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Zhao X, Gao Q, Wang H, Yue J, An D, Li B, Yan F, Carmen SM, Zhao Y, Zhou H, Zhao M. syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in Nicotiana benthamiana. PLANT SIGNALING & BEHAVIOR 2024; 19:2358270. [PMID: 38796845 PMCID: PMC11135832 DOI: 10.1080/15592324.2024.2358270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.
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Affiliation(s)
- Xingyue Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Qian Gao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Haijuan Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianying Yue
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Derong An
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Bin Li
- Department of Tabacco Production, Sichuan Province Company of Tobacco Corporation in China, Chengdu, China
| | - Fangfang Yan
- Panzhihua City company of Sichuan province company of Tobacco Corporation in China, Panzhihua city, Sichuan provience, China
| | | | - Yuanzheng Zhao
- Department of Plant Protection, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingmin Zhao
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
- Department of Plant protection, Key Laboratory of the Development and Resource Utilization of Biological Pesticide in Inner Mongolia, Hohhot, China
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Ebrahimi P, Davoudi E, Sadeghian R, Zadeh AZ, Razmi E, Heidari R, Morowvat MH, Sadeghian I. In vivo and ex vivo gene therapy for neurodegenerative diseases: a promise for disease modification. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:7501-7530. [PMID: 38775852 DOI: 10.1007/s00210-024-03141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/01/2024] [Indexed: 10/04/2024]
Abstract
Neurodegenerative diseases (NDDs), including AD, PD, HD, and ALS, represent a growing public health concern linked to aging and lifestyle factors, characterized by progressive nervous system damage leading to motor and cognitive deficits. Current therapeutics offer only symptomatic management, highlighting the urgent need for disease-modifying treatments. Gene therapy has emerged as a promising approach, targeting the underlying pathology of diseases with diverse strategies including gene replacement, gene silencing, and gene editing. This innovative therapeutic approach involves introducing functional genetic material to combat disease mechanisms, potentially offering long-term efficacy and disease modification. With advancements in genomics, structural biology, and gene editing tools such as CRISPR/Cas9, gene therapy holds significant promise for addressing the root causes of NDDs. Significant progress in preclinical and clinical studies has demonstrated the potential of in vivo and ex vivo gene therapy to treat various NDDs, offering a versatile and precise approach in comparison to conventional treatments. The current review describes various gene therapy approaches employed in preclinical and clinical studies for the treatment of NDDs, including AD, PD, HD, and ALS, and addresses some of the key translational challenges in this therapeutic approach.
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Affiliation(s)
- Pouya Ebrahimi
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Elham Davoudi
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | | | - Amin Zaki Zadeh
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Emran Razmi
- Arak University of Medical Sciences, Arak, Iran
| | - Reza Heidari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Issa Sadeghian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Dume B, Licarete E, Banciu M. Advancing cancer treatments: The role of oligonucleotide-based therapies in driving progress. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102256. [PMID: 39045515 PMCID: PMC11264197 DOI: 10.1016/j.omtn.2024.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Although recent advancements in cancer immunology have resulted in the approval of numerous immunotherapies, minimal progress has been observed in addressing hard-to-treat cancers. In this context, therapeutic oligonucleotides, including interfering RNAs, antisense oligonucleotides, aptamers, and DNAzymes, have gained a central role in cancer therapeutic approaches due to their capacity to regulate gene expression and protein function with reduced toxicity compared with conventional chemotherapeutics. Nevertheless, systemic administration of naked oligonucleotides faces many extra- and intracellular challenges that can be overcome by using effective delivery systems. Thus, viral and non-viral carriers can improve oligonucleotide stability and intracellular uptake, enhance tumor accumulation, and increase the probability of endosomal escape while minimizing other adverse effects. Therefore, gaining more insight into fundamental mechanisms of actions of various oligonucleotides and the challenges posed by naked oligonucleotide administration, this article provides a comprehensive review of the recent progress on oligonucleotide delivery systems and an overview of completed and ongoing cancer clinical trials that can shape future oncological treatments.
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Affiliation(s)
- Bogdan Dume
- Doctoral School in Integrative Biology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Emilia Licarete
- Department of Molecular Biology and Biotechnology, Centre of Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Manuela Banciu
- Department of Molecular Biology and Biotechnology, Centre of Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
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Vempuluru VS, Maniar A, Bakal K, Kaliki S. Role of MYCN in retinoblastoma: A review of current literature. Surv Ophthalmol 2024; 69:697-706. [PMID: 38796108 DOI: 10.1016/j.survophthal.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Chromosomal abnormalities that involve the MYCN gene are rare; however, it is one of the most commonly mutated genes in retinoblastoma (RB) after the RB1 gene. MYCN is amplified in approximately 1-9 % of all RB tumors. It plays a role in RB oncogenesis via many mechanisms, including synergism with RB1 deletion, positive feedback with MDM2, upregulation of cell cycle regulating genes, upregulation of miRNA, and upregulation of glucose metabolism. MYCN amplifications are not mutually exclusive and can occur even in the presence of RB1 gene mutations. Clinically, RB1+/+MYCNA tumors present as sporadic, unilateral, advanced tumors in very young children and tend to follow an aggressive course. Magnetic resonance imaging features include peripheral tumor location, placoid configuration, retinal folding, tumor-associated hemorrhage, and anterior chamber enhancement. Genetic testing for MYCNA is especially recommended in patients with unilateral RB where genetic blood testing and tumor tissue show a lack of RB1 mutation. MYCN-targeted therapies are evolving and hold promise for the future.
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Affiliation(s)
- Vijitha S Vempuluru
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Arpita Maniar
- Duke Eye Center, Duke University, Durham, NC 27705, USA
| | - Komal Bakal
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Swathi Kaliki
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Hyderabad 500034, India.
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Chen G, Lai S, Jiang S, Li F, Sun K, Wu X, Zhou K, Liu Y, Deng X, Chen Z, Xu F, Xu Y, Wang K, Cao G, Xu F, Bi GQ, Zhu Y. Cellular and circuit architecture of the lateral septum for reward processing. Neuron 2024; 112:2783-2798.e9. [PMID: 38959892 DOI: 10.1016/j.neuron.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/29/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
The lateral septum (LS) is composed of heterogeneous cell types that are important for various motivated behaviors. However, the transcriptional profiles, spatial arrangement, function, and connectivity of these cell types have not been systematically studied. Using single-nucleus RNA sequencing, we delineated diverse genetically defined cell types in the LS that play distinct roles in reward processing. Notably, we found that estrogen receptor 1 (Esr1)-expressing neurons in the ventral LS (LSEsr1) are key drivers of reward seeking via projections to the ventral tegmental area, and these neurons play an essential role in methamphetamine (METH) reward and METH-seeking behavior. Extended exposure to METH increases the excitability of LSEsr1 neurons by upregulating hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, thereby contributing to METH-induced locomotor sensitization. These insights not only elucidate the intricate molecular, circuit, and functional architecture of the septal region in reward processing but also reveal a neural pathway critical for METH reward and behavioral sensitization.
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Affiliation(s)
- Gaowei Chen
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shishi Lai
- Yunnan University School of Medicine, Yunnan University, Kunming 650091, China; Southwest United Graduate School, Kunming 650092, China
| | - Shaolei Jiang
- University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fengling Li
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kaige Sun
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shandong Normal University, Jinan 250014, China
| | - Xiaocong Wu
- Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Kuikui Zhou
- University of Health and Rehabilitation Sciences, Qingdao 266000, China
| | - Yutong Liu
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaofei Deng
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zijun Chen
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fang Xu
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yu Xu
- Yunnan Technological Innovation Centre of Drug Addiction Medicine, Yunnan University, Kunming 650091, China
| | - Kunhua Wang
- Yunnan Technological Innovation Centre of Drug Addiction Medicine, Yunnan University, Kunming 650091, China
| | - Gang Cao
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuqiang Xu
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guo-Qiang Bi
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingjie Zhu
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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6
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Yun S, Noh M, Yu J, Kim HJ, Hui CC, Lee H, Son JE. Unlocking biological mechanisms with integrative functional genomics approaches. Mol Cells 2024; 47:100092. [PMID: 39019219 PMCID: PMC11345568 DOI: 10.1016/j.mocell.2024.100092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Reverse genetics offers precise functional insights into genes through the targeted manipulation of gene expression followed by phenotypic assessment. While these approaches have proven effective in model organisms such as Saccharomyces cerevisiae, large-scale genetic manipulations in human cells were historically unfeasible due to methodological limitations. However, recent advancements in functional genomics, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-based screening technologies and next-generation sequencing platforms, have enabled pooled screening technologies that allow massively parallel, unbiased assessments of biological phenomena in human cells. This review provides a comprehensive overview of cutting-edge functional genomic screening technologies applicable to human cells, ranging from short hairpin RNA screens to modern CRISPR screens. Additionally, we explore the integration of CRISPR platforms with single-cell approaches to monitor gene expression, chromatin accessibility, epigenetic regulation, and chromatin architecture following genetic perturbations at the omics level. By offering an in-depth understanding of these genomic screening methods, this review aims to provide insights into more targeted and effective strategies for genomic research and personalized medicine.
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Affiliation(s)
- Sehee Yun
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Minsoo Noh
- Department of Life Sciences, Korea University, Seoul 02841, Korea; Department of Internal Medicine and Laboratory of Genomics and Translational Medicine, Gachon University College of Medicine, Incheon 21565, Korea
| | - Jivin Yu
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyeon-Jai Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hunsang Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Joe Eun Son
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea.
