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Khan MM, Serajuddin M, Bharadwaj M. Potential plasma microRNAs signature miR-190b-5p, miR-215-5p and miR-527 as non-invasive biomarkers for prostate cancer. Biomarkers 2023; 28:227-237. [PMID: 36644827 DOI: 10.1080/1354750x.2022.2163694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BackgroundProstate cancer (PCa) is the most prevalent (20%) pathological cancer among males globally. MicroRNAs (miRNAs) are short (19-22 nucleotide), conserved, noncoding molecules that regulate post-transcriptional processes either by repressing or degrading mRNA or by translation inhibition binding to complementary sites on mRNA. The goal of this study was to find out whether differentially expressed microRNA (DEM) could be used as a potential marker in the prognosis and diagnosis of PCa.MethodologyThe miRNAs profiling was done both from plasma and tissue samples of the same PCa patient (n = 3) by real-time quantitative PCR (qRT-PCR) and compared with BPH (benign prostatic hyperplasia) patients (n = 3) as controls and further validation of selected miRNAs.ResultsWe found 55 significant overexpressed DEMs, 44 significant underexpressed DEMs in plasma and 6 significant overexpressed DEMs, 27 significant underexpressed DEMs in tissue compared between PCa and BPH. Furthermore, there were eight miRNAs namely miR-190b, miR-215, miR-300, miR-329, miR-504, miR-525-3p, miR-527, miR-548a-3p found to be significantly differentially expressed in plasma and tissue samples via profiling, however only three showed concordant expression. After validation, miR-190b-5p were shown to be significantly downexpressed with fold changes of 0.4177 (p value - 0.0072) and 0.7264 (p value - 0.0143) in plasma and tissue samples, respectively. The expression of miR-215-5p was shown to be significantly overexpressed with fold change of 1.820 (p - 0.0016) and 1.476 (p - 0.0407) in plasma and tissue samples, respectively. Furthermore, miR-527 was shown to be significantly downexpressed with fold changes of 0.6018 (p - 0.0095) and 0.6917 (p - 0.0155) in plasma and tissue samples, respectively.ConclusionAccording to our findings, plasma miR-190b-5p, miR-215-5p, miR-527 levels alteration is consistently linked with PCa tissue. For establishing significant miRNAs as biomarkers, additional research of a larger population is needed.
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Affiliation(s)
- Mohd Mabood Khan
- Division of Molecular Genetics & Biochemistry, National Institute of Cancer Prevention & Research (ICMR-NICPR), Noida, India.,Department of Zoology, University of Lucknow, Lucknow, India
| | | | - Mausumi Bharadwaj
- Division of Molecular Genetics & Biochemistry, National Institute of Cancer Prevention & Research (ICMR-NICPR), Noida, India
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Effects of Exosomal microRNAs on Oral Mucosal Epithelial Cells Cocultured with Limbal Niche Cells. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:9794950. [PMID: 36072625 PMCID: PMC9398820 DOI: 10.1155/2022/9794950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022]
Abstract
Autologous cultivated oral mucosal epithelial transplantation (COMET) is an important method for the treatment of limbal stem cell deficiency (LSCD), but the appearance of peripheral corneal neovascularization after COMET has prevented its widespread use in clinical practice. Using limbal niche cells (LNCs) as feeders in the process of coculturing could inhibit the postoperative corneal neovascularization. However, the specific mechanism is still unclear. In this study, LNCs were used as feeder cells to alter the phenotype of cultured oral mucosal epithelial cells (COMECs) by mimicking the primitive limbal microenvironment. The high-throughput sequencing of COMECs cocultured with LNCs or 3T3 cells (named LNCs group and 3T3 groups) was performed, and differential miRNA expression was analyzed. A total of 99 known and 1 newly predicted miRNAs were significantly upregulated in the LNCs group, while 101 known and 8 newly predicted miRNAs were significantly downregulated. A total of 3000 target genes with the 60 most significantly differentially expressed miRNAs were predicted, and 7 upregulated and 7 downregulated miRNAs were ultimately screened. The supernatants obtained from both cocultures were found to be rich in exosomes, indicating that the intercellular communication between COMECs and LNCs or 3T3 cells was highly active. Furthermore, the expression levels of rno-miR-200-5p, rno-miR-204-5p, rno-miR-126a-3p, rno-miR-192-5p, rno-miR-211-5p, rno-miR-143-3p, and rno-miR-184 were significantly higher in the LNCs group compared to the 3T3 group, and the expression levels had a similar trend in exosomes. Meanwhile, sequencing of the cell lines revealed 7 miRNAs that were significantly downregulated in the LNCs group. Interestingly, in that case, rno-miR-23a-3p, rno-miR-379-5p, and rno-miR-127-5p were also significantly downregulated in the exosomes. In summary, this study suggested that signal transduction between cells mediated by exosomal miRNAs may be an important factor for the inhibition of angiogenesis by LNCs nourished COMECs.
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Gregorova J, Vychytilova-Faltejskova P, Sevcikova S. Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development. Cancers (Basel) 2021; 13:1333. [PMID: 33809566 PMCID: PMC8002357 DOI: 10.3390/cancers13061333] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are small non-coding single-stranded RNA molecules regulating gene expression on a post-transcriptional level based on the seed sequence similarity. They are frequently clustered; thus, they are either simultaneously transcribed into a single polycistronic transcript or they may be transcribed independently. Importantly, microRNA families that contain the same seed region and thus target related signaling proteins, may be localized in one or more clusters, which are in a close relationship. MicroRNAs are involved in basic physiological processes, and their deregulation is associated with the origin of various pathologies, including solid tumors or hematologic malignancies. Recently, the interplay between the expression of microRNA clusters and families and epigenetic machinery was described, indicating aberrant DNA methylation or histone modifications as major mechanisms responsible for microRNA deregulation during cancerogenesis. In this review, the most studied microRNA clusters and families affected by hyper- or hypomethylation as well as by histone modifications are presented with the focus on particular mechanisms. Finally, the diagnostic and prognostic potential of microRNA clusters and families is discussed together with technologies currently used for epigenetic-based cancer therapies.
