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Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) loci, which provide a specific immunity against exogenous elements, are hypervariable among distinct prokaryotes. Based on previous researches, this review focuses on concluding systematical genome editing protocols in Streptococcus thermophilus. Firstly, its protocols and optimized conditions in gene editing are introduced. What’s more, classification and diversity analyses of S. thermophilus CRISPR-Cas benefit the further understanding of evolution relationship among Streptococcus. Ability of its foreign segment integration and spacer source analyses also indicate a new direction of phage resistance. Above all, all of these point out its potential to be regarded as another model system other than type II CRISPR-Cas in Streptococcus pyogenes.
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Affiliation(s)
- Mengyuan Hao
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yanhua Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, China
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2
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Landi A, Aligodarzi MT, Khodadadi A, Babiuk LA, van Drunen Littel-van den Hurk S. Defining a standard and weighted mathematical index for maturation of dendritic cells. Immunology 2017; 153:532-544. [PMID: 29068058 DOI: 10.1111/imm.12856] [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: 06/10/2017] [Revised: 10/15/2017] [Accepted: 10/18/2017] [Indexed: 11/26/2022] Open
Abstract
The concept of dendritic cell (DC) maturation generally refers to the changes in morphology and function of DCs. Conventionally, DC maturity is based on three criteria: loss of endocytic ability, gain of high-level capacity to present antigens and induce proliferation of T cells, and mobility of DCs toward high concentrations of CCL19. Impairment of DC maturation has been suggested as the main reason for infectivity or chronicity of several infectious agents. In the case of hepatitis C virus, this has been a matter of controversy for the last two decades. However, insufficient attention has been paid to the method of ex vivo maturation as the possible source of such controversies. We previously reported striking differences between DCs matured with different methods, so we propose the use of a standard quantitative index to determine the level of maturity in DCs as an approach to compare results from different studies. We designed and formulated a mathematically calculated index to numerically define the level of maturity based on experimental data from ex vivo assays. This introduces a standard maturation index (SMI) and weighted maturation index (WMI) based on strictly standardized mean differences between different methods of generating mature DCs. By calculating an SMI and a WMI, numerical values were assigned to the level of maturity achieved by DCs matured with different methods. SMI and WMI could be used as a standard tool to compare diversely generated mature DCs and so better interpret outcomes of ex vivo and in vivo studies with mature DCs.
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Affiliation(s)
- Abdolamir Landi
- Department of Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.,Department of Virology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Ali Khodadadi
- Cancer Petroleum & Environmental Pollutants Research Centre, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Sylvia van Drunen Littel-van den Hurk
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,VIDO-InterVac, University of Saskatchewan, Saskatoon, SK, Canada
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3
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Geng D, Song X, Ning F, Song Q, Yin H. MiR-34a Inhibits Viability and Invasion of Human Papillomavirus-Positive Cervical Cancer Cells by Targeting E2F3 and Regulating Survivin. Int J Gynecol Cancer 2016; 25:707-13. [PMID: 25675046 DOI: 10.1097/igc.0000000000000399] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE Previous studies confirmed that high-risk human papillomavirus (HR-HPV) infection is a risk factor of cervical cancer, and the infection was associated with significantly reduced miR-34a expression during carcinogenesis. However, the downstream targets of miR-34a and their roles are still not well understood. This study explored the regulative role of miR-34a on E2F3 and survivin expression and the viability and invasion of HPV-positive cervical cancer cells. METHODS MiR-34a and survivin expression in 56 cases of HR-HPV-positive patients, 28 cases of HR-HPV-negative patients, and 28 normal cases without HR-HPV infections were measured. Human papillomavirus-18-positive HeLa cervical cancer cells and HPV-16-positive SiHa cells were used to explore the effect of miR-34a on cell viability and invasion. The molecular target of miR-34a was also explored in cervical cancer cells. RESULTS The results showed that miR-34a overexpression could inhibit HPV-positive cancer cell viability, whereas its downregulation promoted cell viability. E2F3 is a direct target of miR-34a in HPV-positive cervical cancer cells. By targeting E2F3, miR-34a could regulate the expression of survivin. Thus, through regulating E2F3 and survivin, miR-34a could reduce the viability and invasion of HPV-positive cervical cancer cells. CONCLUSIONS This study confirmed a novel miR-34a-E2F3-survivin axis in the tumor suppressor role of miR-34a in cervical cancer.