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7
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Lazar NH, Celik S, Chen L, Fay MM, Irish JC, Jensen J, Tillinghast CA, Urbanik J, Bone WP, Gibson CC, Haque IS. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing. Nat Genet 2024; 56:1482-1493. [PMID: 38811841 PMCID: PMC11250378 DOI: 10.1038/s41588-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Affiliation(s)
| | | | - Lu Chen
- Recursion, Salt Lake City, UT, USA
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8
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Haldrup SH, Fabian-Jessing BK, Jakobsen TS, Lindholm AB, Adsersen RL, Aagaard L, Bek T, Askou AL, Corydon TJ. Subretinal AAV delivery of RNAi-therapeutics targeting VEGFA reduces choroidal neovascularization in a large animal model. Mol Ther Methods Clin Dev 2024; 32:101242. [PMID: 38605811 PMCID: PMC11007540 DOI: 10.1016/j.omtm.2024.101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
Neovascular age-related macular degeneration (nAMD) is a frequent cause of vision loss among the elderly in the Western world. Current disease management with repeated injections of anti-VEGF agents accumulates the risk for adverse events and constitutes a burden for society and the individual patient. Sustained suppression of VEGF using gene therapy is an attractive alternative, which we explored using adeno-associated virus (AAV)-based delivery of novel RNA interference (RNAi) effectors in a porcine model of choroidal neovascularization (CNV). The potency of VEGFA-targeting, Ago2-dependent short hairpin RNAs placed in pri-microRNA scaffolds (miR-agshRNA) was established in vitro and in vivo in mice. Subsequently, AAV serotype 8 (AAV2.8) vectors encoding VEGFA-targeting or irrelevant miR-agshRNAs under the control of a tissue-specific promotor were delivered to the porcine retina via subretinal injection before CNV induction by laser. Notably, VEGFA-targeting miR-agshRNAs resulted in a significant and sizable reduction of CNV compared with the non-targeting control. We also demonstrated that single-stranded and self-complementary AAV2.8 vectors efficiently transduce porcine retinal pigment epithelium cells but differ in their transduction characteristics and retinal safety. Collectively, our data demonstrated a robust anti-angiogenic effect of VEGFA-targeting miR-aghsRNAs in a large translational animal model, thereby suggesting AAV-based delivery of anti-VEGFA RNAi therapeutics as a valuable tool for the management of nAMD.
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Affiliation(s)
- Silja Hansen Haldrup
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Bjørn K. Fabian-Jessing
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Thomas Stax Jakobsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Anna Bøgh Lindholm
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Rikke L. Adsersen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Toke Bek
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Anne Louise Askou
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
| | - Thomas J. Corydon
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, 8200 Aarhus N, Denmark
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Meslin PA, Kelly LM, Benbarche S, Lecourt S, Lin K, Rutter J, Bassil C, Itzykson R, Wood K, Puissant A, Lobry C. PitViper: a software for comparative meta-analysis and annotation of functional screening data. NAR Genom Bioinform 2024; 6:lqae059. [PMID: 38800827 PMCID: PMC11127635 DOI: 10.1093/nargab/lqae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/19/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Recent advancements in shRNA and Cas protein technologies have enabled functional screening methods targeting genes or non-coding regions using single or pooled shRNA and sgRNA. CRISPR-based systems have also been developed for modulating DNA accessibility, resulting in CRISPR-mediated interference (CRISPRi) or activation (CRISPRa) of targeted genes or genomic DNA elements. However, there is still a lack of software tools for integrating diverse array of functional genomics screening outputs that could offer a cohesive framework for comprehensive data integration. Here, we developed PitViper, a flexible and interactive open-source software designed to fill this gap, providing reliable results for the type of elements being screened. It is an end-to-end automated and reproducible bioinformatics pipeline integrating gold-standard methods for functional screening analysis. Our sensitivity analyses demonstrate that PitViper is a useful tool for identifying potential super-enhancer liabilities in a leukemia cell line through genome-wide CRISPRi-based screening. It offers a robust, flexible, and interactive solution for integrating data analysis and reanalysis from functional screening methods, making it a valuable resource for researchers in the field.
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Affiliation(s)
- Paul-Arthur Meslin
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Lois M Kelly
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Salima Benbarche
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Séverine Lecourt
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
- Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Kevin H Lin
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Justine C Rutter
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | | | - Raphael Itzykson
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
- Department of Hematology, Saint Louis Hospital, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Alexandre Puissant
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
| | - Camille Lobry
- Université de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France
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10
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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11
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Bains S, Giudicessi JR, Odening KE, Ackerman MJ. State of Gene Therapy for Monogenic Cardiovascular Diseases. Mayo Clin Proc 2024; 99:610-629. [PMID: 38569811 DOI: 10.1016/j.mayocp.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/03/2023] [Indexed: 04/05/2024]
Abstract
Over the past 2 decades, significant efforts have been made to advance gene therapy into clinical practice. Although successful examples exist in other fields, gene therapy for the treatment of monogenic cardiovascular diseases lags behind. In this review, we (1) highlight a brief history of gene therapy, (2) distinguish between gene silencing, gene replacement, and gene editing technologies, (3) discuss vector modalities used in the field with a special focus on adeno-associated viruses, (4) provide examples of gene therapy approaches in cardiomyopathies, channelopathies, and familial hypercholesterolemia, and (5) present current challenges and limitations in the gene therapy field.
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Affiliation(s)
- Sahej Bains
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, MN; Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN
| | - John R Giudicessi
- Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN; Department of Cardiovascular Medicine (Division of Heart Rhythm Services and Circulatory Failure and the Windland Smith Rice Genetic Heart Rhythm Clinic), Mayo Clinic, Rochester, MN
| | - Katja E Odening
- Translational Cardiology, Department of Cardiology and Department of Physiology, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Michael J Ackerman
- Department of Molecular Pharmacology and Experimental Therapeutics (Windland Smith Rice Sudden Death Genomics Laboratory), Mayo Clinic, Rochester, MN; Department of Cardiovascular Medicine (Division of Heart Rhythm Services and Circulatory Failure and the Windland Smith Rice Genetic Heart Rhythm Clinic), Mayo Clinic, Rochester, MN; Department of Pediatric and Adolescent Medicine (Division of Pediatric Cardiology), Mayo Clinic, Rochester, MN.
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12
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Hosseini SM, Borys B, Karimi-Abdolrezaee S. Neural stem cell therapies for spinal cord injury repair: an update on recent preclinical and clinical advances. Brain 2024; 147:766-793. [PMID: 37975820 DOI: 10.1093/brain/awad392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Traumatic spinal cord injury (SCI) is a leading cause of lifelong disabilities. Permanent sensory, motor and autonomic impairments after SCI are substantially attributed to degeneration of spinal cord neurons and axons, and disintegration of neural network. To date, minimal regenerative treatments are available for SCI with an unmet need for new therapies to reconstruct the damaged spinal cord neuron-glia network and restore connectivity with the supraspinal pathways. Multipotent neural precursor cells (NPCs) have a unique capacity to generate neurons, oligodendrocytes and astrocytes. Due to this capacity, NPCs have been an attractive cell source for cellular therapies for SCI. Transplantation of NPCs has been extensively tested in preclinical models of SCI in the past two decades. These studies have identified opportunities and challenges associated with NPC therapies. While NPCs have the potential to promote neuroregeneration through various mechanisms, their low long-term survival and integration within the host injured spinal cord limit the functional benefits of NPC-based therapies for SCI. To address this challenge, combinatorial strategies have been developed to optimize the outcomes of NPC therapies by enriching SCI microenvironment through biomaterials, genetic and pharmacological therapies. In this review, we will provide an in-depth discussion on recent advances in preclinical NPC-based therapies for SCI. We will discuss modes of actions and mechanism by which engrafted NPCs contribute to the repair process and functional recovery. We will also provide an update on current clinical trials and new technologies that have facilitated preparation of medical-grade human NPCs suitable for transplantation in clinical studies.
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Affiliation(s)
- Seyed Mojtaba Hosseini
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Multiple Sclerosis Research Center, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ben Borys
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
| | - Soheila Karimi-Abdolrezaee
- Department of Physiology and Pathophysiology, Spinal Cord Research Centre, Rady Faculty of Health Sciences, University of Manitoba Winnipeg, Manitoba R3E 0J9, Canada
- Manitoba Multiple Sclerosis Research Center, Winnipeg, Manitoba R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
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13
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Le CT, Nguyen TD, Nguyen TA. Two-motif model illuminates DICER cleavage preferences. Nucleic Acids Res 2024; 52:1860-1877. [PMID: 38167721 PMCID: PMC10899750 DOI: 10.1093/nar/gkad1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/25/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
In humans, DICER is a key regulator of gene expression through its production of miRNAs and siRNAs by processing miRNA precursors (pre-miRNAs), short-hairpin RNAs (shRNAs), and long double-stranded RNAs (dsRNAs). To advance our understanding of this process, we employed high-throughput dicing assays using various shRNA variants and both wild-type and mutant DICER. Our analysis revealed that DICER predominantly cleaves shRNAs at two positions, specifically at 21 (DC21) and 22 (DC22) nucleotides from their 5'-end. Our investigation identified two different motifs, mWCU and YCR, that determine whether DICER cleaves at DC21 or DC22, depending on their locations in shRNAs/pre-miRNAs. These motifs can work together or independently to determine the cleavage sites of DICER. Furthermore, our findings indicate that dsRNA-binding domain (dsRBD) of DICER enhances its cleavage, and mWCU strengthens the interaction between dsRBD and RNA, leading to an even greater enhancement of the cleavage. Conversely, YCR functions independently of dsRBD. Our study proposes a two-motif model that sheds light on the intricate regulatory mechanisms involved in gene expression by elucidating how DICER recognizes its substrates, providing valuable insights into this critical biological process.