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Affiliation(s)
- Jana Gregorova
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
| | - Petra Vychytilova-Faltejskova
- Department of Molecular Medicine, Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic;
| | - Sabina Sevcikova
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic;
- Department of Clinical Hematology, University Hospital Brno, 625 00 Brno, Czech Republic
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Fu F, Girma G, Mengiste T. Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. BMC Genomics 2020; 21:760. [PMID: 33143636 PMCID: PMC7641857 DOI: 10.1186/s12864-020-07138-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/11/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Anthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks. RESULTS A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs. CONCLUSIONS We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.
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Affiliation(s)
- Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Present address: Agriculture and Agri-Food Canada, Plant Gene Resources of Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
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Saini S, Saini A, Thakur CJ, Kumar V, Gupta RD, Sharma JK. Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunity. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 9:83-91. [PMID: 32802902 PMCID: PMC7382400 DOI: 10.22099/mbrc.2020.36507.1487] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The current outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China threatened humankind worldwide. The coronaviruses contains the largest RNA genome among all other known RNA viruses, therefore the disease etiology can be understood by analyzing the genome sequence of SARS-CoV-2. In this study, we used an ab-intio based computational tool VMir to scan the complete genome of SARS-CoV-2 to predict pre-miRNAs. The potential pre-miRNAs were identified by ViralMir and mature miRNAs were recognized by Mature Bayes. Additionally, predicted mature miRNAs were analysed against human genome by miRDB server to retrieve target genes. Besides that we also retrieved GO (Gene Ontology) terms for pathways, functions and cellular components. We predicted 26 mature miRNAs from genome of SARS-CoV-2 that targets human genes involved in pathways like EGF receptor signaling, apoptosis signaling, VEGF signaling, FGF receptor signaling. Gene enrichment tool analysis and substantial literature evidences suggests role of genes like BMPR2 and p53 in pulmonary vasculature and antiviral innate immunity respectively. Our findings may help research community to understand virus pathogenesis.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
- Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Varinder Kumar
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Rishabh Dilip Gupta
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Jogesh Kumar Sharma
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
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Chowdhury MR, Basak J, Bahadur RP. Elucidating the Functional Role of Predicted miRNAs in Post- Transcriptional Gene Regulation Along with Symbiosis in Medicago truncatula. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191003114202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background:
microRNAs are small non-coding RNAs which inhibit translational and
post-transcriptional processes whereas long non-coding RNAs are found to regulate both
transcriptional and post-transcriptional gene expression. Medicago truncatula is a well-known
model plant for studying legume biology and is also used as a forage crop. In spite of its
importance in nitrogen fixation and soil fertility improvement, little information is available about
Medicago non-coding RNAs that play important role in symbiosis.
Objective:
In this study we have tried to understand the role of Medicago ncRNAs in symbiosis
and regulation of transcription factors.
Methods:
We have identified novel miRNAs by computational methods considering various
parameters like length, MFEI, AU content, SSR signatures and tried to establish an interaction
model with their targets obtained through psRNATarget server.
Results:
149 novel miRNAs are predicted along with their 770 target proteins. We have also
shown that 51 of these novel miRNAs are targeting 282 lncRNAs.
Conclusion:
In this study role of Medicago miRNAs in the regulation of various transcription
factors are elucidated. Knowledge gained from this study will have a positive impact on the
nitrogen fixing ability of this important model plant, which in turn will improve the soil fertility.
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Affiliation(s)
- Moumita Roy Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Jolly Basak
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan-731235, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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Liu J, Ning C, Li B, Li R, Wu W, Liu H. Hepatic microRNAome reveals potential microRNA-mRNA pairs association with lipid metabolism in pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:1458-1468. [PMID: 30208692 PMCID: PMC6722318 DOI: 10.5713/ajas.18.0438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023]
Abstract
Objective As one of the most important metabolic organs, the liver plays vital roles in modulating the lipid metabolism. This study was to compare miRNA expression profiles of the Large White liver between two different developmental periods and to identify candidate miRNAs for lipid metabolism. Methods Eight liver samples were collected from White Large of 70-day fetus (P70) and of 70-day piglets (D70) (with 4 biological repeats at each development period) to construct sRNA libraries. Then the eight prepared sRNA libraries were sequenced using Illumina next-generation sequencing technology on HiSeq 2500 platform. Results As a result, we obtained 346 known and 187 novel miRNAs. Compared with the D70, 55 down- and 61 up-regulated miRNAs were shown to be significantly differentially expressed (DE). Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis indicated that these DE miRNAs were mainly involved in growth, development and diverse metabolic processes. They were predicted to regulate lipid metabolism through adipocytokine signaling pathway, mitogen-activated protein kinase, AMP-activated protein kinase, cyclic adenosine monophosphate, phosphatidylinositol 3 kinase/protein kinase B, and Notch signaling pathway. The four most abundantly expressed miRNAs were miR-122, miR-26a and miR-30a-5p (miR-122 only in P70), which play important roles in lipid metabolism. Integration analysis (details of mRNAs sequencing data were shown in another unpublished paper) revealed that many target genes of the DE miRNAs (miR-181b, miR-145-5p, miR-199a-5p, and miR-98) might be critical regulators in lipid metabolic process, including acyl-CoA synthetase long chain family member 4, ATP-binding casette A4, and stearyl-CoA desaturase. Thus, these miRNAs were the promising candidates for lipid metabolism. Conclusion Our study provides the main differences in the Large White at miRNA level between two different developmental stages. It supplies a valuable database for the further function and mechanism elucidation of miRNAs in porcine liver development and lipid metabolism.
