD. CONCLUSION In short, circPHC3 promotes cell death and apoptosis in ischemic stroke in vitro model, which might be a novel molecular target for acute cerebrovascular protection.
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Affiliation(s)
- Xiaonan Xu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, People's Republic of China
| | - Zimu Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, People's Republic of China
| | - Hongyan Qiu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, People's Republic of China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518000, Guangdong Province, People's Republic of China
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Shi J, Sun Y, Hua J. Functional Genetic Variation in the 3'-UTRNTRK2 is Associated with Risk of Ischemic Stroke. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2020; 13:577-584. [PMID: 33209049 PMCID: PMC7669521 DOI: 10.2147/pgpm.s270319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/30/2020] [Indexed: 12/05/2022]
Abstract
Background Stroke is a leading cause of death and disability worldwide. It remains difficult to treat brain injury and improve functional rehabilitation after cerebral ischemia. Brain-derived neurotrophic factor (BDNF) is involved in ischemic stroke (IS) through interactions in the CREB1-BDNF-NTRk2 pathway. In this study, we aimed to determine the association of NTRK2 gene polymorphisms and the effects of intergenetic interactions in the Chinese population. Materials and Methods A total of 400 patients diagnosed with IS and 400 healthy controls were enrolled for genotyping. Detailed sequence-based analysis was predicted through bioinformatical investigation. Polymorphisms associated with miRNA were analyzed by a dual-luciferase reporter assay system. Results Analysis of clinical characteristics revealed that IS was highly associated with exposure to cigarette smoking, alcohol intake, as well as metabolic diseases, such as diabetes, hypertension, and higher serum triglyceride concentration. Three polymorphisms in NTRK2 located in the 3ʹ-untranslated region (3ʹ-UTR) were genotyped. Logistic regression analysis showed that IS patients with rs11140793, rs7047042, and rs1221 polymorphisms had a higher risk of stroke and indicated a worse short-term recovery. The mRNA level of NTRK2 was suppressed in a mutant genotype compared with wild genotype. The suppression of NTRK2 was induced by the gain-of-binding ability of certain miRNAs through the direct binding of 3ʹ-UTR. Conclusion Our research indicated that, by influencing the expression of NTRK2, the SNPs rs11140793, rs7047042, and rs1221 in the 3′UTR of NTRK2 can be used as risk factors for IS patients.
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Affiliation(s)
- Jiajia Shi
- Department of Rehabilitation Medicine, Kunshan Rehabilitation Hospital, Suzhou, Jiangsu, People's Republic of China
| | - Ying Sun
- Department of Rehabilitation Medicine, Kunshan Rehabilitation Hospital, Suzhou, Jiangsu, People's Republic of China
| | - Jiajia Hua
- Department of Rehabilitation Medicine, The Sixth People's Hospital of Nantong, Nantong, Jiangsu, People's Republic of China
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