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Affiliation(s)
- Cong Truc Le
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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14
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Zhang F, Qiao W, Wei JA, Tao Z, Chen C, Wu Y, Lin M, Ng KMC, Zhang L, Yeung KWK, Chow BKC. Secretin-dependent signals in the ventromedial hypothalamus regulate energy metabolism and bone homeostasis in mice. Nat Commun 2024; 15:1030. [PMID: 38310104 PMCID: PMC10838336 DOI: 10.1038/s41467-024-45436-3] [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: 04/05/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Secretin, though originally discovered as a gut-derived hormone, is recently found to be abundantly expressed in the ventromedial hypothalamus, from which the central neural system controls satiety, energy metabolism, and bone homeostasis. However, the functional significance of secretin in the ventromedial hypothalamus remains unclear. Here we show that the loss of ventromedial hypothalamus-derived secretin leads to osteopenia in male and female mice, which is primarily induced by diminished cAMP response element-binding protein phosphorylation and upregulation in peripheral sympathetic activity. Moreover, the ventromedial hypothalamus-secretin inhibition also contributes to hyperphagia, dysregulated lipogenesis, and impaired thermogenesis, resulting in obesity in male and female mice. Conversely, overexpression of secretin in the ventromedial hypothalamus promotes bone mass accrual in mice of both sexes. Collectively, our findings identify an unappreciated secretin signaling in the central neural system for the regulation of energy and bone metabolism, which may serve as a new target for the clinical management of obesity and osteoporosis.
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Affiliation(s)
- Fengwei Zhang
- School of Biological Sciences, the University of Hong Kong, Hong Kong, China
| | - Wei Qiao
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, the University of Hong Kong, Hong Kong, China.
- Shenzhen Key Laboratory for Innovative Technology in Orthopaedic Trauma, the University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
| | - Ji-An Wei
- School of Biological Sciences, the University of Hong Kong, Hong Kong, China
- Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Zhengyi Tao
- School of Biological Sciences, the University of Hong Kong, Hong Kong, China
| | - Congjia Chen
- School of Biological Sciences, the University of Hong Kong, Hong Kong, China
| | - Yefeng Wu
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, the University of Hong Kong, Hong Kong, China
| | - Minghui Lin
- School of Biological Sciences, the University of Hong Kong, Hong Kong, China
| | - Ka Man Carmen Ng
- School of Biological Sciences, the University of Hong Kong, Hong Kong, China
| | - Li Zhang
- Key Laboratory of CNS Regeneration (Ministry of Education), GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
- Neuroscience and Neurorehabilitation Institute, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Kelvin Wai-Kwok Yeung
- Shenzhen Key Laboratory for Innovative Technology in Orthopaedic Trauma, the University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China.
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15
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Jamal A, Usman S, Teh MT, Waseem A. Preparation and Use of shRNA for Knocking Down Specific Genes. Methods Mol Biol 2024; 2849:55-72. [PMID: 38411888 DOI: 10.1007/7651_2024_515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Short hairpin RNA (shRNA) is a technique used to silence gene expression stably in various cells. There are however several reported problems. First, the cloning of oligos can lead to ligation of multiple copies; second, premature termination of sequencing reaction during confirmation of hairpin template; third, microdeletions/substitutions in hairpin during cloning; and fourth, off target effects. In this chapter, we have described a retrovirus transduction-based protocol that can be used on cells in culture without encountering any of the reported issues. We have used this protocol to clone shRNA templates for at least 10 different genes and confirmed them by dideoxy sequencing. The knockdown of 75-90% for two mRNA expressing genes, CDH5 and keratin KRT80, and a long non-coding RNA, XIST, is presented here.
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Affiliation(s)
- Ahmad Jamal
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Saima Usman
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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16
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Hinton SD. Understanding Pseudophosphatase Function Through Biochemical Interactions. Methods Mol Biol 2024; 2743:21-41. [PMID: 38147206 DOI: 10.1007/978-1-0716-3569-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pseudophosphatases have been solidified as important signaling molecules that regulate signal transduction cascades. However, their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this does not preclude their having other functions, including as integral elements of signaling networks. Thus, understanding their roles may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [MAPK (mitogen-activated protein kinase) phospho-serine-threonine/tyrosine-binding], which has been linked to tumorigenesis, hepatocellular carcinoma, glioblastoma, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase, so the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalian cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). We also provide a bioinformatic approach to investigating MK-STYX and MK-STYX(active mutant). These bioinformatic approaches can stand alone experimentally but also complement and enhance "wet" bench approaches such as binding assays and/or activity assays. A combination of cellular, molecular, biochemical, proteomic, and bioinformatic techniques has been a powerful tool in identifying novel functions of MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the functions of other pseudophosphatases.
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Affiliation(s)
- Shantá D Hinton
- Department of Biology, College of William and Mary, Williamsburg, VA, USA.
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17
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Liu S. RNA Interference Ex Vivo. Methods Mol Biol 2024; 2766:145-151. [PMID: 38270874 DOI: 10.1007/978-1-0716-3682-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
RNA interference (RNAi) is a widely used technique to regulate the expression of genes and proteins with a high degree of specificity that is not easily accessed by traditional pharmacological approaches. For preclinical research on rheumatoid arthritis (RA), silencing of target genes in primary immune cells can be easily achieved by the application of small interfering RNA (siRNA) and synthetic short hairpin RNA (shRNA). Cellular and systemic administration of siRNA or shRNA has been a significant advance in preclinical research on RA. In this chapter, the basic techniques for gene silencing in human-derived peripheral T cells using liposome-dependent siRNA transfection and lentiviral-mediated shRNA delivery, aiming at gene silencing of therapeutic targets, are introduced.
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Affiliation(s)
- Shuang Liu
- Department of Pharmacology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan.
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18
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Yadav D, Malviya R. Vector-Mediated Delivery of Transgenes and RNA Interference-Based Gene Silencing Sequences to Astrocytes for Disease Management: Advances and Prospectives. Curr Gene Ther 2024; 24:110-121. [PMID: 37921145 DOI: 10.2174/0115665232264527231013072728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 11/04/2023]
Abstract
Astrocytes are a type of important glial cell in the brain that serve crucial functions in regulating neuronal activity, facilitating communication between neurons, and keeping everything in balance. In this abstract, we explore current methods and future approaches for using vectors to precisely target astrocytes in the fight against various illnesses. In order to deliver therapeutic cargo selectively to astrocytes, researchers have made tremendous progress by using viral vectors such as adeno-associated viruses (AAVs) and lentiviruses. It has been established that engineered viral vectors are capable of either crossing the blood-brain barrier (BBB) or being delivered intranasally, which facilitates their entrance into the brain parenchyma. These vectors are able to contain transgenes that code for neuroprotective factors, synaptic modulators, or anti-inflammatory medicines, which pave the way for multiple approaches to disease intervention. Strategies based on RNA interference (RNAi) make vector-mediated astrocyte targeting much more likely to work. Small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) are two types of RNA that can be made to silence disease-related genes in astrocytes. Vector-mediated delivery in conjunction with RNAi techniques provides a powerful toolkit for investigating the complex biological pathways that contribute to disease development. However, there are still a number of obstacles to overcome in order to perfect the specificity, safety, and duration of vector-mediated astrocyte targeting. In order to successfully translate research findings into clinical practise, it is essential to minimise off-target effects and the risk of immunogenicity. To demonstrate the therapeutic effectiveness of these strategies, rigorous preclinical investigation and validation are required.
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Affiliation(s)
- Deepika Yadav
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
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19
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Ma Y, Li S, Lin X, Chen Y. Bioinspired Spatiotemporal Management toward RNA Therapies. ACS NANO 2023; 17:24539-24563. [PMID: 38091941 DOI: 10.1021/acsnano.3c08219] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Ribonucleic acid (RNA)-based therapies have become an attractive topic in disease intervention, especially with some that have been approved by the FDA such as the mRNA COVID-19 vaccine (Comirnaty, Pfizer-BioNTech, and Spikevax, Moderna) and Patisiran (siRNA-based drug for liver delivery). However, extensive applications are still facing challenges in delivering highly negatively charged RNA to the targeted site. Therapeutic delivery strategies including RNA modifications, RNA conjugates, and RNA polyplexes and delivery platforms such as viral vectors, nanoparticle-based delivery platforms, and hydrogel-based delivery platforms as potential nucleic acid-releasing depots have been developed to enhance their cellular uptake and protect nucleic acid from being degraded by immune systems. Here, we review the growing number of viral vectors, nanoparticles, and hydrogel-based RNA delivery systems; describe RNA loading/release mechanism induced by environmental stimulations including light, heat, pH, or enzyme; discuss their physical or chemical interactions; and summarize the RNA therapeutics release period (temporal) and their target cells/organs (spatial). Finally, we describe current concerns, highlight current challenges and future perspectives of RNA-based delivery systems, and provide some possible research areas that provide opportunities for clinical translation of RNA delivery carriers.
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Affiliation(s)
- Yutian Ma
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shiyao Li
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xin Lin
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27705, United States
| | - Yupeng Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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20
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Zareie AR, Verma SC. Nucleolin Regulates the Expression of Kaposi's Sarcoma-Associated Herpesvirus' Latency-Associated Nuclear Antigen through G-Quadruplexes in the mRNA. Viruses 2023; 15:2438. [PMID: 38140679 PMCID: PMC10747643 DOI: 10.3390/v15122438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) establishes life-long latent infection and is linked to several human malignancies. Latency-associated nuclear antigen (LANA) is highly expressed during latency, and is responsible for the replication and maintenance of the viral genome. The expression of LANA is regulated at transcriptional/translational levels through multiple mechanisms, including the secondary structures in the mRNA sequence. LANA mRNA has multiple G-quadruplexes (G4s) that are bound by multiple proteins to stabilize/destabilize these secondary structures for regulating LANA. In this manuscript, we demonstrate the role of Nucleolin (NCL) in regulating LANA expression through its interaction with G-quadruplexes of LANA mRNA. This interaction reduced LANA's protein expression through the sequestration of mRNA into the nucleus, demonstrated by the colocalization of G4-carrying mRNA with NCL. Furthermore, the downregulation of NCL, by way of a short hairpin, showed an increase in LANA translation following an alteration in the levels of LANA mRNA in the cytoplasm. Overall, the data presented in this manuscript showed that G-quadruplexes-mediated translational control could be regulated by NCL, which can be exploited for controlling KSHV latency.