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Affiliation(s)
- Jingge Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Caibo Ning
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bojiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongyang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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Meng X, Guo J, Fang W, Dou L, Li M, Huang X, Zhou S, Man Y, Tang W, Yu L, Li J. Liver MicroRNA-291b-3p Promotes Hepatic Lipogenesis through Negative Regulation of Adenosine 5'-Monophosphate (AMP)-activated Protein Kinase α1. J Biol Chem 2016; 291:10625-34. [PMID: 27013659 DOI: 10.1074/jbc.m116.713768] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
In a microarray study, we found that hepatic miR-291b-3p was significantly increased in leptin-receptor-deficient type 2 mice (db/db), a mouse model of diabetes. The function of miR-291b-3p is unknown. The potential role of miR-291b-3p in regulating hepatic lipid metabolism was explored in this study. High-fat diet (HFD)- and chow-fed mice were injected with an adenovirus expressing a miR-291b-3p inhibitor and a miR-291b-3p mimic through the tail vein. Hepatic lipids and lipogenic gene expression were analyzed. Additionally, gain- and loss-of-function studies were performed in vitro to identify direct targets of miR-291b-3p. MiR-291b-3p expression and the protein levels of sterol regulatory element-binding protein 1 (SREBP1) and fatty acid synthase (FAS) were increased in the steatotic liver of db/db mice and HFD-fed mice versus their respective controls. Inhibition of hepatic miR-291b-3p expression prevented increases in hepatic lipogenesis and steatosis in HFD-fed mice. The opposite was observed when miR-291b-3p was overexpressed in the livers of chow-fed C57BL/6J wild-type mice. In vitro studies revealed that silencing of miR-291b-3p in NCTC1469 hepatic cells ameliorated oleic acid/palmitic acid mixture-induced elevation of cellular triglycerides. Importantly, we identified AMP-activated protein kinase (AMPK)-α1 as a direct target of miR-291b-3p. Using metformin, an activator of AMPK, we showed that AMPK activation-induced inhibition of hepatic lipid accumulation was accompanied by reduced expression of miR-291b-3p in the liver. Liver miR-291b-3p promoted hepatic lipogenesis and lipid accumulation in mice. AMPKα1 is a direct target of miR-291b-3p. In conclusion, our findings indicate that miR-291b-3p promotes hepatic lipogenesis by suppressing AMPKα1 expression and activity, indicating the therapeutic potential of miR-291b-3p inhibitors in fatty liver disease.
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Affiliation(s)
- Xiangyu Meng
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Jun Guo
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Weiwei Fang
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Lin Dou
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Meng Li
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Xiuqing Huang
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Shutong Zhou
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Yong Man
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Weiqing Tang
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China, Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742
| | - Liqing Yu
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742
| | - Jian Li
- From The Key Laboratory of Geriatrics, Beijing Hospital & Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China,
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Jiang WL, Zhang YF, Xia QQ, Zhu J, Yu X, Fan T, Wang F. MicroRNA-19a regulates lipopolysaccharide-induced endothelial cell apoptosis through modulation of apoptosis signal-regulating kinase 1 expression. BMC Mol Biol 2015; 16:11. [PMID: 25982447 PMCID: PMC4446110 DOI: 10.1186/s12867-015-0034-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/19/2015] [Indexed: 01/07/2023] Open
Abstract
Background MicroRNAs, small non-encoding RNAs that post-transcriptionally modulate expression of their target genes, have been implicated as critical regulatory molecules in endothelial cells. Results In the present study, we found that overexpression of miR-19a protects endothelial cells from lipopolysaccharide (LPS)-induced apoptosis through the apoptosis signal-regulating kinase 1 (ASK1)/p38 pathway. Quantitative real-time PCR demonstrated that the expression of miR-19a in endothelial cell was markedly down-regulated by LPS stimulation. Furthermore, LPS-induced apoptosis was significantly inhibited by over-expression of miR-19a. Finally, both a luciferase reporter assay and western blot analysis showed that ASK1 is a direct target of miR-19a. Conclusions MiR-19a regulates ASK1 expression by targeting specific binding sites in the 3’ untranslated region of ASK1 mRNA. Overexpression of miR-19a is an effective method to protect against LPS-induced apoptosis of endothelial cells. Electronic supplementary material The online version of this article (doi:10.1186/s12867-015-0034-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei-Long Jiang
- Department of Respiration, Jiangyin Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Jiangyin City, Jiangsu Province, 214400, China.
| | - Yu-Feng Zhang
- Department of Respiration, Jiangyin Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Jiangyin City, Jiangsu Province, 214400, China.
| | - Qing-Qing Xia
- Department of Respiration, Jiangyin Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Jiangyin City, Jiangsu Province, 214400, China.
| | - Jian Zhu
- Department of Neurology, Jiangyin Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Jiangyin City, Jiangsu Province, 214400, China.
| | - Xin Yu
- Department of Internal Medicine, Jiangyin Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Jiangyin City, Jiangsu Province, 214400, China.
| | - Tao Fan
- Department of Neurology, Jiangyin Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Jiangyin City, Jiangsu Province, 214400, China.
| | - Feng Wang
- Department of Neurology, Shanghai First People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200080, China.
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Xiao F, Yu J, Liu B, Guo Y, Li K, Deng J, Zhang J, Wang C, Chen S, Du Y, Lu Y, Xiao Y, Zhang Z, Guo F. A novel function of microRNA 130a-3p in hepatic insulin sensitivity and liver steatosis. Diabetes 2014; 63:2631-42. [PMID: 24677715 DOI: 10.2337/db13-1689] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, noncoding, short, single-stranded RNAs that are evolutionarily conserved and believed to play a role in controlling a variety of biological processes. The roles of miRNAs in insulin resistance and liver steatosis, however, are largely unknown. The objective of this study was to evaluate the roles of miR-130a in the regulation of insulin sensitivity and liver steatosis. In our current study, we observed that overexpression of miR-130a-3p increases insulin signaling in both HepG2 cells and primary mouse hepatocytes, and silencing of miR-130a-3p has the opposite effects. However, miR-130a-5p has no effect in the regulation of insulin signaling. Consistently, whole-body and hepatic insulin sensitivity are improved in mice injected with adenoviruses that overexpress miR-130a-3p. Furthermore, we provided evidence showing that growth factor receptor-bound protein 10 is required for miR-130a-3p-regulated insulin sensitivity. On the other hand, we observed that expression of miR-130a-3p is decreased in the livers of db/db mice and that adenovirus-mediated overexpression of miR-130a-3p reverses insulin resistance and liver steatosis, the latter of which is achieved via suppressing fatty acid synthase expression in these mice. This study identifies a novel function for hepatic miR-130a-3p in the regulation of insulin sensitivity and liver steatosis.
