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Zhang W, Hou Y, Yin S, Miao Q, Lee K, Zhou X, Wang Y. Advanced gene nanocarriers/scaffolds in nonviral-mediated delivery system for tissue regeneration and repair. J Nanobiotechnology 2024; 22:376. [PMID: 38926780 PMCID: PMC11200991 DOI: 10.1186/s12951-024-02580-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Tissue regeneration technology has been rapidly developed and widely applied in tissue engineering and repair. Compared with traditional approaches like surgical treatment, the rising gene therapy is able to have a durable effect on tissue regeneration, such as impaired bone regeneration, articular cartilage repair and cancer-resected tissue repair. Gene therapy can also facilitate the production of in situ therapeutic factors, thus minimizing the diffusion or loss of gene complexes and enabling spatiotemporally controlled release of gene products for tissue regeneration. Among different gene delivery vectors and supportive gene-activated matrices, advanced gene/drug nanocarriers attract exceptional attraction due to their tunable physiochemical properties, as well as excellent adaptive performance in gene therapy for tissue regeneration, such as bone, cartilage, blood vessel, nerve and cancer-resected tissue repair. This paper reviews the recent advances on nonviral-mediated gene delivery systems with an emphasis on the important role of advanced nanocarriers in gene therapy and tissue regeneration.
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Affiliation(s)
- Wanheng Zhang
- Institute of Geriatrics, School of Medicine, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University, Shanghai, 200444, China
- Department of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Hou
- Institute of Geriatrics, School of Medicine, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University, Shanghai, 200444, China
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education), Shanghai University, Shanghai, 200444, China
| | - Shiyi Yin
- Department of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi Miao
- Department of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Kyubae Lee
- Department of Biomedical Materials, Konyang University, Daejeon, 35365, Republic of Korea
| | - Xiaojian Zhou
- Department of Pediatrics, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200080, China.
| | - Yongtao Wang
- Institute of Geriatrics, School of Medicine, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), Shanghai University, Shanghai, 200444, China.
- Joint International Research Laboratory of Biomaterials and Biotechnology in Organ Repair (Ministry of Education), Shanghai University, Shanghai, 200444, China.
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Cheng L, Lu L, Chen Z, Ma D, Xi Z. Multiple-Gene Regulation for Enhanced Antitumor Efficacy with Branch-PCR-Assembled TP53 and MYC Gene Nanovector. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206943. [PMID: 36296536 PMCID: PMC9609172 DOI: 10.3390/molecules27206943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Multiple proteins are involved in network regulation through the crosstalk of different signaling pathways in cancers. Here, we propose a novel strategy of genome therapy with branch-PCR-assembled gene nanovectors to perform network-based gene regulation at multiple levels for cancer therapy. To validate network-based multiplex-gene regulation for genome therapy, we chose to simultaneously target one tumor suppressor gene (TP53) and one oncogene (MYC) in two different signaling pathways. The results showed that, compared to gene nanovectors targeting single genes (NP-TP53 and NP-shMYC), branch-PCR-assembled gene nanovectors simultaneously expressing p53 proteins and MYC shRNA arrays (NP-TP53-shMYC) showed enhanced antitumor efficacy in both MDA-MB-231 cancer cells and an MDA-MB-231-tumor-bearing mouse model. These findings indicate the feasibility and effectiveness of genome therapy in cancer therapy.
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Affiliation(s)
| | | | | | - Dejun Ma
- Correspondence: (D.M.); (Z.X.); Tel.: +86-022-23504782 (Z.X.)
| | - Zhen Xi
- Correspondence: (D.M.); (Z.X.); Tel.: +86-022-23504782 (Z.X.)