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Affiliation(s)
- Dianzhong Geng
- *Department of Oncology, Binzhou Medical University Hospital; †Department of Obstetrics and Gynecology, Binzhou People's Hospital; and ‡Department of Obstetrics and Gynecology, Zouping Maternal and Child Health-Care Hospital, Shandong, China
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4
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A PCR-Based Method to Construct Lentiviral Vector Expressing Double Tough Decoy for miRNA Inhibition. PLoS One 2015; 10:e0143864. [PMID: 26624995 PMCID: PMC4666662 DOI: 10.1371/journal.pone.0143864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/09/2015] [Indexed: 01/12/2023] Open
Abstract
DNA vector-encoded Tough Decoy (TuD) miRNA inhibitor is attracting increased attention due to its high efficiency in miRNA suppression. The current methods used to construct TuD vectors are based on synthesizing long oligonucleotides (~90 mer), which have been costly and problematic because of mutations during synthesis. In this study, we report a PCR-based method for the generation of double Tough Decoy (dTuD) vector in which only two sets of shorter oligonucleotides (< 60 mer) were used. Different approaches were employed to test the inhibitory potency of dTuDs. We demonstrated that dTuD is the most efficient method in miRNA inhibition in vitro and in vivo. Using this method, a mini dTuD library against 88 human miRNAs was constructed and used for a high-throughput screening (HTS) of AP-1 pathway-related miRNAs. Seven miRNAs (miR-18b-5p, -101-3p, -148b-3p, -130b-3p, -186-3p, -187-3p and -1324) were identified as candidates involved in AP-1 pathway regulation. This novel method allows for an accurate and cost-effective generation of dTuD miRNA inhibitor, providing a powerful tool for efficient miRNA suppression in vitro and in vivo.
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5
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Xu K, Zhang T, Guo L, Xin Y, Zhang L, Zhang Z. Alternative methods for the efficient construction of short hairpin RNA expression vectors. Anal Biochem 2015; 478:23-5. [PMID: 25794926 DOI: 10.1016/j.ab.2015.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 11/22/2022]
Abstract
Short hairpin RNA (shRNA)-mediated RNA interference has become a basic technique in modern molecular biology and biochemistry for studying gene function and biological pathways. Here, we report two alternative and efficient methods to construct shRNA expression vectors based respectively on multiple-step sequential PCR and primer extension-homologous recombination (PE-HR). Neither method requires synthesizing long oligonucleotides containing hairpin sequences as used in traditional approaches. The hairpin sequences may produce mutations during oligo synthesis, pose problems in annealing, and lead to inefficient cloning. The PE-HR method further provides rapid and economical construction of shRNA expression vectors without needing the ligation procedure.
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Affiliation(s)
- Kun Xu
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tingting Zhang
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Lijun Guo
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Xin
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Long Zhang
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zhiying Zhang
- College of Animal Science & Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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6
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Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting. Anal Biochem 2015; 478:131-3. [PMID: 25748774 DOI: 10.1016/j.ab.2015.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 02/08/2023]
Abstract
In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers.