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Affiliation(s)
- Fei Xiao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Junjie Yu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bin Liu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yajie Guo
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Li
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiali Deng
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Molecular Medicine, Ministry of Education, Shanghai Medical College, Fudan University, Shanghai, ChinaInstitutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chunxia Wang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shanghai Chen
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Du
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingli Lu
- Institute and Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuzhong Xiao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhou Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiaotong University, Shanghai, China
| | - Feifan Guo
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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Li X, Kong M, Jiang D, Qian J, Duan Q, Dong A. MicroRNA-150 aggravates H2O2-induced cardiac myocyte injury by down-regulating c-myb gene. Acta Biochim Biophys Sin (Shanghai) 2013; 45:734-41. [PMID: 23824072 DOI: 10.1093/abbs/gmt067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MicroRNAs (miRNAs) are one class of non-coding RNAs that play an important role in post-transcriptional regulation via the degradation or translational inhibition of their target genes. MicroRNA-150 (miR-150) plays a vital role in regulating the development of B and T lymphocytes. Although the dysregulation of miR-150 was confirmed in human myocardial infarction, little is known regarding the biological functions of miR-150 in response to reactive oxygen species (ROS)-mediated gene regulation in cardiac myocytes. Using quantitative real-time reverse transcription-polymerase chain reaction, we demonstrated that the level of miR-150 was up-regulated in cardiac myocytes after treatment with hydrogen peroxide (H2O2). To identify the potential roles of miR-150 in H2O2-mediated gene regulation, we modulated expression of miR-150 using miR-150 inhibitor and miR-150 mimics. Results showed that silencing expression of miR-150 decreased H2O2-induced cardiac cell death and apoptosis. In lymphocytes, c-myb was a direct target of miR-150. In cardiac myocytes, we found that c-myb was also involved in miR-150-mediated H2O2-induced cardiac cell death. These results suggested that miR-150 participates in H2O2-mediated gene regulation and functional modulation in cardiac myocytes. MiR-150 may play an essential role in heart diseases related to ROS, such as cardiac hypertrophy, heart failure, myocardial infarction, and myocardial ischemia/reperfusion injury.
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Affiliation(s)
- Xuebiao Li
- Department of Cardiothoracic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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12
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QI YIMING, LI YING, ZHANG LIN, HUANG JUNQI. microRNA expression profiling and bioinformatic analysis of dengue virus-infected peripheral blood mononuclear cells. Mol Med Rep 2013; 7:791-8. [DOI: 10.3892/mmr.2013.1288] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 01/07/2013] [Indexed: 11/06/2022] Open
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Kukreja RC, Yin C, Salloum FN. MicroRNAs: new players in cardiac injury and protection. Mol Pharmacol 2011; 80:558-64. [PMID: 21737570 DOI: 10.1124/mol.111.073528] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as a novel class of endogenous, small, noncoding RNAs that negatively regulate gene expression via degradation or translational inhibition of their target mRNAs. Over 700 miRNAs have been identified and sequenced in humans, and the number of miRNA genes is estimated at more than 1000. Individual miRNA is functionally important as a transcription factor because it has the ability to regulate the expression of multiple genes through binding to its target with imperfect or perfect complement. In the heart, miRNAs have been involved in several clinical scenarios, such as ischemia/reperfusion (I/R) injury and heart failure suggesting that regulation of their function could be used as a novel cardioprotective strategy. In particular, miRNA-1, miRNA-21, miRNA-24, miRNA-29, miRNA-92a, miRNA-126, miRNA-133, miRNA-320, miRNA-199a, miRNA-208, and miRNA-195 have been shown to be regulated after I/R injury. Because tissue miRNAs can be released into circulating blood, they also offer exciting new opportunities for developing sensitive biomarkers, including miRNA-1, miRNA-126, miR-208, and miRNA-499, for acute myocardial infarction and other cardiac diseases.
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Affiliation(s)
- Rakesh C Kukreja
- Division of Cardiology, Virginia Commonwealth University, Richmond, VA 23298, USA.
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MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors. PLoS One 2010; 5:e11843. [PMID: 20700506 PMCID: PMC2917354 DOI: 10.1371/journal.pone.0011843] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 06/08/2010] [Indexed: 11/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small, single stranded RNAs with a key role in post-transcriptional regulation of thousands of genes across numerous species. While several computational methods are currently available for identifying miRNA genes, accurate prediction of the mature miRNA remains a challenge. Existing approaches fall short in predicting the location of mature miRNAs but also in finding the functional strand(s) of miRNA precursors. Methodology/Principal Findings Here, we present a computational tool that incorporates a Naive Bayes classifier to identify mature miRNA candidates based on sequence and secondary structure information of their miRNA precursors. We take into account both positive (true mature miRNAs) and negative (same-size non-mature miRNA sequences) examples to optimize sensitivity as well as specificity. Our method can accurately predict the start position of experimentally verified mature miRNAs for both human and mouse, achieving a significantly larger (often double) performance accuracy compared with two existing methods. Moreover, the method exhibits a very high generalization performance on miRNAs from two other organisms. More importantly, our method provides direct evidence about the features of miRNA precursors which may determine the location of the mature miRNA. We find that the triplet of positions 7, 8 and 9 from the mature miRNA end towards the closest hairpin have the largest discriminatory power, are relatively conserved in terms of sequence composition (mostly contain a Uracil) and are located within or in very close proximity to the hairpin loop, suggesting the existence of a possible recognition site for Dicer and associated proteins. Conclusions This work describes a novel algorithm for identifying the start position of mature miRNA(s) produced by miRNA precursors. Our tool has significantly better (often double) performance than two existing approaches and provides new insights about the potential use of specific sequence/structural information as recognition signals for Dicer processing. Web Tool available at: http://mirna.imbb.forth.gr/MatureBayes.html
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15
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Characterization of evolutionarily conserved microRNAs in amphioxus. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 8:10-21. [PMID: 20451158 PMCID: PMC5054118 DOI: 10.1016/s1672-0229(10)60002-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amphioxus is an extant species closest to the ancestry of vertebrates. Observation of microRNA (miRNA) distribution of amphioxus would lend some hints for evolutionary research of vertebrates. In this study, using the publicly available scaffold data of the Florida amphioxus (Branchiostoma floridae) genome, we screened and characterized homologs of miRNAs that had been identified in other species. In total, 68 pieces of such homologs were obtained and classified into 33 families. Most of these miRNAs were distributed as clusters in genome. Inter-species comparison showed that many miRNAs, which had been thought as vertebrate- or mammal-specific before, were also present in amphioxus, while some miRNAs that had been considered as protostome-specific before also existed in amphioxus. Compared with ciona, amphioxus had an apparent miRNA gene expansion, but phylogenetic analysis showed that the duplicated miRNAs or clusters of amphioxus had a higher homology level than those duplicated ones in vertebrates.
