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Nerva L, Gambino G, Moffa L, Spada A, Falginella L, De Luca E, Zambon Y, Chitarra W. Conjoined partners: efficacy and side effects of grafting and dsRNA application on the microbial endophyte population of grapevine plants inoculated with two esca-related fungal pathogens. JOURNAL OF EXPERIMENTAL BOTANY 2024:erae461. [PMID: 39699194 DOI: 10.1093/jxb/erae461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 11/11/2024] [Indexed: 12/20/2024]
Abstract
Grafting has been exploited since 7000 BC to enhance productivity, disease resistance, and adaptability of cultivated plants to stressful conditions especially in woody crops such as grapevine (Vitis spp.). In contrast, the application of sequence specific double-stranded RNAs (dsRNAs) to control fungal pathogens and insect pests has only been recently developed. The possibility of combining these approaches to enhance plant resilience, reducing reliance on pesticides, offers new perspectives for a more sustainable agriculture. In this study, we assessed the potential of utilizing dsRNAs to enhance resilience against esca-related wood fungal pathogens in grapevine, considering various rootstock-scion combinations. The results showed that the scion genotype modulates the ability of the rootstock to cope with the inoculated wood fungal pathogens, mainly by altering the efficacy of producing stilbene compounds. Additionally, we found that dsRNAs reduced the growth of two inoculated esca-related fungal pathogens but they did not completely stop their colonization. Furthermore, wood microbiome data showed that the scion genotype (always belonging to Vitis vinifera species) was also able to influence the rootstock-associated microbiota, with a major effect on the fungal community. Lastly, adverse effects on non-target microorganisms are reported, raising questions on the environmental fate of dsRNAs and how dsRNAs can directly or indirectly affect plant-associated microbial communities.
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Affiliation(s)
- Luca Nerva
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Loredana Moffa
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Alberto Spada
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
- University of Padova, Department of Agronomy, Food, Natural resources, Animals and Environment, Via dell'Università 16, 35020 Legnaro (PD), Italy
| | - Luigi Falginella
- VCR Research Center, Via Ruggero Forti 4, 33095 Rauscedo (PN), Italy
| | - Elisa De Luca
- VCR Research Center, Via Ruggero Forti 4, 33095 Rauscedo (PN), Italy
| | - Yuri Zambon
- VCR Research Center, Via Ruggero Forti 4, 33095 Rauscedo (PN), Italy
| | - Walter Chitarra
- Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy
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Salman Hameed M, Ren Y, Tuda M, Basit A, Urooj N. Role of Argonaute proteins in RNAi pathway in Plutella xylostella: A review. Gene 2024; 903:148195. [PMID: 38295911 DOI: 10.1016/j.gene.2024.148195] [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: 12/04/2023] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Argonaute (Ago) proteins act as key elements in RNA interference (RNAi) pathway, orchestrating the intricate machinery of gene regulation within eukaryotic cells. Within the RNAi pathway, small RNA molecules, including microRNA (miRNA), small interfering RNA (siRNA), and PIWI-interacting RNA (piRNA), collaborate with Ago family member proteins such as Ago1, Ago2, and Ago3 to form the RNA-induced silencing complex (RISC). This RISC complex, in turn, either cleaves the target mRNA or inhibits the process of protein translation. The precise contributions of Ago proteins have been well-established in numerous animals and plants, although they still remain unclear in some insect species. This review aims to shed light on the specific roles played by Ago proteins within the RNAi mechanism in a destructive lepidopteran pest, the diamondback moth (Plutella xylostella). Furthermore, we explore the potential of double-stranded RNA (dsRNA)-mediated RNAi as a robust genetic tool in pest management strategies. Through an in-depth examination of Ago proteins and dsRNA-mediated RNAi, this review seeks to contribute to our understanding of innovative approaches for controlling this pest and potentially other insect species of agricultural significance.
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Affiliation(s)
- Muhammad Salman Hameed
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Yanliang Ren
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China.
| | - Midori Tuda
- Institute of Biological Control, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Abdul Basit
- Institute of Entomology, Guizhou University Guiyang 550025, Guizhou China
| | - Nida Urooj
- Department of Business Administrative, Bahaudin Zakriya University, Multan, Pakistan
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3
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Dabin A, Stirnemann G. Atomistic simulations of RNA duplex thermal denaturation: Sequence- and forcefield-dependence. Biophys Chem 2024; 307:107167. [PMID: 38262278 DOI: 10.1016/j.bpc.2023.107167] [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: 10/02/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that greatly improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université de Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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Chen S, Liu W, Xiong L, Tao Z, Zhao D. Tissue-specific silencing of integrated transgenes achieved through endogenous RNA interference in Caenorhabditis elegans. RNA Biol 2024; 21:1-10. [PMID: 38531838 PMCID: PMC10978027 DOI: 10.1080/15476286.2024.2332856] [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] [Revised: 01/22/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Transgene silencing is a common phenomenon observed in Caenorhabditis elegans, particularly in the germline, but the precise mechanisms underlying this process remain elusive. Through an analysis of the transcription factors profile of C. elegans, we discovered that the expression of several transgenic reporter lines exhibited tissue-specific silencing, specifically in the intestine of C. elegans. Notably, this silencing could be reversed in mutants defective in endogenous RNA interference (RNAi). Further investigation using knock-in strains revealed that these intestine-silent genes were indeed expressed in vivo, indicating that the organism itself regulates the intestine-specific silencing. This tissue-specific silencing appears to be mediated through the endo-RNAi pathway, with the main factors of this pathway, mut-2 and mut-16, are significantly enriched in the intestine. Additionally, histone modification factors, such as met-2, are involved in this silencing mechanism. Given the crucial role of the intestine in reproduction alongside the germline, the transgene silencing observed in the intestine reflects the self-protective mechanisms employed by the organisms. In summary, our study proposed that compared to other tissues, the transgenic silencing of intestine is specifically regulated by the endo-RNAi pathway.