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7
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Guo P, Xiao X, El-Gohary Y, Criscimanna A, Prasadan K, Rymer C, Shiota C, Wiersch J, Gaffar I, Esni F, Gittes GK. Specific transduction and labeling of pancreatic ducts by targeted recombinant viral infusion into mouse pancreatic ducts. J Transl Med 2013; 93:1241-53. [PMID: 24100509 DOI: 10.1038/labinvest.2013.113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/05/2013] [Accepted: 08/16/2013] [Indexed: 02/08/2023] Open
Abstract
Specific labeling of pancreatic ducts has proven to be quite difficult. Such labeling has been highly sought after because of the power it would confer to studies of pancreatic ductal carcinogenesis, as well as studies of the source of new insulin-producing β-cells. Cre-loxp recombination could, in theory, lineage-tag pancreatic ducts, but results have been conflicting, mainly due to low labeling efficiencies. Here, we achieved a high pancreatic duct labeling efficiency using a recombinant adeno-associated virus (rAAV) with a duct-specific sox9 promoter infused into the mouse common biliary/pancreatic duct. We saw rapid, diffuse duct-specific labeling, with 50 and 89% labeling in the pancreatic tail and head region, respectively. This highly specific labeling of ducts should greatly enhance our ability to study the role of pancreatic ducts in numerous aspects of pancreatic growth, development and function.
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Affiliation(s)
- Ping Guo
- Division of Pediatric General and Thoracic Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, One Children Hospital Drive, Pittsburgh, PA, USA
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A single-step mixing cloning method for assembly of lentiviral short hairpin RNA expression vectors for gene silencing. Anal Biochem 2013; 438:39-41. [DOI: 10.1016/j.ab.2013.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/04/2013] [Accepted: 03/07/2013] [Indexed: 11/18/2022]
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9
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Liang G, He H, Li Y, Yu D. A new strategy for construction of artificial miRNA vectors in Arabidopsis. PLANTA 2012; 235:1421-1429. [PMID: 22350768 DOI: 10.1007/s00425-012-1610-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 01/26/2012] [Indexed: 05/31/2023]
Abstract
MicroRNAs are a class of small RNAs that specifically suppress their target genes by transcript cleavage or/and translation repression. Natural miRNA precursors have been used for the backbones of artificial miRNA precursors, which can give rise to expected artificial miRNAs with which to repress specific target genes. Artificial miRNA technology is a powerful tool to silence genes of interest. However, it is costly and time-consuming to construct artificial miRNA precursors by the use of an overlapping PCR method. We describe a new strategy to construct artificial miRNAs. A miRNA gene consists of three components (upstream, stem-loop, and downstream regions). Upstream and downstream regions of a natural miRNA transcript were amplified in conjunction with the introduction of two suitable restriction sites in the amplicons, which were inserted into a plasmid to form a median vector. Production of an artificial miRNA vector was easily achieved by insertion of an artificial stem-loop into the median vector. The artificial miRNAs produced by this method efficiently repressed their target genes in Arabidopsis. In addition, two artificial miRNA constructs were expressed as one polycistron driven by the CaMV 35S promoter and their targets were suppressed simultaneously in Arabidopsis. Thus, artificial miRNAs are a powerful tool with which to analyze rapidly the functions of not only a single gene or multiple homologous genes, but also multiple non-homologous genes.