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A translational study of circulating cell-free microRNA-1 in acute myocardial infarction. Clin Sci (Lond) 2010; 119:87-95. [PMID: 20218970 DOI: 10.1042/cs20090645] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
miRNAs (microRNAs) participate in many diseases including cardiovascular disease. In contrast with our original hypothesis, miRNAs exist in circulating blood and are relatively stable due to binding with other materials. The aim of the present translational study is to establish a method of determining the absolute amount of an miRNA in blood and to determine the potential applications of circulating cell-free miR-1 (microRNA-1) in AMI (acute myocardial infarction). The results revealed that miR-1 is the most abundant miRNA in the heart and is also a heart- and muscle-specific miRNA. In a cardiac cell necrosis model induced by Triton X-100 in vitro, we found that cardiac miR-1 can be released into the culture medium and is stable at least for 24 h. In a rat model of AMI induced by coronary ligation, we found that serum miR-1 is quickly increased after AMI with a peak at 6 h, in which an increase in miR-1 of over 200-fold was demonstrated. The miR-1 level returned to basal levels at 3 days after AMI. Moreover, the serum miR-1 level in rats with AMI had a strong positive correlation with myocardial infarct size. To verify further the relationship between myocardial size and miR-1 level, an IP (ischaemic preconditioning) model was used. The results showed that IP significantly reduced circulating miR-1 levels and myocardial infract size induced by I/R (ischaemia/reperfusion) injury. Finally, the levels of circulating cell-free miR-1 were significantly increased in patients with AMI and had a positive correlation with serum CK-MB (creatine kinase-MB) levels. In conclusion, the results suggest that serum miR-1 could be a novel sensitive diagnostic biomarker for AMI.
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Chen F, Chen YPP. Exploring the ncRNA-ncRNA patterns based on bridging rules. J Biomed Inform 2010; 43:569-77. [PMID: 20152932 DOI: 10.1016/j.jbi.2010.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 11/11/2009] [Accepted: 02/05/2010] [Indexed: 10/19/2022]
Abstract
ncRNAs play an important role in the regulation of gene expression. However, many of their functions have not yet been fully discovered. There are complicated relationships between ncRNAs in different categories. Finding these relationships can contribute to identify ncRNAs' functions and properties. We extend the association rule to represent the relationship between two ncRNAs. Based on this rule, we can speculate the ncRNA's function when it interacts with other ncRNAs. We propose two measures to explore the relationships between ncRNAs in different categories. Entropy theory is to calculate how close two ncRNAs are. Association rule is to represent the interactions between ncRNAs. We use three datasets from miRBase and RNAdb. Two from miRBase are designed for finding relationships between miRNAs; the other from RNAdb is designed for relationships among miRNA, snoRNA and piRNA. We evaluate our measures from both biological significance and performance perspectives. All the cross-species patterns regarding miRNA that we found are proven correct using miRNAMap 2.0. In addition, we find novel cross-genomes patterns such as (hsa-mir-190b-->hsa-mir-153-2). According to the patterns we find, we can (1) explore one ncRNA's function from another with known function and (2) speculate the functions of both of them based on the relationship even we do no understand either of them. Our methods' merits also include: (1) they are suitable for any ncRNA datasets and (2) they are not sensitive to the parameters.
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Affiliation(s)
- Feng Chen
- Faculty of Science, Technology and Engineering, La Trobe University, Bundoora, Vic. 3086, Australia
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18
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Du J, Wu Y, Zhang Y, Wu L, Wang X, Tao S. Large-scale information entropy analysis of important sites in mature and precursor miRNA sequences. ACTA ACUST UNITED AC 2009; 52:771-9. [PMID: 19727596 DOI: 10.1007/s11427-009-0099-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 02/12/2009] [Indexed: 01/12/2023]
Abstract
In order to find evidence of consistent sequence conservation or the base correlation degree in miRNA, some important sites in the sequences of reported miRNA and their precursors (pre-miRNA) were investigated via information entropy analysis. Twelve different groups of sites were obtained from special locations (head, tail) in miRNAs of different sources according to taxonomy (animal, plant and virus) and then analyzed by measuring the single base information redundancy (D(1)(L)) and the adjacent base related information redundancy (D(2)(L)). The results showed that D(2)(L) has more information than D(1)(L), though D(1)(L) changes roughly consistently with D(2)(L) in each group. Viral pre-miRNAs are more conservative than those belonging to animals or plants. In addition, U is dominant in most sites compared with other nucleotides. It was also found that in the middle of several groups, there were sites where miRNAs were cut down from pre-miRNAs by Enzyme Dicer which were significantly conservative. This phenomenon shows that the conservatism is an aspect of the of miRNA and may be involved in the recognition and cutting by the Dicer. Those results provided another perspective for understanding more about the primary structure of pre-miRNA.