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3
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Miele D, Xia X, Catenacci L, Sorrenti M, Rossi S, Sandri G, Ferrari F, Rossi JJ, Bonferoni MC. Chitosan Oleate Coated PLGA Nanoparticles as siRNA Drug Delivery System. Pharmaceutics 2021; 13:1716. [PMID: 34684009 PMCID: PMC8539707 DOI: 10.3390/pharmaceutics13101716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Oligonucleotide therapeutics such as miRNAs and siRNAs represent a class of molecules developed to modulate gene expression by interfering with ribonucleic acids (RNAs) and protein synthesis. These molecules are characterized by strong instability and easy degradation due to nuclease enzymes. To avoid these drawbacks and ensure efficient delivery to target cells, viral and non-viral vectors are the two main approaches currently employed. Viral vectors are one of the major vehicles in gene therapy; however, the potent immunogenicity and the insertional mutagenesis is a potential issue for the patient. Non-viral vectors, such as polymeric nanocarriers, provide a safer and more efficient delivery of RNA-interfering molecules. The aim of this work is to employ PLGA core nanoparticles shell-coated with chitosan oleate as siRNA carriers. An siRNA targeted on HIV-1, directed against the viral Tat/Rev transcripts was employed as a model. The ionic interaction between the oligonucleotide's moieties, negatively charged, and the positive surface charges of the chitosan shell was exploited to associate siRNA and nanoparticles. Non-covalent bonds can protect siRNA from nuclease degradation and guarantee a good cell internalization and a fast release of the siRNA into the cytosolic portion, allowing its easy activation.
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Affiliation(s)
- Dalila Miele
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
| | - Xin Xia
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1218 Fifth Avenue, Duarte, CA 91010, USA;
| | - Laura Catenacci
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
| | - Milena Sorrenti
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
| | - Silvia Rossi
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
| | - Giuseppina Sandri
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
| | - Franca Ferrari
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1218 Fifth Avenue, Duarte, CA 91010, USA;
| | - Maria Cristina Bonferoni
- Department Drug Sciences, University of Pavia, Vle Taramelli 12, 27100 Pavia, Italy; (D.M.); (L.C.); (M.S.); (S.R.); (G.S.); (F.F.)
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4
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Cao C, Cai Z, Xiao X, Rao J, Chen J, Hu N, Yang M, Xing X, Wang Y, Li M, Zhou B, Wang X, Wang J, Xue Y. The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun 2021; 12:3917. [PMID: 34168138 PMCID: PMC8225788 DOI: 10.1038/s41467-021-22785-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly "unentangled globule" conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.
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Affiliation(s)
- Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Xiao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Rao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Juan Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minnan Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaorui Xing
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongle Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Manman Li
- School of Life Sciences, Henan Normal University, Xinxiang, China
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianwei Wang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Zhang K, Zhang Z, Kang J, Chen J, Liu J, Gao N, Fan L, Zheng P, Wang Y, Sun J. CRISPR/Cas13d-Mediated Microbial RNA Knockdown. Front Bioeng Biotechnol 2020; 8:856. [PMID: 32850723 PMCID: PMC7406568 DOI: 10.3389/fbioe.2020.00856] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-guided and RNA-targeting type IV-D CRISPR/Cas systems (CRISPR/Cas13d) have recently been identified and employed for efficient and specific RNA knockdown in mammalian and plant cells. Cas13d possesses dual RNase activities and is capable of processing CRISPR arrays and cleaving target RNAs in a protospacer flanking sequence (PFS)-independent manner. These properties make this system a promising tool for multiplex gene expression regulation in microbes. Herein, we aimed to establish a CRISPR/Cas13d-mediated RNA knockdown platform for bacterial chassis. CasRx, Cas13d from Ruminococcus flavefaciens XPD3002, was selected due to its high activity. However, CasRx was found to be highly toxic to both Escherichia coli and Corynebacterium glutamicum, especially when it cooperated with its guide and target RNAs. After employing a low copy number vector, a tightly controlled promoter, and a weakened ribosome binding site, we successfully constructed an inducible expression system for CasRx and applied it for repressing the expression of a green fluorescent protein (GFP) in E. coli. Despite our efforts to optimize inducer usage, guide RNA (gRNA) architecture and combination, and target gene expression level, the highest gene repression efficiency was 30–50% at the protein level and ∼70% at the mRNA level. The moderate RNA knockdown is possibly caused by the collateral cleavage activity toward bystander RNAs, which acts as a mechanism of type IV-D immunity and perturbs microbial metabolism. Further studies on cellular response to CRISPR/Cas13d and improvement in RNA knockdown efficiency are required prior to practical application of this system in microbes.