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Affiliation(s)
- Gang Liang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
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10
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Kumar B, Yadav A, Lang J, Teknos TN, Kumar P. Dysregulation of microRNA-34a expression in head and neck squamous cell carcinoma promotes tumor growth and tumor angiogenesis. PLoS One 2012; 7:e37601. [PMID: 22629428 PMCID: PMC3358265 DOI: 10.1371/journal.pone.0037601] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 04/26/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND MicroRNAs (miRs) are small non-coding RNAs that play an important role in cancer development where they can act as oncogenes or as tumor-suppressors. miR-34a is a tumor-suppressor that is frequently downregulated in a number of tumor types. However, little is known about the role of miR-34a in head and neck squamous cell carcinoma (HNSCC). METHODS AND RESULTS miR-34a expression in tumor samples, HNSCC cell lines and endothelial cells was examined by real time PCR. Lipofectamine-2000 was used to transfect miR-34a in HNSCC cell lines and human endothelial cells. Cell-proliferation, migration and clonogenic survival was examined by MTT, Xcelligence system, scratch assay and colony formation assay. miR-34a effect on tumor growth and tumor angiogenesis was examined by in vivo SCID mouse xenograft model. Our results demonstrate that miR-34a is significantly downregulated in HNSCC tumors and cell lines. Ectopic expression of miR-34a in HNSCC cell lines significantly inhibited tumor cell proliferation, colony formation and migration. miR-34a overexpression also markedly downregulated E2F3 and survivin levels. Rescue experiments using microRNA resistant E2F3 isoforms suggest that miR-34a-mediated inhibition of cell proliferation and colony formation is predominantly mediated by E2F3a isoform. In addition, tumor samples from HNSCC patients showed an inverse relationship between miR-34a and survivin as well as miR-34a and E2F3 levels. Overexpression of E2F3a completely rescued survivin expression in miR-34a expressing cells, thereby suggesting that miR-34a may be regulating survivin expression via E2F3a. Ectopic expression of miR-34a also significantly inhibited tumor growth and tumor angiogenesis in a SCID mouse xenograft model. Interestingly, miR-34a inhibited tumor angiogenesis by blocking VEGF production by tumor cells as well as directly inhibiting endothelial cell functions. CONCLUSIONS Taken together, these findings suggest that dysregulation of miR-34a expression is common in HNSCC and modulation of miR34a activity might represent a novel therapeutic strategy for the treatment of HNSCC.
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MESH Headings
- Animals
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Down-Regulation
- Endothelial Cells/metabolism
- Endothelial Cells/pathology
- Gene Expression Regulation, Neoplastic
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/pathology
- Humans
- Inhibitor of Apoptosis Proteins/genetics
- Inhibitor of Apoptosis Proteins/metabolism
- Mice
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Survivin
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Affiliation(s)
- Bhavna Kumar
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Arti Yadav
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - James Lang
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Theodoros N. Teknos
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Pawan Kumar
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, Ohio, United States of America
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Huang Y, Zou Q, Shen XJ, Yu XL, Wang ZB, Cheng XC. Construction of baculovirus expression vector of miRNAs and its expression in insect cells. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2012. [DOI: 10.3103/s0891416812020036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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MicroRNA-34a affects the occurrence of laryngeal squamous cell carcinoma by targeting the antiapoptotic gene survivin. Med Oncol 2012; 29:2473-80. [DOI: 10.1007/s12032-011-0156-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 12/30/2011] [Indexed: 01/22/2023]
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13
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Huang Y, Zou Q, Wang SP, Tang SM, Zhang GZ, Shen XJ. Construction and detection of expression vectors of microRNA-9a in BmN cells. J Zhejiang Univ Sci B 2011; 12:527-33. [PMID: 21726059 DOI: 10.1631/jzus.b1000296] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs molecules, approximately 21-23 nucleotides in length, which regulate gene expression by base-pairing with 3' untranslated regions (UTRs) of target mRNAs. However, the functions of only a few miRNAs in organisms are known. Recently, the expression vector of artificial miRNA has become a promising tool for gene function studies. Here, a method for easy and rapid construction of eukaryotic miRNA expression vector was described. The cytoplasmic actin 3 (A3) promoter and flanked sequences of miRNA-9a (miR-9a) precursor were amplified from genomic DNA of the silkworm (Bombyx mori) and was inserted into pCDNA3.0 vector to construct a recombinant plasmid. The enhanced green fluorescent protein (EGFP) gene was used as reporter gene. The Bombyx mori N (BmN) cells were transfected with recombinant miR-9a expression plasmid and were harvested 48 h post transfection. Total RNAs of BmN cells transfected with recombinant vectors were extracted and the expression of miR-9a was evaluated by reverse transcriptase polymerase chain reaction (RT-PCR) and Northern blot. Tests showed that the recombinant miR-9a vector was successfully constructed and the expression of miR-9a with EGFP was detected.