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Affiliation(s)
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA;
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21
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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22
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Chen K, Wei X, Wang R, Yang L, Zou D, Wang Y. BMP7 alleviates trigeminal neuralgia by reducing oligodendrocyte apoptosis and demyelination. J Headache Pain 2023; 24:143. [PMID: 37875834 PMCID: PMC10594892 DOI: 10.1186/s10194-023-01681-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND BMP7 has been shown to have neuroprotective effects and to alleviate demyelination. However, its role in trigeminal neuralgia (TN) has not been well investigated. The current study aims to determine whether BMP7 plays a role in demyelination, its effects on pain behaviors and mechanism of action in rats with TN. METHODS We used an infraorbital-nerve chronic-constriction injury (ION-CCI) to establish a rat model of TN. Adeno-associated viruses (AAVs) were injected into the rats to upregulate or downregulate BMP7. The mechanical withdrawal thresholds (MWT) of the injured rats were detected using Von Frey filaments. The changes in expression levels of BMP7 and oligodendrocyte (OL) markers were examined by western blotting, quantitative real-time PCR, immunofluorescence, and transmission electron microscopy. RESULTS The ION-CCI induced mechanical allodynia, demyelination, and loss of OLs with a reduction of BMP7. Short-hairpin RNA (shRNA)-BMP7 that inhibited BMP7 expression also caused mechanical allodynia, demyelination, and loss of OLs, and its mechanism may be OL apoptosis. Overexpressing BMP7 in the trigeminal spinal subnucleus caudalis(VC) with AAV-BMP7 relieved all three phenotypes induced by the CCI, and its mechanism may be alleviating OLs apoptosis. Two signal pathways associated with apoptosis, STAT3 and p65, were significantly downregulated in the VC after CCI and rescued by BMP7 overexpression. CONCLUSION BMP7 can alleviate TN by reducing OLs apoptosis and subsequent demyelination. The mechanism behind this protection could be BMP7-mediated activation of the STAT3 and NF-κB/p65 signaling pathway and subsequent decrease in OL apoptosis. Importantly, our study presents clear evidence in support of BMP7 as a possible therapeutic target for the treatment of TN.
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Affiliation(s)
- Kai Chen
- Department of Pain Management and Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Pain Medicine in Hunan Province, Changsha, Hunan, China
| | - Xiaojin Wei
- Department of Pain Management and Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100054, China
| | - Ruixuan Wang
- Bourns Engineering, The University of California, Riverside, CA, 92521, USA
| | - Lin Yang
- Department of Pain Management and Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Pain Medicine in Hunan Province, Changsha, Hunan, China
| | - Dingquan Zou
- Department of Pain Management and Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center for Pain Medicine in Hunan Province, Changsha, Hunan, China
| | - Yaping Wang
- Department of Pain Management and Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Pain Medicine in Hunan Province, Changsha, Hunan, China.
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23
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Du Y, Luo L, Xu X, Yang X, Yang X, Xiong S, Yu J, Liang T, Guo L. Unleashing the Power of Synthetic Lethality: Augmenting Treatment Efficacy through Synergistic Integration with Chemotherapy Drugs. Pharmaceutics 2023; 15:2433. [PMID: 37896193 PMCID: PMC10610204 DOI: 10.3390/pharmaceutics15102433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Cancer is the second leading cause of death in the world, and chemotherapy is one of the main methods of cancer treatment. However, the resistance of cancer cells to chemotherapeutic drugs has always been the main reason affecting the therapeutic effect. Synthetic lethality has emerged as a promising approach to augment the sensitivity of cancer cells to chemotherapy agents. Synthetic lethality (SL) refers to the specific cell death resulting from the simultaneous mutation of two non-lethal genes, which individually allow cell survival. This comprehensive review explores the classification of SL, screening methods, and research advancements in SL inhibitors, including Poly (ADP-ribose) polymerase (PARP) inhibitors, Ataxia telangiectasia and Rad3-related (ATR) inhibitors, WEE1 G2 checkpoint kinase (WEE1) inhibitors, and protein arginine methyltransferase 5 (PRMT5) inhibitors. Emphasizing their combined use with chemotherapy drugs, we aim to unveil more effective treatment strategies for cancer patients.
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Affiliation(s)
- Yajing Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.D.); (L.L.); (X.X.); (X.Y.)
| | - Lulu Luo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.D.); (L.L.); (X.X.); (X.Y.)
| | - Xinru Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.D.); (L.L.); (X.X.); (X.Y.)
| | - Xinbing Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.D.); (L.L.); (X.X.); (X.Y.)
| | - Xueni Yang
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (X.Y.); (S.X.)
| | - Shizheng Xiong
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (X.Y.); (S.X.)
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China;
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.D.); (L.L.); (X.X.); (X.Y.)
| | - Li Guo
- Department of Bioinformatics, Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (X.Y.); (S.X.)
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Koo J, Gurusamy D, Palli SR. Inefficient uptake of small interfering RNAs is responsible for their inability to trigger RNA interference in Colorado potato beetle cells. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-12. [PMID: 37452750 PMCID: PMC10528746 DOI: 10.1002/arch.22036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
There has been limited success in the usage of exogenous small interference RNA (siRNA) or small hairpin RNA (shRNA) to trigger RNA interference (RNAi) in insects. Instead, long double-stranded RNAs (dsRNA) are used to induce knockdown of target genes in insects. Here, we compared the potency of si/sh RNAs and dsRNA in Colorado potato beetle (CPB) cells. CPB cells showed highly efficient RNAi response to dsRNA. However, si/sh RNAs were inefficient in triggering RNAi in CPB cells. Confocal microscopy observations of Cy3 labeled-si/sh RNA cellular uptake revealed reduced si/sh RNA uptake compared to dsRNA. si/sh RNAs were stable in the conditioned media of CPB cells. Although in a small amount, when internalized by CPB cells, the si/sh RNAs were processed by the Dicer enzyme. Lipid-mediated transfection and chimeric dsRNA approaches were used to improve the delivery of si/sh RNAs. Our results suggest that the uptake of si/sh RNAs is inefficient in CPB cells, resulting in ineffective RNAi response. However, with the help of effective delivery methods, si/sh RNA could be a useful option for developing target-specific RNAi-mediated biopesticides.
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Affiliation(s)
- Jinmo Koo
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
| | - Dhandapani Gurusamy
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
- Current address, Department of Botany, Kongunadu Arts and Science College (Autonomous), Bharathiar University, Coimbatore, India
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
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Corydon IJ, Fabian-Jessing BK, Jakobsen TS, Jørgensen AC, Jensen EG, Askou AL, Aagaard L, Corydon TJ. 25 years of maturation: A systematic review of RNAi in the clinic. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:469-482. [PMID: 37583575 PMCID: PMC10424002 DOI: 10.1016/j.omtn.2023.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The year 2023 marks the 25th anniversary of the discovery of RNAi. RNAi-based therapeutics enable sequence-specific gene knockdown by eliminating target RNA molecules through complementary base-pairing. A systematic review of published and ongoing clinical trials was performed. Web of Science, PubMed, and Embase were searched from January 1, 1998, to December 30, 2022 for clinical trials using RNAi. Following inclusion, data from the articles were extracted according to a predefined protocol. A total of 90 trials published in 81 articles were included. In addition, ongoing clinical trials were retrieved from ClinicalTrials.gov, resulting in the inclusion of 48 trials. We investigated how maturation of RNAi-based therapeutics and developments in delivery platforms, administration routes, and potential targets shape the current landscape of clinically applied RNAi. Notably, most contemporary clinical trials used either N-acetylgalactosamine delivery and subcutaneous administration or lipid nanoparticle delivery and intravenous administration. In conclusion, RNAi therapeutics have gained great momentum during the past decade, resulting in five approved therapeutics targeting the liver for treatment of severe diseases, and the trajectory depicted by the ongoing trials emphasizes that even more RNAi-based medicines also targeting extra-hepatic tissues are likely to be available in the years to come.
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Affiliation(s)
- Ida Juhl Corydon
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Bjørn Kristensen Fabian-Jessing
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| | - Thomas Stax Jakobsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| | | | - Emilie Grarup Jensen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Anne Louise Askou
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
| | - Thomas Juhl Corydon
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 167, Aarhus N, Denmark
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26
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Teotia S, Wang X, Zhou N, Wang M, Liu H, Qin J, Han D, Li C, Li CE, Pan S, Tang H, Kang W, Zhang Z, Tang X, Peng T, Tang G. A high-efficiency gene silencing in plants using two-hit asymmetrical artificial MicroRNAs. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1799-1811. [PMID: 37392408 PMCID: PMC10440985 DOI: 10.1111/pbi.14091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/21/2023] [Accepted: 05/15/2023] [Indexed: 07/03/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. They are produced through an enzyme-guided process called dicing and have an asymmetrical structure with two nucleotide overhangs at the 3' ends. Artificial microRNAs (amiRNAs or amiRs) are designed to mimic the structure of miRNAs and can be used to silence specific genes of interest. Traditionally, amiRNAs are designed based on an endogenous miRNA precursor with certain mismatches at specific positions to increase their efficiency. In this study, the authors modified the highly expressed miR168a in Arabidopsis thaliana by replacing the single miR168 stem-loop/duplex with tandem asymmetrical amiRNA duplexes that follow the statistical rules of miRNA secondary structures. These tandem amiRNA duplexes, called "two-hit" amiRNAs, were shown to have a higher efficiency in silencing GFP and endogenous PDS reporter genes compared to traditional "one-hit" amiRNAs. The authors also demonstrated the effectiveness of "two-hit" amiRNAs in silencing genes involved in miRNA, tasiRNA, and hormone signalling pathways, individually or in families. Importantly, "two-hit" amiRNAs were also able to over-express endogenous miRNAs for their functions. The authors compare "two-hit" amiRNA technology with CRISPR/Cas9 and provide a web-based amiRNA designer for easy design and wide application in plants and even animals.