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Affiliation(s)
- Kun Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianan Kang
- College of Life Engineering, Shenyang Institute of Technology, Fushun, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Gao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liwen Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
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Chen Y, Guo E, Zhang J, Si T. Advances in RNAi-Assisted Strain Engineering in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2020; 8:731. [PMID: 32714914 PMCID: PMC7343710 DOI: 10.3389/fbioe.2020.00731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Saccharomyces cerevisiae is a widely used eukaryotic model and microbial cell factory. RNA interference (RNAi) is a conserved regulatory mechanism among eukaryotes but absent from S. cerevisiae. Recent reconstitution of RNAi machinery in S. cerevisiae enables the use of this powerful tool for strain engineering. Here we first discuss the introduction of heterologous RNAi pathways in S. cerevisiae, and the design of various expression cassettes of RNAi precursor reagents for tunable, dynamic, and genome-wide regulation. We then summarize notable examples of RNAi-assisted functional genomics and metabolic engineering studies in S. cerevisiae. We conclude with the future challenges and opportunities of RNAi-based approaches, as well as the potential of other regulatory RNAs in advancing yeast engineering.
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Affiliation(s)
- Yongcan Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianzhi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Anwar A, Kim JK. Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives. Int J Mol Sci 2020; 21:E2695. [PMID: 32295026 PMCID: PMC7216248 DOI: 10.3390/ijms21082695] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.
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Affiliation(s)
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea;
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Moradpour M, Abdulah SNA. CRISPR/dCas9 platforms in plants: strategies and applications beyond genome editing. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:32-44. [PMID: 31392820 PMCID: PMC6920162 DOI: 10.1111/pbi.13232] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) and Cas9-associated protein systems provide a powerful genetic manipulation tool that can drive plant research forward. Nuclease-dead Cas9 (dCas9) is an enzymatically inactive mutant of Cas9 in which its endonuclease activity is non-functional. The applications of CRISPR/dCas9 have expanded and diversified in recent years. Originally, dCas9 was used as a CRISPR/Cas9 re-engineering tool that enables targeted expression of any gene or multiple genes through recruitment of transcriptional effector domains without introducing irreversible DNA-damaging mutations. Subsequent applications have made use of its ability to recruit modifying enzymes and reporter proteins to DNA target sites. In this paper, the most recent progress in the applications of CRISPR/dCas9 in plants, which include gene activation and repression, epigenome editing, modulation of chromatin topology, live-cell chromatin imaging and DNA-free genetic modification, will be reviewed. The associated strategies for exploiting the CRISPR/dCas9 system for crop improvement with a dimer of the future of the CRISPR/dCas9 system in the functional genomics of crops and the development of traits will be briefly discussed.
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Affiliation(s)
- Mahdi Moradpour
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Siti Nor Akmar Abdulah
- Laboratory of Science and TechnologyInstitute of Plantation StudiesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Department of Agricultural TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangSelangorMalaysia
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Ye W, Liu T, Zhu M, Zhang W, Huang Z, Li S, Li H, Kong Y, Chen Y. An Easy and Efficient Strategy for the Enhancement of Epothilone Production Mediated by TALE-TF and CRISPR/dcas9 Systems in Sorangium cellulosum. Front Bioeng Biotechnol 2019; 7:334. [PMID: 32039165 PMCID: PMC6988809 DOI: 10.3389/fbioe.2019.00334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/30/2019] [Indexed: 11/23/2022] Open
Abstract
Epothilones are a kind of macrolides with strong cytotoxicity toward cancer cells and relatively lower side effects compared with taxol. Epothilone B derivate ixabepilone has been used for the clinical treatment of advanced breast cancer. However, the low yield of epothilones and the difficulty in the genetic manipulation of Sorangium cellulosum limited their wider application. Transcription activator-like effectors-Trancriptional factor (TALE-TF)-VP64 and clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-VP64 have been demonstrated as effective systems for the transcriptional improvement. In this study, a promoter for the epothilone biosynthesis cluster was obtained and the function has been verified. The TALE-TF-VP64 and CRISPR/dcas9-VP64 target P3 promoter were electroporated into S. cellulosum strain So ce M4, and the transcriptional levels of epothilone biosynthesis-related genes were