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Affiliation(s)
- Yong Huang
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang 212018, China
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Chen Y, Zhu X, Zhang X, Liu B, Huang L. Nanoparticles modified with tumor-targeting scFv deliver siRNA and miRNA for cancer therapy. Mol Ther 2010; 18:1650-6. [PMID: 20606648 DOI: 10.1038/mt.2010.136] [Citation(s) in RCA: 385] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Targeted delivery of RNA-based therapeutics for cancer therapy remains a challenge. We have developed a LPH (liposome-polycation-hyaluronic acid) nanoparticle formulation modified with tumor-targeting single-chain antibody fragment (scFv) for systemic delivery of small interfering RNA (siRNA) and microRNA (miRNA) into experimental lung metastasis of murine B16F10 melanoma. The siRNAs delivered by the scFv targeted nanoparticles efficiently downregulated the target genes (c-Myc/MDM2/VEGF) in the lung metastasis. Two daily intravenous injections of the combined siRNAs in the GC4-targeted nanoparticles significantly reduced the tumor load in the lung. miRNA-34a (miR-34a) induced apoptosis, inhibited survivin expression, and downregulated MAPK pathway in B16F10 cells. miR-34a delivered by the GC4-targeted nanoparticles significantly downregulated the survivin expression in the metastatic tumor and reduced tumor load in the lung. When miR-34a and siRNAs were co-formulated in GC4-targeted nanoparticles, an enhanced anticancer effect was observed.
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Affiliation(s)
- Yunching Chen
- Division of Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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15
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Watashi K, Yeung ML, Starost MF, Hosmane RS, Jeang KT. Identification of small molecules that suppress microRNA function and reverse tumorigenesis. J Biol Chem 2010; 285:24707-16. [PMID: 20529860 DOI: 10.1074/jbc.m109.062976] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) act in post-transcriptional gene silencing and are proposed to function in a wide spectrum of pathologies, including cancers and viral diseases. Currently, to our knowledge, no detailed mechanistic characterization of small molecules that interrupt miRNA pathways have been reported. In screening a small chemical library, we identified compounds that suppress RNA interference activity in cultured cells. Two compounds were characterized; one impaired Dicer activity while the other blocked small RNA-loading into an Argonaute 2 (AGO2) complex. We developed a cell-based model of miRNA-dependent tumorigenesis, and using this model, we observed that treatment of cells with either of the two compounds effectively neutralized tumor growth. These findings indicate that miRNA pathway-suppressing small molecules could potentially reverse tumorigenesis.
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Affiliation(s)
- Koichi Watashi
- Molecular Virology Section, Laboratory of Molecular Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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Kato M, Natarajan R. microRNA cascade in diabetic kidney disease: Big impact initiated by a small RNA. Cell Cycle 2010; 8:3613-4. [PMID: 19884793 DOI: 10.4161/cc.8.22.9816] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Kato M, Arce L, Natarajan R. MicroRNAs and their role in progressive kidney diseases. Clin J Am Soc Nephrol 2009; 4:1255-66. [PMID: 19581401 DOI: 10.2215/cjn.00520109] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRs) are a family of short non-coding RNAs. These endogenously produced factors have been shown to play important roles in gene regulation. The discovery of miRs has greatly expanded our knowledge of gene regulation at the posttranscriptional level. miRs inhibit target gene expression by blocking protein translation or by inducing mRNA degradation and therefore have the potential to modulate physiologic and pathologic processes. The imperative need to determine their cellular targets and disease relevance has sparked an unprecedented explosion of research in the miR field. Recent findings have revealed critical functions for specific miRs in cellular events such as proliferation, differentiation, development, and immune responses and in the regulation of genes relevant to human diseases. Of particular interest to renal researchers are recent reports that key miRs are highly expressed in the kidney and can act as effectors of TGF-beta actions and high glucose in diabetic kidney disease. Moreover, podocyte-specific deletion of Dicer, a key enzyme involved in miR biogenesis, led to proteinuria and severe renal dysfunction in mice. Hence, studies aimed at determining the in vitro and in vivo functions of miRs in the kidney could determine their value as therapeutic targets for progressive renal glomerular and tubular diseases. Translational approaches could be facilitated by the development of effective inhibitors of specific miRs and methods for optimal delivery of anti-miRs to the kidney. The major goal of this review is to highlight key functions of these miRs and their relationships to human diseases, with special emphasis on diabetic kidney disease.