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Affiliation(s)
- JiangFeng Du
- Bioinformatics Center, Northwest Science and Technology University of Agriculture, Yangling, 712100, China
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19
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Dong S, Cheng Y, Yang J, Li J, Liu X, Wang X, Wang D, Krall TJ, Delphin ES, Zhang C. MicroRNA expression signature and the role of microRNA-21 in the early phase of acute myocardial infarction. J Biol Chem 2009; 284:29514-25. [PMID: 19706597 DOI: 10.1074/jbc.m109.027896] [Citation(s) in RCA: 359] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Several recent reports have suggested that microRNAs (miRNAs) might play critical roles in acute myocardial infarction (AMI). However, the miRNA expression signature in the early phase of AMI has not been identified. In this study, the miRNA expression signature was investigated in rat hearts 6 h after AMI. Compared with the expression signature in the noninfarcted areas, 38 miRNAs were differentially expressed in infarcted areas and 33 miRNAs were aberrantly expressed in the border areas. Remarkably, miR-21 expression was significantly down-regulated in infarcted areas, but was up-regulated in border areas. The down-regulation of miR-21 in the infarcted areas was inhibited by ischemic preconditioning, a known cardiac protective method. Overexpression of miR-21 via adenovirus expressing miR-21 (Ad-miR-21) decreased myocardial infarct size by 29% at 24 h and decreased the dimension of left ventricles at 2 weeks after AMI. Using both gain-of-function and loss-of-function approaches in cultured cardiac myocytes, we identified that miR-21 had a protective effect on ischemia-induced cell apoptosis that was associated with its target gene programmed cell death 4 and activator protein 1 pathway. The protective effect of miR-21 against ischemia-induced cardiac myocyte damage was further confirmed in vivo by decreased cell apoptosis in the border and infarcted areas of the infarcted rat hearts after treatment with Ad-miR-21. The results suggest that miRNAs such as miR-21 may play critical roles in the early phase of AMI.
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Affiliation(s)
- Shimin Dong
- Department of Anesthesiology, RNA and Cardiovascular Research Laboratory, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101, USA
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Cheng Y, Liu X, Zhang S, Lin Y, Yang J, Zhang C. MicroRNA-21 protects against the H(2)O(2)-induced injury on cardiac myocytes via its target gene PDCD4. J Mol Cell Cardiol 2009; 47:5-14. [PMID: 19336275 DOI: 10.1016/j.yjmcc.2009.01.008] [Citation(s) in RCA: 300] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 01/02/2009] [Accepted: 01/09/2009] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species (ROS)-induced cardiac cell injury via expression changes of multiple genes plays a critical role in the pathogenesis of numerous heart diseases. MicroRNAs (miRNAs) comprise a novel class of endogenous, small, noncoding RNAs that negatively regulate about 30% of the genes in a cell via degradation or translational inhibition of their target mRNAs. Currently, the effects of ROS on miRNA expression and the roles of miRNAs in ROS-mediated injury on cardiac myocytes are uncertain. Using quantitative real-time RT-PCR (qRT-PCR), we demonstrated that microRNA-21 (miR-21) was upregulated in cardiac myocytes after treatment with hydrogen peroxide (H(2)O(2)). To determine the potential roles of miRNAs in H(2)O(2)-mediated gene regulation and cellular injury, miR-21 expression was downregulated by miR-21 inhibitor and upregulated by pre-miR-21. H(2)O(2)-induced cardiac cell death and apoptosis were increased by miR-21 inhibitor and was decreased by pre-miR-21. Programmed cell death 4 (PDCD4) that was regulated by miR-21 and was a direct target of miR-21 in cardiac myocytes. Pre-miR-21-mediated protective effect on cardiac myocyte injury was inhibited in H(2)O(2)-treated cardiac cells via adenovirus-mediated overexpression of PDCD4 without miR-21 binding site. Moreover, Activator protein 1 (AP-1) was a downstream signaling molecule of PDCD4 that was involved in miR-21-mediated effect on cardiac myocytes. The results suggest that miR-21 is sensitive to H(2)O(2) stimulation. miR-21 participates in H(2)O(2)-mediated gene regulation and functional modulation in cardiac myocytes. miR-21 might play an essential role in heart diseases related to ROS such as cardiac hypertrophy, heart failure, myocardial infarction, and myocardial ischemia/reperfusion injury.
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Affiliation(s)
- Yunhui Cheng
- RNA and Cardiovascular Research Laboratory, Department of Anesthesiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07101-1709, USA
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21
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Lin Y, Liu X, Cheng Y, Yang J, Huo Y, Zhang C. Involvement of MicroRNAs in hydrogen peroxide-mediated gene regulation and cellular injury response in vascular smooth muscle cells. J Biol Chem 2009; 284:7903-13. [PMID: 19158092 DOI: 10.1074/jbc.m806920200] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) comprise a novel class of endogenous, small, noncoding RNAs that negatively regulate approximately 30% of genes in a cell via degradation or translational inhibition of their target mRNAs. However, the effects of reactive oxygen species (ROS) on miRNA expression and the roles of miRNAs in ROS-mediated gene regulation and biological functions of vascular cells are unclear. Using microarray analysis, we demonstrated that miRNAs are aberrantly expressed in vascular smooth muscle cells (VSMCs) after treatment with hydrogen peroxide (H(2)O(2)). H(2)O(2)-mediated up-regulation of microRNA-21 (miR-21) was further confirmed by quantitative real-time PCR. To determine the potential roles of miRNAs in H(2)O(2)-mediated gene regulation and cellular effects, miR-21 expression was down-regulated by miR-21 inhibitor and up-regulated by pre-miR-21. H(2)O(2)-induced VSMC apoptosis and death were increased by miR-21 inhibitor and decreased by pre-miR-21. Programmed cell death 4(PDCD4) was a direct target of miR-21 that was involved in miR-21-mediated effects on VSMCs. Pre-miR-21-mediated protective effect on VSMC apoptosis and death was blocked via adenovirus-mediated overexpression of PDCD4 without the miR-21 binding site. Moreover, activator protein 1 was a downstream signaling molecule of PDCD4 in miR-21-modulated VSMCs. The results suggest that miRNAs in VSMCs are sensitive to H(2)O(2) stimulation. miRN-21 participates in H(2)O(2)-mediated gene regulation and cellular injury response through PDCD4 and the activator protein 1 pathway. miRNAs might play a role in vascular diseases related to ROS.