significantly upregulated. The yield of epothilone B was improved by 2.89- and 1.53-fold by the introduction of recombinant TALE-TF-VP64-P3 and dCas9-VP64-P3 elements into So ce M4, respectively. The epothilone D yield was also improved by 1.12- and 2.18-fold in recombinant dCas9-So ce M4 and TALE-VP64 strains, respectively. The transcriptional regulation mechanism of TALE-TF-VP64 and the competition mechanism with endogenous transcriptional factor were investigated by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP), demonstrating the combination of the P3 promoter and TALE-TF element and the competition between TALE-TF and endogenous transcriptional protein. This is the first report on the transcriptional regulation of the epothilone biosynthetic gene cluster in S. cellulosum using the TALE-TF and dCas9-VP64 systems, and the regulatory mechanism of the TALE-TF system for epothilone biosynthesis in S. cellulosum was also firstly revealed, thus shedding light on the metabolic engineering of S. cellulosum to improve epothilone yields substantially and promoting the application of epothilones in the biomedical industry.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zilei Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Saini Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yali Kong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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10
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Marshall EA, Stewart GL, Sage AP, Lam WL, Brown CJ. Beyond sequence homology: Cellular biology limits the potential of XIST to act as a miRNA sponge. PLoS One 2019; 14:e0221371. [PMID: 31419261 PMCID: PMC6697314 DOI: 10.1371/journal.pone.0221371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/05/2019] [Indexed: 01/13/2023] Open
Abstract
Introduction The sponging of microRNAs by a long non-coding RNA (lncRNA) away from their coding gene targets is a conceptually-simple, yet biologically-complex method of lncRNA-mediated gene regulation. Currently, predictions of genes that participate in sponge-based regulation are largely based on sequence homology alone, which may not adequately reflect the cellular environment in which lncRNA:miRNA pairs interact. The vast number of potential interactions generated by these predictions impedes the identification of functional gene regulatory relationships, which necessitates an approach that considers biological context. XIST, the female-specific lncRNA canonically involved in silencing the X chromosome, has been suggested by many studies to act as a miRNA sponge. The sex-specificity of XIST provides the opportunity to study the biological feasibility of proposed XIST-miRNA interactions. Here we take a comprehensive approach by considering factors that affect possible regulation through XIST-miRNA sponging. Results To identify the most feasible candidates in a particular tissue (lung adenocarcinomas), we considered protein-coding genes that (1) were positively correlated with XIST expression within sexes, (2) were targeted by miRNAs shared with XIST, and (3) expressed in lung adenocarcinoma. This revealed a robust set of 124 genes potentially positively regulated by XIST through the sequestration of 804 shared miRNAs. We then used the basic sex-specific nature of XIST to compare the changes in miRNA-target gene relationships in endogenously high-XIST and low-XIST systems to discover a high-confidence set of only 13 miRNA-gene pairs. As XIST is expressed exclusively in the nucleus, we validated the nuclear presence of several of these high-confidence miRNAs using RT-qPCR, confirming the co-localization required for XIST to interact with these species. Conclusions We use a biology-driven approach to identify genes defended from miRNA-based inhibition by the lncRNA XIST. Importantly, we identify that only a small subset of miRNAs predicted by sequence homology alone have the capacity to mediate the XIST-target gene axis, as they are enriched in the nucleus and able to co-localize with XIST for sponging. Our results reinforce the necessary consideration of biological features in future studies of lncRNA:miRNA interactions.
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Affiliation(s)
- Erin A. Marshall
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Greg L. Stewart
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
| | - Adam P. Sage
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
| | - Carolyn J. Brown
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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11
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Ras proteins as therapeutic targets. Biochem Soc Trans 2018; 46:1303-1311. [PMID: 30154091 DOI: 10.1042/bst20170529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/25/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
Oncogenic mutations in RAS genes underlie the pathogenesis of many human tumours, and there has been intense effort for over 30 years to develop effective and tolerated targeted therapeutics for patients with Ras-driven cancers. This review summarises the progress made in Ras drug discovery, highlighting some of the recent developments in directly targeting Ras through advances in small molecule drug design and novel therapeutic strategies.