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Affiliation(s)
- Mitsuo Kato
- Gonda Diabetes Center, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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TGF-beta activates Akt kinase through a microRNA-dependent amplifying circuit targeting PTEN. Nat Cell Biol 2009; 11:881-9. [PMID: 19543271 PMCID: PMC2744130 DOI: 10.1038/ncb1897] [Citation(s) in RCA: 486] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 03/20/2009] [Indexed: 01/20/2023]
Abstract
Akt kinase is activated by transforming growth factor-beta1 (TGF-β) in diabetic kidneys and plays important roles in fibrosis, hypertrophy and cell survival in glomerular mesangial cells (MC)1–11. However, the mechanisms of Akt activation by TGF-β are not fully understood. Here we show that TGF-β activates Akt in MC by inducing microRNA-216a (miR-216a) and miR-217, both of which target phosphatase and tensin homologue (PTEN). Both these miRs are located within the second intron of a non-coding RNA (RP23-298H6.1-001). The RP23 promoter was activated by TGF-β and also by miR-192 via E-box-regulated mechanisms as shown previously3. Akt activation by these miRs also led to MC survival and hypertrophy similar to TGF-β. These studies reveal a mechanism of Akt activation via PTEN downregulation by two miRs regulated by upstream miR-192 and TGF-β. Due to the diversity of PTEN function12, 13, this miR amplifying circuit may play key roles not only in kidney disorders, but also other diseases.
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Cloning and identification of microRNAs in bovine alveolar macrophages. Mol Cell Biochem 2009; 332:9-16. [DOI: 10.1007/s11010-009-0168-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 05/21/2009] [Indexed: 12/19/2022]
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20
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Xu J, Zeng JQ, Wan G, Hu GB, Yan H, Ma LX. Construction of siRNA/miRNA expression vectors based on a one-step PCR process. BMC Biotechnol 2009; 9:53. [PMID: 19490634 PMCID: PMC2700792 DOI: 10.1186/1472-6750-9-53] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 06/02/2009] [Indexed: 11/20/2022] Open
Abstract
Background RNA interference (RNAi) has become a powerful means for silencing target gene expression in mammalian cells and is envisioned to be useful in therapeutic approaches to human disease. In recent years, high-throughput, genome-wide screening of siRNA/miRNA libraries has emerged as a desirable approach. Current methods for constructing siRNA/miRNA expression vectors require the synthesis of long oligonucleotides, which is costly and suffers from mutation problems. Results Here we report an ingenious method to solve traditional problems associated with construction of siRNA/miRNA expression vectors. We synthesized shorter primers (< 50 nucleotides) to generate a linear expression structure by PCR. The PCR products were directly transformed into chemically competent E. coli and converted to functional vectors in vivo via homologous recombination. The positive clones could be easily screened under UV light. Using this method we successfully constructed over 500 functional siRNA/miRNA expression vectors. Sequencing of the vectors confirmed a high accuracy rate. Conclusion This novel, convenient, low-cost and highly efficient approach may be useful for high-throughput assays of RNAi libraries.
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Affiliation(s)
- Jun Xu
- Institute of Molecular Biology, Biology Faculty of Hubei University, Wuhan, Hubei Province, PR China.