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Affiliation(s)
- Ying Lin
- RNA and Cardiovascular Research Laboratory, Department of Anesthesiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101, USA
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Heikkinen L, Asikainen S, Wong G. Identification of phylogenetically conserved sequence motifs in microRNA 5' flanking sites from C. elegans and C. briggsae. BMC Mol Biol 2008; 9:105. [PMID: 19036124 PMCID: PMC2613404 DOI: 10.1186/1471-2199-9-105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 11/26/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, noncoding RNA molecules that act as post-transcriptional regulators of gene expression. Studies concerning transcriptional regulation of miRNAs have so far concentrated on those located within the intergenic region of the genome and the search for putative promoters, thus leaving open the question of the existence of possible regulatory elements common to all miRNAs including those located in introns of protein coding genes. RESULTS In this study, we initially searched for motifs occurring in the area 1000 bp upstream from all miRNAs independent of their genomic location. We discovered a previously unknown sequence motif GANNNNGA that displayed a conserved distribution in the nematode worms Caenorhabditis elegans and Caenorhabditis briggsae. This motif had a peak occurrence at 500 bp upstream, with a sharp drop-off toward the miRNA start site. Further analysis indicated that this motif was locally restricted and not enriched 1000-5000 bp upstream or 0-2000 bp downstream of the miRNA start site. In addition, this motif was observed to be most abundant in the upstream sequences of two important miRNAs, mir-1 and mir-124. This abundance was also conserved in phylogenetically distant species including human and mouse. CONCLUSION The results show that the motif GANNNNGA is conserved close to miRNA precursor start sites, suggesting that it may be involved in miRNA sequence recognition or regulation. This data provides important knowledge for the identification and computational prediction of miRNA sequences.
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Affiliation(s)
- Liisa Heikkinen
- Department of Biosciences, University of Kuopio, Kuopio, Finland.
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Thatcher EJ, Bond J, Paydar I, Patton JG. Genomic organization of zebrafish microRNAs. BMC Genomics 2008; 9:253. [PMID: 18510755 PMCID: PMC2427041 DOI: 10.1186/1471-2164-9-253] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 05/29/2008] [Indexed: 11/24/2022] Open
Abstract
Background microRNAs (miRNAs) are small (~22 nt) non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family) contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.
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Abstract
Genomic evidence reveals that gene expression in humans is precisely controlled in cellular, tissue-type, temporal, and condition-specific manners. Completely understanding the regulatory mechanisms of gene expression is therefore one of the most important issues in genomic medicine. Surprisingly, recent analyses of the human and animal genomes have demonstrated that the majority of RNA transcripts are relatively small, noncoding RNAs (sncRNAs), rather than large, protein coding message RNAs (mRNAs). Moreover, these sncRNAs may represent a novel important layer of regulation for gene expression. The most important breakthrough in this new area is the discovery of microRNAs (miRNAs). miRNAs comprise a novel class of endogenous, small, noncoding RNAs that negatively regulate gene expression via degradation or translational inhibition of their target mRNAs. As a group, miRNAs may directly regulate approximately 30% of the genes in the human genome. In keeping with the nomenclature of RNomics, which is to study sncRNAs on the genomic scale, "microRNomics" is coined here to describe a novel subdiscipline of genomics that studies the identification, expression, biogenesis, structure, regulation of expression, targets, and biological functions of miRNAs on the genomic scale. A growing body of exciting evidence suggests that miRNAs are important regulators of cell differentiation, proliferation/growth, mobility, and apoptosis. These miRNAs therefore play important roles in development and physiology. Consequently, dysregulation of miRNA function may lead to human diseases such as cancer, cardiovascular disease, liver disease, immune dysfunction, and metabolic disorders. microRNomics may be a newly emerging approach for human disease biology.
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Affiliation(s)
- Chunxiang Zhang
- RNA and Cardiovascular Research Laboratory, Department of Anesthesiology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07101-1709, USA.
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Cheng Y, Ji R, Yue J, Yang J, Liu X, Chen H, Dean DB, Zhang C. MicroRNAs are aberrantly expressed in hypertrophic heart: do they play a role in cardiac hypertrophy? THE AMERICAN JOURNAL OF PATHOLOGY 2007; 170:1831-40. [PMID: 17525252 PMCID: PMC1899438 DOI: 10.2353/ajpath.2007.061170] [Citation(s) in RCA: 412] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs) are a recently discovered class of endogenous, small, noncoding RNAs that regulate gene expression. Although miRNAs are highly expressed in the heart, their roles in heart diseases are currently unclear. Using microarray analysis designed to detect the majority of mammalian miRNAs identified thus far, we demonstrated that miRNAs are aberrantly expressed in hypertrophic mouse hearts. The time course of the aberrant miRNA expression was further identified in mouse hearts at 7, 14, and 21 days after aortic banding. Nineteen of the most significantly dysregulated miRNAs were further confirmed by Northern blot and/or real-time polymerase chain reaction, in which miR-21 was striking because of its more than fourfold increase when compared with the sham surgical group. Similar aberrant expression of the most up-regulated miRNA, miR-21, was also found in cultured neonatal hypertrophic cardiomyocytes stimulated by angiotensin II or phenylephrine. Modulating miR-21 expression via antisense-mediated depletion (knockdown) had a significant negative effect on cardiomyocyte hypertrophy. The results suggest that miRNAs are involved in cardiac hypertrophy formation. miRNAs might be a new therapeutic target for cardiovascular diseases involving cardiac hypertrophy such as hypertension, ischemic heart disease, valvular diseases, and endocrine disorders.