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12
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Pizzino G, Irrera N, Galfo F, Pallio G, Mannino F, D'amore A, Pellegrino E, Ieni A, Russo GT, Calapai M, Altavilla D, Squadrito F, Bitto A. Effects of the antagomiRs 15b and 200b on the altered healing pattern of diabetic mice. Br J Pharmacol 2018; 175:644-655. [PMID: 29178246 DOI: 10.1111/bph.14113] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND PURPOSE Diabetic patients with non-healing ulcers have a reduced expression of VEGF. Genetically diabetic mice have an altered expression pattern of VEGF and its receptor, VEGF receptor 2 (VEGFR-2). In diabetic wounds, the microRNAs, miR15b and miR200b, which respectively inhibit VEGF and VEGF-R2 mRNAs, are up-regulated, further affecting the impaired angiogenesis. We investigated whether anti-miRs directed toward miR15b and miR200b could improve wound repair in genetically diabetic mice. EXPERIMENTAL APPROACH Skin wounds were produced on the backs of female diabetic mice. The anti-miRs (antimiR15b, antimiR200b or antimiR15b/200b) at 10 mg·kg-1 , or vehicle were applied to the wound edge. Mice were killed on days 7, 14 and at time of complete wound closure. Levels of mRNA and protein of angiogenic mediators and their receptors were measured with RT-qPCR and Western blotting. Wounds were examined by histological and immunochemical methods. KEY RESULTS mRNA expression of VEGF, VEGFR-2, angiopoietin-1 and its receptor TEK were evaluated after 7 and 14 days. Protein levels of VEGF and transglutaminase II were measured at day 7, while VEGFR-2 and Angiopoietin-1 were measured at day 14. Histological features and the time to achieve a complete wound closure were also examined. Treatment with the anti-miRs improved the analysed parameters and the co-treatment resulted the most effective. CONCLUSION AND IMPLICATIONS The results suggest that the inhibition of miR15b and miR200b may have a potential application in diabetes-related wound disorders.
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Affiliation(s)
- Gabriele Pizzino
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Natasha Irrera
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Federica Galfo
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Giovanni Pallio
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Federica Mannino
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Angelica D'amore
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Enrica Pellegrino
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Antonio Ieni
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Giuseppina T Russo
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Marco Calapai
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Domenica Altavilla
- Department of Biomedical Sciences, Dentistry and Morphological and Functional Images, University of Messina, Messina, Italy
| | - Francesco Squadrito
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
| | - Alessandra Bitto
- Department of Clinical and Experimental Medicine, Section of Pharmacology, Medical School, University of Messina, Messina, Italy
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13
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Heffler E, Allegra A, Pioggia G, Picardi G, Musolino C, Gangemi S. MicroRNA Profiling in Asthma: Potential Biomarkers and Therapeutic Targets. Am J Respir Cell Mol Biol 2017; 57:642-650. [PMID: 28489455 DOI: 10.1165/rcmb.2016-0231tr] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Asthma is a heterogeneous chronic inflammatory disorder in which different endotypes contribute to define clinical inflammatory phenotypes. MicroRNAs (miRNAs) are a group of minute, endogenous 22-25 nt RNA elements that join to particular mRNAs to reduce translation and increase messenger RNA degradation. miRNAs operate in post-transcriptional control and regulate physiological and pathological processes in several illnesses. The purpose of this work is to review and discuss the current knowledge about the function of miRNAs in asthma, focusing particularly on their biological properties, pathophysiologic actions, and possible use as markers and treatments for asthma.