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Hu T, Fu Q, Chen P, Ma L, Sin O, Guo D. Construction of an artificial MicroRNA expression vector for simultaneous inhibition of multiple genes in mammalian cells. Int J Mol Sci 2009; 10:2158-2168. [PMID: 19564946 PMCID: PMC2695274 DOI: 10.3390/ijms10052158] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 04/16/2009] [Accepted: 05/14/2009] [Indexed: 12/20/2022] Open
Abstract
Recently, artificial microRNA (amiRNA) has become a promising RNA interference (RNAi) technology. Here, we describe a flexible and reliable method for constructing both single- and multi-amiRNA expression vectors. Two universal primers, together with two specific primers carrying the encoding sequence of amiRNA were designed and utilized to synthesize the functional amiRNA cassette through a one-step PCR. With appropriate restriction sites, the synthesized amiRNA cassettes can be cloned into any site of different destination vectors. Using the method, we constructed both single- and multi-amiRNA expression vectors to target three reporter genes, which code firefly luciferase (Fluc), enhanced green fluorescent protein (EGFP) and β-galactosidase (LacZ), respectively. The expressions of three genes were all specifically inhibited by either the corresponding single- or the multi-amiRNA expression vector in 293T cells. And the RNAi efficiency of each amiRNA produced by both single- and multi-amiRNA expression vectors was comparable.
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Affiliation(s)
- Tao Hu
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Qiong Fu
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Ping Chen
- Department of Pathophysiology, Basic Medical College, Zhengzhou University, Zhengzhou 450001, China; E-Mail:
(P.C.)
| | - Li Ma
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Onsam Sin
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
| | - Deyin Guo
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, China; E-Mails:
(T.H.);
(Q.F.);
(L.M.);
(O.S.)
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +86-27-6875-2506; Fax: +86-27-6875-2897
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Lai A, Cairns MJ, Tran N, Zhang HP, Cullen L, Arndt GM. RNA modulators of complex phenotypes in mammalian cells. PLoS One 2009; 4:e4758. [PMID: 19270743 PMCID: PMC2650256 DOI: 10.1371/journal.pone.0004758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 02/12/2009] [Indexed: 12/03/2022] Open
Abstract
RNA-mediated gene silencing, in the form of RNA interference (RNAi) or microRNAs (miRNAs) has provided novel tools for gene discovery and validation in mammalian cells. Here, we report on the construction and application of a random small RNA expression library for use in identifying small interfering RNA (siRNA) effectors that can modify complex cellular phenotypes in mammalian cells. The library is based in a retroviral vector and uses convergent promoters to produce unique small complementary RNAs. Using this library, we identify a range of small RNA-encoding gene inserts that overcome resistance to 5-fluorouracil (5-FU)- or tumour necrosis factor alpha (TNF-α)- induced cell death in colorectal cancer cells. We demonstrate the utility of this technology platform by identifying a key RNA effector, in the form of a siRNA, which overcomes cell death induced by the chemotherapeutic 5-FU. The technology described has the potential to identify both functional RNA modulators capable of altering physiological systems and the cellular target genes altered by these modulators.
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Affiliation(s)
- Angela Lai
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia
| | - Murray J. Cairns
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia
| | - Nham Tran
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia
- The Sydney Head and Neck Cancer Institute, Sydney Cancer Centre, Royal Prince Alfred Hospital and University of Sydney, Sydney, New South Wales, Australia
| | - Hong-Ping Zhang
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia
| | - Lara Cullen
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia
| | - Greg M. Arndt
- Johnson and Johnson Research Pty Ltd, Australian Technology Park, Eveleigh, New South Wales, Australia
- * E-mail:
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Dickson ME, Tian X, Liu X, Davis DR, Sigmund CD. Upstream stimulatory factor is required for human angiotensinogen expression and differential regulation by the A-20C polymorphism. Circ Res 2008; 103:940-7. [PMID: 18802024 DOI: 10.1161/circresaha.108.180653] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Among naturally occurring polymorphisms in the 5' flanking region of the human angiotensinogen (AGT) gene, the -20 and -217 polymorphisms have the strongest effects on AGT regulation in AGT-expressing cells derived from liver, kidney, brain, and fat. These polymorphisms may affect allele-specific transcription factor binding, and the high-expressing alleles are both relatively common. We show herein that the -20C allele has higher transcriptional activity than -20A, and the -20A allele confers no additional transactivation potential beyond that of a mutated vector. Gel-shift assays show that upstream stimulatory factor (USF)1 and USF2 preferentially bind the -20C allele, whereas the -20A allele retains a low affinity USF binding site. Plasmid immunoprecipitation assays confirmed preferential association of USF1 with the -20C allele in transfected HepG2 cells. Chromatin immunoprecipitation confirmed that USF1 binds to the endogenous AGT -20C allele in CCF cells, the only cell line tested that carries the -20C allele, and to the human AGT promoter in liver and adipose tissue from transgenic mice. Transduction of AGT-expressing cells with short hairpin RNAs specifically targeting USF1 or USF2, resulted in cell- and allele-specific attenuation of AGT promoter activity. In vivo, knockdown of USF expression in the liver of transgenic mice expressing the -20C allele of AGT resulted in lower AGT expression, a decrease in circulating human AGT protein but no change in expression of GAPDH or hepatocyte nuclear factor-4alpha. We conclude that USF1 functionally and differentially regulates AGT expression via the -20 polymorphism and that the differential expression exhibited by -20 can be accounted for by differential association with USF1.