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Affiliation(s)
- Sachin Teotia
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
- Department of Biological SciencesMichigan Technological UniversityHoughtonMichiganUSA
- Department of BiotechnologySharda UniversityGreater NoidaIndia
| | - Xiaoran Wang
- School of Life SciencesHenan Agricultural UniversityZhengzhouChina
| | - Na Zhou
- School of Life SciencesHenan Agricultural UniversityZhengzhouChina
| | - Mengmeng Wang
- School of Life SciencesHenan Agricultural UniversityZhengzhouChina
| | - Haiping Liu
- Department of Biological SciencesMichigan Technological UniversityHoughtonMichiganUSA
| | - Jun Qin
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Dianwei Han
- Department of Computer ScienceUniversity of KentuckyLexingtonKentuckyUSA
| | - Chingwen Li
- SQS Lexington Delivery CenterLexingtonKentuckyUSA
| | | | - Shangjin Pan
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Haifeng Tang
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Wenjun Kang
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Zhanhui Zhang
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiaoqing Tang
- Department of Biological SciencesMichigan Technological UniversityHoughtonMichiganUSA
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Ting Peng
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Guiliang Tang
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
- Department of Biological SciencesMichigan Technological UniversityHoughtonMichiganUSA
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development CenterUniversity of KentuckyLexingtonKentuckyUSA
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
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Adugna A. Therapeutic strategies and promising vaccine for hepatitis C virus infection. Immun Inflamm Dis 2023; 11:e977. [PMID: 37647422 PMCID: PMC10461427 DOI: 10.1002/iid3.977] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 09/01/2023] Open
Abstract
Hepatitis C virus (HCV) infection is still a significant global health problem despite therapeutic advancements. Ribavirin and interferon therapy have been the sole available treatments for HCV infection for a number of years with low efficacy. Thus, currently, a number of therapeutic strategies are being used, including nanoparticles (NPs), micro-RNAs such as small interfering RNA (siRNA), RNAi-based gene silencing and antisense oligonucleotide-based microRNA-122, microRNA-155, and short hairpin RNAs (shRNAs), and immunotherapeutic approaches such as anti-programmed cell death 1(PD-1), monoclonal antibodies (mAb or moAb), and monocyte-derived dendritic cells (Mo-DCs). Furthermore, direct-acting antivirals (DAAs) and host-targeting agents (HTA) were also the current therapeutic approaches with great efficacy. In spite of different clinical trials on HCV vaccine developments, nowadays there is no effective HCV vaccine in opposition to virus due to various challenges including genetic diversity, lack of immunocompetent small animal models, shortage of HCV vaccination testing alternatives, lack of an effective tissue culture method for replicating HCV, and inadequate knowledge regarding to immune responses against HCV infection. Nowadays, mRNA vaccine, recombinant viral vector, peptides vaccine, virus-like particles, DNA vaccine, rational designed vaccine, and recombinant polyantigenic T-cell-based vaccine are novel promising candidates for HCV vaccine based on various clinical trials. This review summarizes the different therapeutic approaches and the advancements of vaccine candidates for HCV infection.
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Affiliation(s)
- Adane Adugna
- Medical Microbiology, Medical Laboratory Sciences, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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28
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Papaioannou I, Owen JS, Yáñez‐Muñoz RJ. Clinical applications of gene therapy for rare diseases: A review. Int J Exp Pathol 2023; 104:154-176. [PMID: 37177842 PMCID: PMC10349259 DOI: 10.1111/iep.12478] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 03/08/2023] [Accepted: 04/16/2023] [Indexed: 05/15/2023] Open
Abstract
Rare diseases collectively exact a high toll on society due to their sheer number and overall prevalence. Their heterogeneity, diversity, and nature pose daunting clinical challenges for both management and treatment. In this review, we discuss recent advances in clinical applications of gene therapy for rare diseases, focusing on a variety of viral and non-viral strategies. The use of adeno-associated virus (AAV) vectors is discussed in the context of Luxturna, licenced for the treatment of RPE65 deficiency in the retinal epithelium. Imlygic, a herpes virus vector licenced for the treatment of refractory metastatic melanoma, will be an example of oncolytic vectors developed against rare cancers. Yescarta and Kymriah will showcase the use of retrovirus and lentivirus vectors in the autologous ex vivo production of chimeric antigen receptor T cells (CAR-T), licenced for the treatment of refractory leukaemias and lymphomas. Similar retroviral and lentiviral technology can be applied to autologous haematopoietic stem cells, exemplified by Strimvelis and Zynteglo, licenced treatments for adenosine deaminase-severe combined immunodeficiency (ADA-SCID) and β-thalassaemia respectively. Antisense oligonucleotide technologies will be highlighted through Onpattro and Tegsedi, RNA interference drugs licenced for familial transthyretin (TTR) amyloidosis, and Spinraza, a splice-switching treatment for spinal muscular atrophy (SMA). An initial comparison of the effectiveness of AAV and oligonucleotide therapies in SMA is possible with Zolgensma, an AAV serotype 9 vector, and Spinraza. Through these examples of marketed gene therapies and gene cell therapies, we will discuss the expanding applications of such novel technologies to previously intractable rare diseases.
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Affiliation(s)
| | - James S. Owen
- Division of MedicineUniversity College LondonLondonUK
| | - Rafael J. Yáñez‐Muñoz
- AGCTlab.orgCentre of Gene and Cell TherapyCentre for Biomedical SciencesDepartment of Biological SciencesSchool of Life Sciences and the EnvironmentRoyal Holloway University of LondonEghamUK
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29
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Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. MICROMACHINES 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
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Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
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30
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Abstract
Mouse models of colorectal cancer (CRC) have been crucial in the identification of the role of genes responsible for the full range of pathology of the human disease and have proved to be dependable for testing anti-cancer drugs. Recent research points toward the relevance of tumor, angiogenic, and immune microenvironments in CRC progression to late-stage disease, as well as the treatment of it. This study examines important mouse models in CRC, discussing inherent strengths and weaknesses disclosed during their construction. It endeavors to provide both a synopsis of previous work covering how investigators have defined various models and to evaluate critically how researchers are most likely to use them in the future. Accumulated evidence regarding the metastatic process and the hope of using checkpoint inhibitors and immunological inhibitor therapies points to the need for a genetically engineered mouse model that is both immunocompetent and autochthonous.
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Affiliation(s)
- Melanie Haas Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
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31
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Yan F, Xiao X, Long C, Tang L, Wang C, Zhang M, Zhang J, Lin H, Huang H, Zhang Y, Li S. Molecular Characterization of U6 Promoters from Orange-Spotted Grouper (Epinephelus coioides) and Its Application in DNA Vector-Based RNAi Technology. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10212-9. [PMID: 37154998 DOI: 10.1007/s10126-023-10212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
The U6 promoter, a typical RNA polymerase III promoter, is widely used to transcribe small RNAs in vector-based siRNA systems. The RNAi efficiency is mainly dependent on the transcriptional activity of the U6 promoter. However, studies have found that U6 promoters isolated from some fishes do not work well in distantly related species. To isolate a U6 promoter with high transcriptional efficiency from fish, in this study, we cloned five U6 promoters in orange-spotted grouper, of which only the grouper U6-1 (GU6-1) promoter contains the OCT element in the distant region. Functional studies revealed that the GU6-1 promoter has high transcriptional ability, which could efficiently transcribe shRNA and result in target gene knockdown in vitro and in vivo. Subsequently, the deletion or mutation of the OCT motif resulted in a significant decrease in promoter transcriptional activity, demonstrating that the OCT element plays an important role in enhancing the grouper U6 promoter transcription. Moreover, the transcriptional activity of the GU6-1 promoter showed little species specificity. It not only works in the grouper but also possesses high transcriptional activity in the zebrafish. Knockdown of the mstn gene in zebrafish and grouper through shRNA driven by the GU6-1 promoter could promote fish growth, suggesting that the GU6-1 promoter can be used as a potential molecular tool in aquaculture practice.
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Affiliation(s)
- Fengying Yan
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Xinxun Xiao
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Chen Long
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Lin Tang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Chongwei Wang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Mingqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Jin Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266373, Qingdao, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, 572022, Sanya, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266373, Qingdao, China.
| | - Shuisheng Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China.
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32
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Borzooee Moghadam N, Avatefi M, Karimi M, Mahmoudifard M. Graphene family in cancer therapy: recent progress in cancer gene/drug delivery applications. J Mater Chem B 2023; 11:2568-2613. [PMID: 36883982 DOI: 10.1039/d2tb01858f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
In the past few years, the development in the construction and architecture of graphene based nanocomplexes has dramatically accelerated the use of nano-graphene for therapeutic and diagnostic purposes, fostering a new area of nano-cancer therapy. To be specific, nano-graphene is increasingly used in cancer therapy, where diagnosis and treatment are coupled to deal with the clinical difficulties and challenges of this lethal disease. As a distinct family of nanomaterials, graphene derivatives exhibit outstanding structural, mechanical, electrical, optical, and thermal capabilities. Concurrently, they can transport a wide variety of synthetic agents, including medicines and biomolecules, such as nucleic acid sequences (DNA and RNA). Herewith, we first provide an overview of the most effective functionalizing agents for graphene derivatives and afterward discuss the significant improvements in the gene and drug delivery composites based on graphene.