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Affiliation(s)
- Enrico Heffler
- 1 Personalized Medicine Asthma and Allergy Clinic, Humanitas Research Hospital, and.,2 Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Alessandro Allegra
- 3 Division of Hematology, Department of General Surgery and Oncology, University of Messina
| | - Giovanni Pioggia
- 4 Institute of Applied Sciences and Intelligent Systems-Messina Unit, and
| | - Giuseppe Picardi
- 5 Respiratory Diseases and Allergy, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Caterina Musolino
- 3 Division of Hematology, Department of General Surgery and Oncology, University of Messina
| | - Sebastiano Gangemi
- 4 Institute of Applied Sciences and Intelligent Systems-Messina Unit, and.,6 School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University Hospital "G. Martino," Messina, Italy; and
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14
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Sharma D, Turkistani AA, Chang W, Hu C, Xu Z, Chang TKH. Negative Regulation of Human Pregnane X Receptor by MicroRNA-18a-5p: Evidence for Suppression of MicroRNA-18a-5p Expression by Rifampin and Rilpivirine. Mol Pharmacol 2017; 92:48-56. [DOI: 10.1124/mol.116.107003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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15
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Bhadra U, Patra P, Chhatai J, Pal-Bhadra M. Pigmy MicroRNA: surveillance cops in Therapies kingdom. Mol Med 2016; 22:759-775. [PMID: 27704139 PMCID: PMC5193465 DOI: 10.2119/molmed.2016.00136] [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: 05/25/2016] [Accepted: 09/13/2016] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are well preserved in every animal. These pigmy sized non-coding RNAs (21-23 nt), scattered in genome, are responsible for micromanaging the versatile gene regulations. Involvement of miRNAs was surveillance cops in all human diseases including cardiovascular defects, tumor formation, reproductive pathways, and neurological and autoimmune disorders. The effective functional role of miRNA can be reduced by chemical entities of antisense oligonucleotides and versatile small molecules that support the views of novel therapy of different human diseases. In this study, we have updated our current understanding for designing and synthesizing miRNA-controlling therapeutic chemicals. We have also proposed various in-vivo delivery strategies and their ongoing challenges to combat the incorporation hurdles in live cells and animals. Lastly, we have demonstrated the current progress of miRNA modulation in the treatment of different human diseases that provides an alternative approach of gene therapy.
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Affiliation(s)
- Utpal Bhadra
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Pradipta Patra
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Jagamohan Chhatai
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Manika Pal-Bhadra
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Uppal Road, Hyderabad, India
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16
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Sun WC, Pei L. rno-miR-665 targets BCL2L1 (Bcl-xl) and increases vulnerability to propofol in developing astrocytes. J Neurochem 2016; 138:233-42. [PMID: 27121046 DOI: 10.1111/jnc.13647] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/25/2016] [Accepted: 03/21/2016] [Indexed: 11/29/2022]
Abstract
Propofol exerts a cytotoxic influence over immature neurocytes. Our previous study revealed that clinically relevant doses of propofol accelerated apoptosis of primary cultured astrocytes of developing rodent brains via rno-miR-665 regulation. However, the role of rno-miR-665 during the growth spurt of neonatal rodent brains in vivo is still uncertain. Post-natal day 7 (P7) rats received a single injection of propofol 30 mg/kg intraperitoneally (i.p.), and neuroapoptosis of hippocampal astrocytes was analyzed by immunofluorescence and scanning electron microscopy. The differential expression of rno-miR-665, BCL2L1 (Bcl-xl), and cleaved caspase 3 (CC3) was surveyed by qRT-PCR and western blotting. In addition, the utility of A-1155463, a highly potent and BCL2L1-selective antagonist, was aimed to assess the contribution of BCL2L1 for neuroglial survival. Following the intraventricular injection of lentivirus rno-miR-665, neuroprotection was detected by 5-point scale measurement. The single dose of propofol 30 mg/kg triggered dose-dependent apoptosis of developing hippocampal astrocytes. Meanwhile, propofol triggered both rno-miR-665 and CC3, and depressed BCL2L1, which was predicted as one target gene of rno-miR-665. Combination treatment with A-1155463 and propofol induced lower mRNA and protein levels of BCL2L1 and more CC3 activation than propofol treatment alone in vivo. The lentivirus-mediated knockdown of rno-miR-665 elevated BCL2L1 and attenuated CC3 levels, whereas up-regulation of rno-miR-665 suppressed BCL2L1 and induced CC3 expression in vivo. More importantly, rno-miR-665 antagomir infusion improved neurological outcomes of pups receiving propofol during the brain growth spurt. Rno-miR-665, providing a potential target for alternative therapeutics for pediatric anesthesia, is susceptible to propofol by negatively targeting antiapoptotic BCL2L1. Relatively little is known about the association between exposure of astrocytes to brief propofol anaesthesia and risk for impairment. Here, it revealed that propofol-related neurotoxicity of neonatal astrocytes was under rno-miR-665 regulation during the brain growth spurt. Rno-miR-665 might act as a clinically alternative therapeutic target for treatment of neurological disorders in peadiatric anesthesia or sedation with propofol in future.