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Affiliation(s)
- Yunhui Cheng
- Cardiovascular Research Laboratory, Vascular Biology Center and Department of Surgery, University of Tennessee Health Science Center, 956 Court Avenue, Memphis, TN 38163, USA
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Abstract
Identification of microRNAs (miRNAs) is essential to studying their physiological functions. Due to the difficulties in discovering truly expressed miRNAs from genomic random hairpin secondary structure sequences, it is beneficial to predict them from expressed sequences--expressed sequence tags (ESTs) and intronic sequences. We used a modified scanning pipeline using criteria based on the features of known pre-miRNAs and phylogenetic conservation for predicting intronic miRNAs. Upon examination, we found that 25% of known human miRNAs belong to intronic regions of known protein-coding genes. About 50% of these intronic miRNAs reside in introns whose length is longer than 5,000 bps. It is likely that these intronic miRNAs can have their own independently regulated transcription units, which can be regulated by RNA polymerase II (Pol II) or RNA polymerase III (Pol III). It was recently demonstrated that RNA Pol III could transcribe human miRNAs through associated repetitive elements. Since various repetitive elements are often found to be present in the intronic regions, the distribution of intronic miRNAs and their possible transcription regulation are presented. Although the intronic miRNAs and their host genes could be regulated independently, it is possible that the intronic miRNA can still down-regulate its own host protein-coding gene by targeting the untranslated region (UTR) of the host gene. Another biological implication is that intronic miRNAs could play an important role as negative feedback regulators. We propose hypothetical models of such feedback regulation on host protein-coding genes by selecting the transcription factors as miRNA targets or by protein-protein interactions between intronic miRNA host gene product and miRNA target gene products.
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Affiliation(s)
- Sung-Chou Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
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27
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Ji R, Cheng Y, Yue J, Yang J, Liu X, Chen H, Dean DB, Zhang C. MicroRNA Expression Signature and Antisense-Mediated Depletion Reveal an Essential Role of MicroRNA in Vascular Neointimal Lesion Formation. Circ Res 2007; 100:1579-88. [PMID: 17478730 DOI: 10.1161/circresaha.106.141986] [Citation(s) in RCA: 714] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are a recently discovered class of endogenous, small, noncoding RNAs that regulate about 30% of the encoding genes of the human genome. However, the role of miRNAs in vascular disease is currently completely unknown. Using microarray analysis, we demonstrated for the first time that miRNAs are aberrantly expressed in the vascular walls after balloon injury. The aberrantly expressed miRNAs were further confirmed by Northern blot and quantitative real-time polymerase chain reaction. Modulating an aberrantly overexpressed miRNA, miR-21, via antisense-mediated depletion (knock-down) had a significant negative effect on neointimal lesion formation. In vitro, the expression level of miR-21 in dedifferentiated vascular smooth muscle cells was significantly higher than that in fresh isolated differentiated cells. Depletion of miR-21 resulted in decreased cell proliferation and increased cell apoptosis in a dose-dependent manner. MiR-21-mediated cellular effects were further confirmed in vivo in balloon-injured rat carotid arteries. Western blot analysis demonstrated that PTEN and Bcl-2 were involved in miR-21-mediated cellular effects. The results suggest that miRNAs are novel regulatory RNAs for neointimal lesion formation. MiRNAs may be a new therapeutic target for proliferative vascular diseases such as atherosclerosis, postangioplasty restenosis, transplantation arteriopathy, and stroke.
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MESH Headings
- Angioplasty, Balloon
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- Base Sequence
- Blotting, Northern
- Carotid Arteries/cytology
- Carotid Arteries/drug effects
- Carotid Arteries/metabolism
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cell Survival/genetics
- Cells, Cultured
- Disease Models, Animal
- Down-Regulation
- Male
- MicroRNAs/antagonists & inhibitors
- MicroRNAs/genetics
- MicroRNAs/metabolism
- MicroRNAs/physiology
- Molecular Sequence Data
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Oligonucleotides, Antisense/pharmacology
- Proteins
- Rats
- Rats, Sprague-Dawley
- Tunica Intima/drug effects
- Tunica Intima/growth & development
- Tunica Intima/metabolism
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Affiliation(s)
- Ruirui Ji
- Cardiovascular Research Laboratory, Vascular Biology Center & Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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28
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Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA. Computational identification of microRNAs and their targets. Comput Biol Chem 2006; 30:395-407. [PMID: 17123865 DOI: 10.1016/j.compbiolchem.2006.08.006] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 08/28/2006] [Accepted: 08/29/2006] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are one class of newly identified riboregulators of gene expression in many eukaryotic organisms. They play important roles in multiple biological and metabolic processes, including developmental timing, signal transduction, cell maintenance and differentiation, diseases and cancers. miRNAs regulate gene expression at the posttranscriptional level by directly cleaving targeted mRNAs or repressing translation. Although the founding members of miRNAs were discovered by genetic screening approaches, experimental approaches were limited by their low efficiency, time consuming, and high cost. As an alternative, computational approaches were developed. Computational approaches for identifying miRNAs are based on the following major characteristics of miRNAs: hairpin-shaped secondary structures, high conservation for some miRNAs, and high minimal folding free energy index (MFEI). Computational approaches also play an important role in identifying miRNA targets. A majority of known miRNAs and their targets were identified by computational approaches. Several web-based or non-web-based computer software programs are publicly available for predicting miRNAs and their targets.
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Affiliation(s)
- Baohong Zhang
- The Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409-1163, USA.
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29
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Abstract
One of the most important advances in biology in recent years may be the discovery of RNAs that can regulate gene expression. As one kind of such functional noncoding RNAs, microRNAs (miRNAs) form a class of endogenous 19-23-nucleotide RNAs that can have important regulatory roles in animals and plants by targeting transcripts for cleavage or translational repression. Since the discovery of the very first miRNAs, computational methods have been an invaluable tool that can complement experimental approaches to understand the biology of miRNAs. Most computational approaches associated with miRNA research can be classified into two broad categories, namely miRNA gene identification and miRNA target prediction. In this review, we summarize the principles of in silico prediction of miRNAs and their targets, and provide a comprehensive survey of specific methods that have been proposed in the field.
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Affiliation(s)
- Sungroh Yoon
- Computer Systems Laboratory, Stanford University, CA 94305, USA.
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