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Affiliation(s)
- Negin Borzooee Moghadam
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Manizheh Avatefi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Mahnaz Karimi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Matin Mahmoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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33
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Structure of the human DICER-pre-miRNA complex in a dicing state. Nature 2023; 615:331-338. [PMID: 36813958 DOI: 10.1038/s41586-023-05723-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/14/2022] [Indexed: 02/24/2023]
Abstract
Dicer has a key role in small RNA biogenesis, processing double-stranded RNAs (dsRNAs)1,2. Human DICER (hDICER, also known as DICER1) is specialized for cleaving small hairpin structures such as precursor microRNAs (pre-miRNAs) and has limited activity towards long dsRNAs-unlike its homologues in lower eukaryotes and plants, which cleave long dsRNAs. Although the mechanism by which long dsRNAs are cleaved has been well documented, our understanding of pre-miRNA processing is incomplete because structures of hDICER in a catalytic state are lacking. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state and uncover the structural basis of pre-miRNA processing. hDICER undergoes large conformational changes to attain the active state. The helicase domain becomes flexible, which allows the binding of pre-miRNA to the catalytic valley. The double-stranded RNA-binding domain relocates and anchors pre-miRNA in a specific position through both sequence-independent and sequence-specific recognition of the newly identified 'GYM motif'3. The DICER-specific PAZ helix is also reoriented to accommodate the RNA. Furthermore, our structure identifies a configuration of the 5' end of pre-miRNA inserted into a basic pocket. In this pocket, a group of arginine residues recognize the 5' terminal base (disfavouring guanine) and terminal monophosphate; this explains the specificity of hDICER and how it determines the cleavage site. We identify cancer-associated mutations in the 5' pocket residues that impair miRNA biogenesis. Our study reveals how hDICER recognizes pre-miRNAs with stringent specificity and enables a mechanistic understanding of hDICER-related diseases.
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34
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Akbarimotlagh M, Azizi A, Shams-Bakhsh M, Jafari M, Ghasemzadeh A, Palukaitis P. Critical points for the design and application of RNA silencing constructs for plant virus resistance. Adv Virus Res 2023; 115:159-203. [PMID: 37173065 DOI: 10.1016/bs.aivir.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Control of plant virus diseases is a big challenge in agriculture as is resistance in plant lines to infection by viruses. Recent progress using advanced technologies has provided fast and durable alternatives. One of the most promising techniques against plant viruses that is cost-effective and environmentally safe is RNA silencing or RNA interference (RNAi), a technology that could be used alone or along with other control methods. To achieve the goals of fast and durable resistance, the expressed and target RNAs have been examined in many studies, with regard to the variability in silencing efficiency, which is regulated by various factors such as target sequences, target accessibility, RNA secondary structures, sequence variation in matching positions, and other intrinsic characteristics of various small RNAs. Developing a comprehensive and applicable toolbox for the prediction and construction of RNAi helps researchers to achieve the acceptable performance level of silencing elements. Although the attainment of complete prediction of RNAi robustness is not possible, as it also depends on the cellular genetic background and the nature of the target sequences, some important critical points have been discerned. Thus, the efficiency and robustness of RNA silencing against viruses can be improved by considering the various parameters of the target sequence and the construct design. In this review, we provide a comprehensive treatise regarding past, present and future prospective developments toward designing and applying RNAi constructs for resistance to plant viruses.
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Affiliation(s)
- Masoud Akbarimotlagh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Abdolbaset Azizi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.
| | - Masoud Shams-Bakhsh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Majid Jafari
- Department of Plant Protection, Higher Education Complex of Saravan, Saravan, Iran
| | - Aysan Ghasemzadeh
- Plant Pathology Department, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Peter Palukaitis
- Department of Horticulture Sciences, Seoul Women's University, Seoul, Republic of Korea.
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35
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Chen J, Huang F, Fang X, Li S, Liang Y. Silencing TLR4 using an ultrasound-targeted microbubble destruction-based shRNA system reduces ischemia-induced seizures in hyperglycemic rats. Open Life Sci 2022; 17:1689-1697. [PMID: 36619717 PMCID: PMC9795576 DOI: 10.1515/biol-2022-0526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/28/2022] [Accepted: 10/12/2022] [Indexed: 12/28/2022] Open
Abstract
The toll-like receptor 4 (TLR4) pathway is involved in seizures. We investigated whether ultrasound-targeted microbubble destruction (UTMD)-mediated delivery of short hairpin RNA (shRNA) targeting the TLR4 gene (shRNA-TLR4) can reduce ischemia-induced seizures in rats with hyperglycemia. A total of 100 male Wistar rats were randomly assigned to five groups: (1) Sham; (2) normal saline (NS); (3) shRNA-TLR4, where rats were injected with shRNA-TLR4; (4) shRNA-TLR4 + US, where rats were injected with shRNA-TLR4 followed by ultrasound (US) irradiation; and (5) shRNA-TLR4 + microbubbles (MBs) + US, where rats were injected with shRNA-TLR4 mixed with MBs followed by US irradiation. Western blot and immunohistochemical staining were used to measure TLR4-positive cells. Half of the rats in the NS group developed tonic-clonic seizures, and TLR4 expression in the CA3 region of the hippocampus was increased in these rats. In addition, the NS group showed an increased number of TLR4-positive cells compared with the Sham group, while there was a decreased number of TLR4-positive cells in the shRNA, shRNA + US, and shRNA + MBs + US groups. Our findings indicate that the TLR4 pathway is involved in the pathogenesis of ischemia-induced seizures in hyperglycemic rats and that UTMD technology may be a promising strategy to treat brain diseases.
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Affiliation(s)
- Jia Chen
- Department of Neurology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, 510150, China
| | - Fami Huang
- Department of Intensive Care Unit, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511500, China
| | - Xiaobo Fang
- Department of Neurology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, 510150, China
| | - Siying Li
- Department of Neurology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, 510150, China
| | - Yanling Liang
- Department of Neurology, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, 510150, China,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China
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36
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Evaluation of a Novel Oncolytic Adenovirus Silencing SYVN1. Int J Mol Sci 2022; 23:ijms232315430. [PMID: 36499754 PMCID: PMC9737683 DOI: 10.3390/ijms232315430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/23/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Oncolytic adenoviruses are promising new anticancer agents. To realize their full anticancer potential, they are being engineered to express therapeutic payloads. Tumor suppressor p53 function contributes to oncolytic adenovirus activity. Many cancer cells carry an intact TP53 gene but express p53 inhibitors that compromise p53 function. Therefore, we hypothesized that oncolytic adenoviruses could be made more effective by suppressing p53 inhibitors in selected cancer cells. To investigate this concept, we attenuated the expression of the established p53 inhibitor synoviolin (SYVN1) in A549 lung cancer cells by RNA interference. Silencing SYVN1 inhibited p53 degradation, thereby increasing p53 activity, and promoted adenovirus-induced A549 cell death. Based on these observations, we constructed a new oncolytic adenovirus that expresses a short hairpin RNA against SYVN1. This virus killed A549 cells more effectively in vitro and inhibited A549 xenograft tumor growth in vivo. Surprisingly, increased susceptibility to adenovirus-mediated cell killing by SYVN1 silencing was also observed in A549 TP53 knockout cells. Hence, while the mechanism of SYVN1-mediated inhibition of adenovirus replication is not fully understood, our results clearly show that RNA interference technology can be exploited to design more potent oncolytic adenoviruses.
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37
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McLean B, Istadi A, Clack T, Vankan M, Schramek D, Neely GG, Pajic M. A CRISPR Path to Finding Vulnerabilities and Solving Drug Resistance: Targeting the Diverse Cancer Landscape and Its Ecosystem. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200014. [PMID: 36911295 PMCID: PMC9993475 DOI: 10.1002/ggn2.202200014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Cancer is the second leading cause of death globally, with therapeutic resistance being a major cause of treatment failure in the clinic. The dynamic signaling that occurs between tumor cells and the diverse cells of the surrounding tumor microenvironment actively promotes disease progression and therapeutic resistance. Improving the understanding of how tumors evolve following therapy and the molecular mechanisms underpinning de novo or acquired resistance is thus critical for the identification of new targets and for the subsequent development of more effective combination regimens. Simultaneously targeting multiple hallmark capabilities of cancer to circumvent adaptive or evasive resistance may lead to significantly improved treatment response in the clinic. Here, the latest applications of functional genomics tools, such as clustered regularly interspaced short palindromic repeats (CRISPR) editing, to characterize the dynamic cancer resistance mechanisms, from improving the understanding of resistance to classical chemotherapeutics, to deciphering unique mechanisms that regulate tumor responses to new targeted agents and immunotherapies, are discussed. Potential avenues of future research in combating therapeutic resistance, the contribution of tumor-stroma signaling in this setting, and how advanced functional genomics tools can help streamline the identification of key molecular determinants of drug response are explored.
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Affiliation(s)
- Benjamin McLean
- The Kinghorn Cancer CentreThe Garvan Institute of Medical Research384 Victoria St, DarlinghurstSydneyNew South Wales2010Australia
| | - Aji Istadi
- The Kinghorn Cancer CentreThe Garvan Institute of Medical Research384 Victoria St, DarlinghurstSydneyNew South Wales2010Australia
| | - Teleri Clack
- Dr. John and Anne Chong Lab for Functional GenomicsCharles Perkins CentreCentenary InstituteUniversity of SydneyCamperdownNew South Wales2006Australia
| | - Mezzalina Vankan
- Dr. John and Anne Chong Lab for Functional GenomicsCharles Perkins CentreCentenary InstituteUniversity of SydneyCamperdownNew South Wales2006Australia
| | - Daniel Schramek
- Centre for Molecular and Systems BiologyLunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioM5G 1X5Canada
- Department of Molecular GeneticsFaculty of MedicineUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - G. Gregory Neely
- Dr. John and Anne Chong Lab for Functional GenomicsCharles Perkins CentreCentenary InstituteUniversity of SydneyCamperdownNew South Wales2006Australia
| | - Marina Pajic
- The Kinghorn Cancer CentreThe Garvan Institute of Medical Research384 Victoria St, DarlinghurstSydneyNew South Wales2010Australia
- St Vincent's Clinical SchoolFaculty of MedicineUniversity of NSW SydneySydneyNew South Wales2052Australia
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38
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Bryl R, Piwocka O, Kawka E, Mozdziak P, Kempisty B, Knopik-Skrocka A. Cancer Stem Cells-The Insight into Non-Coding RNAs. Cells 2022; 11:cells11223699. [PMID: 36429127 PMCID: PMC9688207 DOI: 10.3390/cells11223699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Since their initial identification three decades ago, there has been extensive research regarding cancer stem cells (CSCs). It is important to consider the biology of cancer stem cells with a particular focus on their phenotypic and metabolic plasticity, the most important signaling pathways, and non-coding RNAs (ncRNAs) regulating these cellular entities. Furthermore, the current status of therapeutic approaches against CSCs is an important consideration regarding employing the technology to improve human health. Cancer stem cells have claimed to be one of the most important group of cells for the development of several common cancers as they dictate features, such as resistance to radio- and chemotherapy, metastasis, and secondary tumor formation. Therapies which could target these cells may develop into an effective strategy for tumor eradication and a hope for patients for whom this disease remains uncurable.