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Affiliation(s)
- Wen-Chong Sun
- Department of Anesthesiology, the First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Ling Pei
- Department of Anesthesiology, the First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
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17
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Shatizadeh Malekshahi S, Arefian E, Salimi V, Mokhtari Azad T, Yavarian J. Potential siRNA Molecules for Nucleoprotein and M2/L Overlapping Region of Respiratory Syncytial Virus: In Silico Design. Jundishapur J Microbiol 2016; 9:e34304. [PMID: 27303618 PMCID: PMC4902852 DOI: 10.5812/jjm.34304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/05/2015] [Accepted: 02/16/2016] [Indexed: 11/28/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in the pediatric population, elderly and in immunosuppressed individuals. Respiratory syncytial virus is also responsible for bronchiolitis, pneumonia, and chronic obstructive pulmonary infections in all age groups. With this high disease burden and the lack of an effective RSV treatment and vaccine, there is a clear need for discovery and development of novel, effective and safe drugs to prevent and treat RSV disease. The most innovative approach is the use of small interfering RNAs (siRNAs) which represent a revolutionary new concept in human therapeutics. The nucleoprotein gene of RSV which is known as the most conserved gene and the M2/L mRNA, which encompass sixty-eight overlapping nucleotides, were selected as suitable targets for siRNA design. Objectives The present study is aimed to design potential siRNAs for silencing nucleoprotein and an overlapping region of M2-L coding mRNAs by computational analysis. Materials and Methods Various computational methods (target alignment, similarity search, secondary structure prediction, and RNA interaction calculation) have been used for siRNA designing against different strains of RSV. Results In this study, seven siRNA molecules were rationally designed against the nucleoprotein gene and validated using various computational methods for silencing different strains of RSV. Additionally, three effective siRNA molecules targeting the overlapping region of M2/L mRNA were designed. Conclusions This approach provides insight and a validated strategy for chemical synthesis of an antiviral RNA molecule which meets many sequence features for efficient silencing and treatment at the genomic level.
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Affiliation(s)
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, IR Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Talat Mokhtari Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Jila Yavarian, Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran. Tel/Fax: +98-2188962343, E-mail:
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Khatodia S, Bhatotia K, Passricha N, Khurana SMP, Tuteja N. The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops. FRONTIERS IN PLANT SCIENCE 2016; 7:506. [PMID: 27148329 PMCID: PMC4835450 DOI: 10.3389/fpls.2016.00506] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2016] [Indexed: 05/18/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE) crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses.
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Affiliation(s)
- Surender Khatodia
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Kirti Bhatotia
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Nishat Passricha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - S. M. P. Khurana
- Amity Institute of Biotechnology, Amity University HaryanaGurgaon, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
- Amity Institute of Microbial Technology, Amity UniversityNoida, India
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19
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Challenges and opportunities for siRNA-based cancer treatment. Cancer Lett 2016; 387:77-83. [PMID: 27045474 DOI: 10.1016/j.canlet.2016.03.045] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/29/2016] [Accepted: 03/29/2016] [Indexed: 12/14/2022]
Abstract
As one of the life-threatening diseases involving multi-step genetic and epigenetic disorders, cancer has long been a dynamic research area for siRNA-based therapy as half of the current siRNA-based clinical trials are involved in oncology. However, despite consistent enthusiasm in the academic world, siRNA-based cancer treatment still faces obstacles and difficulties in clinical development. In this article, we discuss key challenges facing siRNA-based cancer treatment revealed from recent clinical and preclinical studies, including chemical modification, tumour penetration, endosomal escape, target selection and off-target effects. In addition, opportunities and avenues for translating siRNA technology from bench to oncologic clinics are explored.
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20
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Mayrhofer M, Mione M. The Toolbox for Conditional Zebrafish Cancer Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:21-59. [PMID: 27165348 DOI: 10.1007/978-3-319-30654-4_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Here we describe the conditional zebrafish cancer toolbox, which allows for fine control of the expression of oncogenes or downregulation of tumor suppressors at the spatial and temporal level. Methods such as the Gal4/UAS or the Cre/lox systems paved the way to the development of elegant tumor models, which are now being used to study cancer cell biology, clonal evolution, identification of cancer stem cells and anti-cancer drug screening. Combination of these tools, as well as novel developments such as the promising genome editing system through CRISPR/Cas9 and clever application of light reactive proteins will enable the development of even more sophisticated zebrafish cancer models. Here, we introduce this growing toolbox of conditional transgenic approaches, discuss its current application in zebrafish cancer models and provide an outlook on future perspectives.