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Affiliation(s)
- Matthew E Dickson
- Genetics and Medical Scientist Training Programs, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Genome-wide screens for effective siRNAs through assessing the size of siRNA effects. BMC Res Notes 2008; 1:33. [PMID: 18710486 PMCID: PMC2526086 DOI: 10.1186/1756-0500-1-33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2008] [Accepted: 06/23/2008] [Indexed: 11/14/2022] Open
Abstract
Background RNA interference (RNAi) has been seen as a revolution in functional genomics and system biology. Genome-wide RNAi research relies on the development of RNAi high-throughput screening (HTS) assays. One of the most fundamental challenges in RNAi HTS is to glean biological significance from mounds of data, which relies on the development of effective analytic methods for selecting effective small interfering RNAs (siRNAs). Findings Based on a recently proposed parameter, strictly standardized mean difference (SSMD), I propose an analytic method for genome-wide screens of effective siRNAs through assessing and testing the size of siRNA effects. Central to this method is the capability of SSMD in quantifying siRNA effects. This method has relied on normal approximation, which works only in the primary screens but not in the confirmatory screens. In this paper, I explore the non-central t-distribution property of SSMD estimates and use this property to extend the SSMD-based method so that it works effectively in either primary or confirmatory screens as well as in any HTS screens with or without replicates. The SSMD-based method maintains a balanced control of false positives and false negatives. Conclusion The central interest in genome-wide RNAi research is the selection of effective siRNAs which relies on the development of analytic methods to measure the size of siRNA effects. The new analytic method for hit selection provided in this paper offers a good analytic tool for selecting effective siRNAs, better than current analytic methods, and thus may have broad utility in genome-wide RNAi research.
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Li XX, Jia HW, Quan JX, Jiao YL, Yang YH, Wang BL, Yao Z. An efficient approach for constructing shRNA expression vectors based on short oligonucleotide synthesis. Anal Biochem 2008; 381:163-5. [PMID: 18601895 DOI: 10.1016/j.ab.2008.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/07/2008] [Accepted: 06/09/2008] [Indexed: 11/29/2022]
Abstract
Traditional strategies for establishing shRNA expression constructs are inefficient, error-prone, or costly. We describe a simple approach that overcomes these drawbacks. Briefly, the sense and antisense strands of the short hairpin RNA coding sequence are segmented into two parts, respectively, at asymmetric sites. The four resulting short oligonucleotides are synthesized. Each oligonucleotide is annealed with its opposite, resulting in a double-stranded fragment with sticky termini at both ends. The two fragments so generated can be easily spliced by simple ligation to reconstitute the full-length short hairpin RNA coding sequence which can then be cloned into an appropriately restricted vector.
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Affiliation(s)
- Xiao-Xia Li
- Key Lab of Ministry of Health for Hormone and Development, Institute of Endocrinology, Tianjin Medical University, Tianjin 300070, People's Republic of China
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