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Affiliation(s)
- Rut Bryl
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Oliwia Piwocka
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Emilia Kawka
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Bartosz Kempisty
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA
- Department of Human Morphology and Embryology, Division of Anatomy, Medical University of Wrocław, 50-367 Wroclaw, Poland
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, 87-100 Torun, Poland
- Correspondence: or
| | - Agnieszka Knopik-Skrocka
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
- Department of Cell Biology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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39
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Sun J, Li X, Hou X, Cao S, Cao W, Zhang Y, Song J, Wang M, Wang H, Yan X, Li Z, Roeder RG, Wang W. Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Nat Commun 2022; 13:6871. [PMID: 36369505 PMCID: PMC9652321 DOI: 10.1038/s41467-022-34639-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a "wrap-around" mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system.
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Affiliation(s)
- Jianfeng Sun
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Xue Li
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xuben Hou
- grid.27255.370000 0004 1761 1174School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Sujian Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Wenjin Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Ye Zhang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Jinyang Song
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Manfu Wang
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Hao Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xiaodong Yan
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Zengpeng Li
- grid.453137.70000 0004 0406 0561Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Robert G. Roeder
- grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Wei Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Interventional Medicine Department, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033 China
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40
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Panagopoulos A, Samant S, Bakhos JJ, Liu M, Khan B, Makadia J, Muhammad F, Kievit FM, Agrawal DK, Chatzizisis YS. Triggering receptor expressed on myeloid cells-1 (TREM-1) inhibition in atherosclerosis. Pharmacol Ther 2022; 238:108182. [DOI: 10.1016/j.pharmthera.2022.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 03/14/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
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41
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Lama L, Ryan K. Starting and stopping RNA polymerase III transcription on single-stranded DNA oligonucleotides. RNA (NEW YORK, N.Y.) 2022; 28:1315-1324. [PMID: 35853667 PMCID: PMC9479740 DOI: 10.1261/rna.078981.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Circularized single-stranded DNA oligonucleotides, or coligos, show promise as promoter-independent RNA polymerase III (Pol III) transcription templates for generating small RNA in human cells. Using a modified small RNA-seq method, we studied the sequence and secondary structure characteristics that determine Pol III initiation and termination on six coligo templates. The coligos each consisted of an imperfectly base-paired stem flanked by one larger and one smaller loop and were unrelated in sequence. Small RNA-seq data from Pol III coligo transcripts revealed a strong preference for initiating transcription within a 5-nucleotide (nt) window spanning the stem-larger loop junction (loop size 11-24 nt). Transcription in all cases proceeded into the stem rather than into the larger loop, indicating the junction is a site-specific, secondary structure-based Pol III transcription initiator. On average, 81% of sequencing reads showed initiation within this 5 nt junction region, with a template start site nucleotide preference of C > T >> A > G, and a requirement for a template purine at Tss-1. Termination was less precise than initiation and occurred in the larger loop at the same end of the stem where transcription initiated. Termination efficiency was on average 82% and was distributed among the first 11 single-stranded larger loop nt following the stem. The size heterogeneity of Pol III coligo transcripts is thus mainly due to 3' end heterogeneity, whereas the RNA 5' ends were more predictable and homogeneous. Transcription termination did not require an oligo dA template sequence, indicating that termination in this context may be mechanistically different than Pol III's normal gene-context termination. A stepwise model for coligo transcription by Pol III is proposed.
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Affiliation(s)
- Lodoe Lama
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Biochemistry and Chemistry Ph.D. Programs, The City University of New York Graduate Center, New York, New York 10016, USA
| | - Kevin Ryan
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, USA
- Biochemistry and Chemistry Ph.D. Programs, The City University of New York Graduate Center, New York, New York 10016, USA
- Chemistry Ph.D. Programs, The City University of New York Graduate Center, New York, New York 10016, USA
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42
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Kelley CP, Haerle MC, Wang ET. Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells. Cell Rep 2022; 40:111226. [PMID: 35977479 PMCID: PMC9809062 DOI: 10.1016/j.celrep.2022.111226] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
CRISPR-Cas13 RNA endonucleases show promise for programmable RNA knockdown. However, sequence-specific binding of Cas13 unleashes non-specific bystander RNA cleavage, or collateral activity, raising concerns for experiments and therapeutic applications. Although robust in cell-free and bacterial environments, collateral activity in mammalian cells remains disputed. We investigate Cas13d collateral activity in a therapeutic context for myotonic dystrophy type 1, caused by a transcribed CTG repeat expansion. We find that, when targeting CUGn RNA in mammalian cells, Cas13d depletes endogenous and transgenic RNAs, interferes with critical cellular processes, and activates stress response and apoptosis. Collateral effects also occur when targeting abundant endogenous transcripts. To minimize collateral activity for repeat-targeting approaches, we introduce GENO, an adeno-associated virus-compatible strategy that leverages guide RNA processing to control Cas13d expression. We argue that thorough assessment of collateral activity is necessary when applying Cas13 in mammalian cells and that GENO illustrates advantages of compact regulatory systems for Cas-based gene therapies.
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Affiliation(s)
- Chase P Kelley
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32608, USA
| | - Maja C Haerle
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Myology Institute, University of Florida, Gainesville, FL 32608, USA.
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43
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Dionisi S, Piera K, Baumschlager A, Khammash M. Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase. ACS Synth Biol 2022; 11:2650-2661. [PMID: 35921263 PMCID: PMC9396705 DOI: 10.1021/acssynbio.2c00067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Optogenetic tools are widely used to control gene expression
dynamics
both in prokaryotic and eukaryotic cells. These tools are used in
a variety of biological applications from stem cell differentiation
to metabolic engineering. Despite some tools already available in
bacteria, no light-inducible system currently exists to control gene
expression independently from mammalian transcriptional and/or translational
machineries thus working orthogonally to endogenous regulatory mechanisms.
Such a tool would be particularly important in synthetic biology,
where orthogonality is advantageous to achieve robust activation of
synthetic networks. Here we implement, characterize, and optimize
a new optogenetic tool in mammalian cells based on a previously published
system in bacteria called Opto-T7RNAPs. The tool is orthogonal to
the cellular machinery for transcription and consists of a split T7
RNA polymerase coupled with the blue light-inducible magnets system
(mammalian OptoT7–mOptoT7). In our study we exploited the T7
polymerase’s viral origins to tune our system’s expression
level, reaching up to an almost 20-fold change activation over the
dark control. mOptoT7 is used here to generate mRNA for protein expression,
shRNA for protein inhibition, and Pepper aptamer for RNA visualization.
Moreover, we show that mOptoT7 can mitigate the gene expression burden
when compared to another optogenetic construct. These properties make
mOptoT7 a powerful new tool to use when orthogonality and viral RNA
species (that lack endogenous RNA modifications) are desired.
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Affiliation(s)
- Sara Dionisi
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Karol Piera
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Armin Baumschlager
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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44
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Duran AG, Schwestka M, Nazari-Shafti TZ, Neuber S, Stamm C, Gossen M. Limiting Transactivator Amounts Contribute to Transgene Mosaicism in Tet-On All-in-One Systems. ACS Synth Biol 2022; 11:2623-2635. [PMID: 35815862 DOI: 10.1021/acssynbio.2c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MicroRNAs play an essential role in cell homeostasis and have been proposed as therapeutic agents. One strategy to deliver microRNAs is to genetically engineer target cells to express microRNAs of interest. However, to control dosage and timing, as well as to limit potential side-effects, microRNAs' expression should ideally be under exogenous, inducible control. Conditional expression of miRNA-based short hairpin RNAs (shRNAmirs) via gene regulatory circuits such as the Tet-system is therefore a promising strategy to control shRNAmirs' expression in research and therapy. Single vector approaches like Tet-On all-in-one designs are more compatible with potential clinical applications by providing the Tet-On system components in a single round of genetic engineering. However, all-in-one systems often come at the expense of heterogeneous and unstable expression. In this study, we aimed to understand the causes that lead to such erratic transgene expression. By using a reporter cell, we found that the degree of heterogeneity mostly correlated with reverse tetracycline transactivator (rtTA) expression levels. Moreover, the targeted integration of a potent rtTA expression cassette into a genomic safe harbor locus functionally rescued previously silenced rtTA-responsive transcription units. Overall, our results suggest that ensuring homogenous and stable rtTA expression is essential for the robust and reliable performance of future Tet-On all-in-one designs.
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Affiliation(s)
- Ana G Duran
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Timo Z Nazari-Shafti
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Sebastian Neuber
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Christof Stamm
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
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45
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Chilamkurthy R, White AA, Pater AA, Jensik PJ, Gagnon KT. Efficient Cloning and Sequence Validation of Repetitive and High GC-Content shRNAs. Hum Gene Ther 2022; 33:829-839. [PMID: 35726380 DOI: 10.1089/hum.2021.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Short hairpin RNAs, or shRNAs, are a proven tool for gene knockdown and a promising therapeutic approach for suppression of disease-associated genes. The efficient preparation of shRNA-expressing vectors can sometimes become a bottleneck due to the complexity of shRNA hairpin sequence and structure, especially for repetitive or high GC-content targets. Here we present improved shRNA cloning and validation methods that enabled efficient and rapid cloning of several shRNAs targeting disease-associated repeat expansions, including GGGGCC, CAG, CTG, CCTG, and CGG into modified pLKO.1 vectors. Improvements included shRNA insert design and preparation, recombination-based cloning, and sequencing-based validation that included Sanger and nanopore long-read sequencing. This improved method should enable practical, efficient cloning of nearly any shRNA sequence.