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Affiliation(s)
- Marie Mayrhofer
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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21
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Regulatory RNA-assisted genome engineering in microorganisms. Curr Opin Biotechnol 2015; 36:85-90. [DOI: 10.1016/j.copbio.2015.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/18/2015] [Accepted: 08/09/2015] [Indexed: 01/05/2023]
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22
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Laganà A, Ferro A, Croce CM. Editorial: Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges. Front Bioeng Biotechnol 2015; 3:156. [PMID: 26501059 PMCID: PMC4597103 DOI: 10.3389/fbioe.2015.00156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/25/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - Alfredo Ferro
- Department of Clinical and Molecular Biomedicine, University of Catania , Catania , Italy
| | - Carlo Maria Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University , Columbus, OH , USA
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Wostenberg C, Ceres P, Polaski JT, Batey RT. A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol 2015; 427:3473-3490. [PMID: 26343759 DOI: 10.1016/j.jmb.2015.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/24/2023]
Abstract
RNA folding in vivo is significantly influenced by transcription, which is not necessarily recapitulated by Mg(2+)-induced folding of the corresponding full-length RNA in vitro. Riboswitches that regulate gene expression at the transcriptional level are an ideal system for investigating this aspect of RNA folding as ligand-dependent termination is obligatorily co-transcriptional, providing a clear readout of the folding outcome. The folding of representative members of the SAM-I family of riboswitches has been extensively analyzed using approaches focusing almost exclusively upon Mg(2+) and/or S-adenosylmethionine (SAM)-induced folding of full-length transcripts of the ligand binding domain. To relate these findings to co-transcriptional regulatory activity, we have investigated a set of structure-guided mutations of conserved tertiary architectural elements of the ligand binding domain using an in vitro single-turnover transcriptional termination assay, complemented with phylogenetic analysis and isothermal titration calorimetry data. This analysis revealed a conserved internal loop adjacent to the SAM binding site that significantly affects ligand binding and regulatory activity. Conversely, most single point mutations throughout key conserved features in peripheral tertiary architecture supporting the SAM binding pocket have relatively little impact on riboswitch activity. Instead, a secondary structural element in the peripheral subdomain appears to be the key determinant in observed differences in regulatory properties across the SAM-I family. These data reveal a highly coupled network of tertiary interactions that promote high-fidelity co-transcriptional folding of the riboswitch but are only indirectly linked to regulatory tuning.
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Affiliation(s)
- Christopher Wostenberg
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Pablo Ceres
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Jacob T Polaski
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA.
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Ho HL, Haynes K. Candida glabrata: new tools and technologies-expanding the toolkit. FEMS Yeast Res 2015; 15:fov066. [PMID: 26205243 PMCID: PMC4629792 DOI: 10.1093/femsyr/fov066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/29/2015] [Accepted: 07/15/2015] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a noticeable rise in fungal infections related to non-albicans Candida species, including Candida glabrata which has both intrinsic resistance to and commonly acquired resistance to azole antifungals. Phylogenetically, C. glabrata is more closely related to the mostly non-pathogenic model organism Saccharomyces cerevisiae than to other Candida species. Despite C. glabrata's designation as a pathogen by Wickham in 1957, relatively little is known about its mechanism of virulence. Over the past few years, technology to analyse the molecular basis of infection has developed rapidly, and here we briefly review the major advances in tools and technologies available to explore and investigate the virulence of C. glabrata that have occurred over the past decade.
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Affiliation(s)
- Hsueh-lui Ho
- Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Ken Haynes
- Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, UK
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Abstract
The most widely used approach for defining gene function is to reduce or completely disrupt its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to disrupt gene expression in many organisms. However, new biotechnological tools--specifically CRISPR-based technologies--have become available and are squeezing out RNAi dominance in mammalian cell studies. These seemingly competing technologies leave research investigators with the question: "Which technology should I use in my experiment?" This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools.
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Affiliation(s)
- Michael Boettcher
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, CA 94143, USA.
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