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Affiliation(s)
- Ramadevi Chilamkurthy
- Southern Illinois University School of Medicine, 12249, Biochemistry & Molecular Biology, Carbondale, Illinois, United States;
| | - Adam A White
- Southern Illinois University School of Medicine, 12249, Biochemistry & Molecular Biology, Carbondale, Illinois, United States;
| | - Adrian A Pater
- Southern Illinois University Carbondale, 2254, Chemistry & Biochemistry, Carbondale, Illinois, United States;
| | - Philip J Jensik
- Southern Illinois University School of Medicine, 12249, Physiology, Carbondale, Illinois, United States;
| | - Keith T Gagnon
- Southern Illinois University Carbondale, 2254, Biochemistry & Molecular Biology, 1245 Lincoln Dr., 229 Neckers Bldg., Carbondale, Illinois, United States, 62901-6632;
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Alsing S, Doktor TK, Askou AL, Jensen EG, Ahmadov U, Kristensen LS, Andresen BS, Aagaard L, Corydon TJ. VEGFA-targeting miR-agshRNAs combine efficacy with specificity and safety for retinal gene therapy. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:58-76. [PMID: 35356684 PMCID: PMC8933642 DOI: 10.1016/j.omtn.2022.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Retinal gene therapy using RNA interference (RNAi) to silence targeted genes requires both efficacy and safety. Short hairpin RNAs (shRNAs) are useful for RNAi, but high expression levels and activity from the co-delivered passenger strand may cause undesirable cellular responses. Ago2-dependent shRNAs (agshRNAs) produce no passenger strand activity. To enhance efficacy and to investigate improvements in safety, we have generated VEGFA-targeting agshRNAs and microRNA (miRNA)-embedded agshRNAs (miR-agshRNAs) and inserted these RNAi effectors in Pol II/III-driven expression cassettes and lentiviral vectors (LVs). Compared with corresponding shRNAs, agshRNAs and miR-agshRNAs increased specificity and safety, while retaining a high knockdown efficacy and abolishing passenger strand activity. The agshRNAs also caused significantly smaller reductions in cell viability and reduced competition with the processing of endogenous miR21 compared with their shRNA counterparts. RNA sequencing (RNA-seq) analysis of LV-transduced ARPE19 cells revealed that expression of shRNAs in general leads to more changes in gene expression levels compared with their agshRNA counterparts and activation of immune-related pathways. In mice, subretinal delivery of LVs encoding tissue-specific miR-agshRNAs resulted in retinal pigment epithelium (RPE)-restricted expression and significant knockdown of Vegfa in transduced RPE cells. Collectively, our data suggest that agshRNAs and miR-agshRNA possess important advantages over shRNAs, thereby posing a clinically relevant approach with respect to efficacy, specificity, and safety.
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Tanner AR, Kennedy VC, Lynch CS, Hord TK, Winger QA, Rozance PJ, Anthony RV. In vivo investigation of ruminant placenta function and physiology-a review. J Anim Sci 2022; 100:skac045. [PMID: 35648127 PMCID: PMC9159061 DOI: 10.1093/jas/skac045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/10/2022] [Indexed: 12/16/2022] Open
Abstract
The placenta facilitates the transport of nutrients to the fetus, removal of waste products from the fetus, immune protection of the fetus and functions as an endocrine organ, thereby determining the environment for fetal growth and development. Additionally, the placenta is a highly metabolic organ in itself, utilizing a majority of the oxygen and glucose derived from maternal circulation. Consequently, optimal placental function is required for the offspring to reach its genetic potential in utero. Among ruminants, pregnant sheep have been used extensively for investigating pregnancy physiology, in part due to the ability to place indwelling catheters within both maternal and fetal vessels, allowing for steady-state investigation of blood flow, nutrient uptakes and utilization, and hormone secretion, under non-stressed and non-anesthetized conditions. This methodology has been applied to both normal and compromised pregnancies. As such, our understanding of the in vivo physiology of pregnancy in sheep is unrivalled by any other species. However, until recently, a significant deficit existed in determining the specific function or significance of individual genes expressed by the placenta in ruminants. To that end, we developed and have been using in vivo RNA interference (RNAi) within the sheep placenta to examine the function and relative importance of genes involved in conceptus development (PRR15 and LIN28), placental nutrient transport (SLC2A1 and SLC2A3), and placenta-derived hormones (CSH). A lentiviral vector is used to generate virus that is stably integrated into the infected cell's genome, thereby expressing a short-hairpin RNA (shRNA), that when processed within the cell, combines with the RNA Induced Silencing Complex (RISC) resulting in specific mRNA degradation or translational blockage. To accomplish in vivo RNAi, day 9 hatched and fully expanded blastocysts are infected with the lentivirus for 4 to 5 h, and then surgically transferred to synchronized recipient uteri. Only the trophectoderm cells are infected by the replication deficient virus, leaving the inner cell mass unaltered, and we often obtain ~70% pregnancy rates following transfer of a single blastocyst. In vivo RNAi coupled with steady-state study of blood flow and nutrient uptake, transfer and utilization can now provide new insight into the physiological consequences of modifying the translation of specific genes expressed within the ruminant placenta.
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Affiliation(s)
- Amelia R Tanner
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Victoria C Kennedy
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Cameron S Lynch
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Taylor K Hord
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Quinton A Winger
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Paul J Rozance
- Department of Pediatrics, Division of Neonatology, College of Medicine, University of Colorado, Aurora, CO 80045, USA
| | - Russell V Anthony
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
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Secondary structure RNA elements control the cleavage activity of DICER. Nat Commun 2022; 13:2138. [PMID: 35440644 PMCID: PMC9018771 DOI: 10.1038/s41467-022-29822-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/23/2022] [Indexed: 12/05/2022] Open
Abstract
The accurate and efficient cleavage of shRNAs and pre-miRNAs by DICER is crucial for their gene-silencing activity. Here, we conduct high-throughput DICER cleavage assays for more than ~20,000 different shRNAs and show the comprehensive cleavage activities of DICER on these sequences. We discover a single-nucleotide bulge (22-bulge), which facilitates the cleavage activity of DICER on shRNAs and human pre-miRNAs. As a result, this 22-bulge enhances the gene-silencing activity of shRNAs and the accuracy of miRNA biogenesis. In addition, various single-nucleotide polymorphism-edited 22-bulges are found to govern the cleavage sites of DICER on pre-miRNAs and thereby control their functions. Finally, we identify the single cleavage of DICER and reveal its molecular mechanism. Our findings improve the understanding of the DICER cleavage mechanism, provide a foundation for the design of accurate and efficient shRNAs for gene-silencing, and indicate the function of bulges in regulating miRNA biogenesis. MicroRNA precursors are cleaved by DICER to generate mature microRNAs in the cytoplasm. Here the authors employ high-throughput analysis of DICER cleavage activity and identify RNA secondary elements in precursor miRNAs and shRNAs, including a single nucleotide bulge, which govern its cleavage efficiency and accuracy.
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Engineering Novel Lentiviral Vectors for Labelling Tumour Cells and Oncogenic Proteins. Bioengineering (Basel) 2022; 9:bioengineering9030091. [PMID: 35324780 PMCID: PMC8945451 DOI: 10.3390/bioengineering9030091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
Lentiviral vectors are unique and highly efficient genetic tools to incorporate genetic materials into the genome of a variety of cells whilst conserving biosafety. Their rapid acceptance made it necessary to improve existing protocols, including molecular engineering and cloning, production of purified lentiviral particles, and efficient infection of target cells. In addition to traditional protocols, which can be time-consuming, several biotechnology companies are providing scientists with commercially available lentiviral constructs and particles. However, these constructs are limited by their original form, tend to be costly, and lack the flexibility to re-engineer based on the ever-changing needs of scientific projects. Therefore, the current study organizes the existing methods and integrates them with novel ideas to establish a protocol that is simple and efficient to implement. In this study we, (i) generated an innovative site-directed nucleotide attachment/replacement and DNA insertion method using unique PCR primers, (ii) improved traditional methods by integrating plasmid clarification steps, (iii) utilized endogenous mRNA as a resource to construct new lentiviruses, and (iv) identified an existing purification method and incorporated it into an organized workflow to produce high-yield lentiviral particle collection. Finally, (v) we verified and demonstrated the functional validity of our methods using an infection strategy.
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He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W. Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells. J Am Chem Soc 2022; 144:4289-4293. [PMID: 35138101 DOI: 10.1021/jacs.1c11041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a prevalent protein modification that plays fundamental roles in both cell physiology and pathology. O-GlcNAc is catalyzed solely by O-GlcNAc transferase (OGT). The study of protein O-GlcNAc function is limited by the lack of tools to control OGT activity with spatiotemporal resolution in cells. Here, we report light control of OGT activity in cells by replacing a catalytically essential lysine residue with a genetically encoded photocaged lysine. This enables the expression of a transiently inactivated form of OGT, which can be rapidly reactivated by photo-decaging. We demonstrate the activation of OGT activity by monitoring the time-dependent increase of cellular O-GlcNAc and profile glycoproteins using mass-spectrometry-based quantitative proteomics. We further apply this activation strategy to control the morphological contraction of fibroblasts. Furthermore, we achieved spatial activation of OGT activity predominantly in the cytosol. Thus, our approach provides a valuable chemical tool to control cellular O-GlcNAc with much needed spatiotemporal precision, which aids in a better understanding of O-GlcNAc function.
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Affiliation(s)
- Jiahui He
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhiya Fan
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yinping Tian
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.,Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiwei Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yichao Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiang Zhu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wen Yi
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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