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Affiliation(s)
- Siyu Chen
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Institute of Sport, Exercise & Health, Tianjin University of Sport, Tianjin, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Weihong Liu
- Intelligent Perception Lab, Hanwang Technology Co. Ltd, Beijing, China
| | - Lei Xiong
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhiju Tao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Di Zhao
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, Institute of Sport, Exercise & Health, Tianjin University of Sport, Tianjin, China
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Garcia-Rubio VG, Cabrera-Becerra SE, Ocampo-Ortega SA, Blancas-Napoles CM, Sierra-Sánchez VM, Romero-Nava R, Gutiérrez-Rojas RA, Huang F, Hong E, Villafaña S. siRNA Targeting PDE5A Partially Restores Vascular Damage Due to Type 1 Diabetes in a Streptozotocin-Induced Rat Model. Sci Pharm 2023; 91:52. [DOI: 10.3390/scipharm91040052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025] Open
Abstract
Diabetes mellitus is a metabolic disease that can produce different alterations such as endothelial dysfunction, which is defined as a decrease in the vasodilator responses of the mechanisms involved such as the nitric oxide (NO) pathway. The overexpression of PDE5A has been reported in diabetes, which causes an increase in the hydrolysis of cGMP and a decrease in the NO pathway. For this reason, the aim of this study was to evaluate whether siRNAs targeting PDE5A can reduce the endothelial dysfunction associated with diabetes. We used male Wistar rats (200–250 g) that were administered streptozotocin (STZ) (60 mg/kg i.p) to induce diabetes. Two weeks after STZ administration, the siRNAs or vehicle were administered and then, at 4 weeks, dose–response curves to acetylcholine were performed and PDE5A mRNA levels were measured by RT-PCR. siRNAs were designed by the bioinformatic analysis of human–rat FASTA sequences and synthesised in the Mermade-8 equipment. Our results showed that 4 weeks of diabetes produces a decrease in the vasodilator responses to acetylcholine and an increase in the expression of PDE5A mRNA, while the administration of siRNAs partially restores the vasodilator response and decreases PDE5A expression. We conclude that the administration of siRNAs targeting PDE5A partially reverts the endothelial impairment associated with diabetes.
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Affiliation(s)
- Vanessa Giselle Garcia-Rubio
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
| | - Sandra Edith Cabrera-Becerra
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
| | - Sergio Adrian Ocampo-Ortega
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
| | - Citlali Margarita Blancas-Napoles
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
| | - Vivany Maydel Sierra-Sánchez
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
| | - Rodrigo Romero-Nava
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
| | | | - Fengyang Huang
- Departamento de Farmacología y Toxicología, “Hospital Infantil de México Federico Gómez” (HIMFG), Ciudad de México 06720, Mexico
| | - Enrique Hong
- Departamento de Neurofarmacobiología, Centro de Investigación y de Estudios Avanzados, Ciudad de México 07360, Mexico
| | - Santiago Villafaña
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Ciudad de México 11340, Mexico
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Koyasu K, Chandela A, Ueno Y. Non-terminal conjugation of small interfering RNAs with spermine improves duplex binding and serum stability with position-specific incorporation. RSC Adv 2023; 13:25169-25181. [PMID: 37622021 PMCID: PMC10445083 DOI: 10.1039/d3ra04918c] [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: 07/21/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
The conjugation of small interfering RNAs (siRNAs) has been studied using lipid and ligand conjugates for efficient delivery. However, most conjugates have been inserted at the terminal position; very few have been inserted at non-terminal positions. Herein, we synthesized a 4'-C-propyllevulinate-2'-O-methyluridine analog for non-terminal conjugation of spermine into the passenger strand of siRNA. Solid-phase oligonucleotide synthesis using this analog was successful, with the conjugation of one or two spermine molecules. The siRNAs conjugated with spermine displayed improved thermodynamic stability and resistance against nucleases, which depended on the site of conjugation in each case. Circular dichroism spectroscopy revealed that the A-type helical structure of the RNA duplex was not altered by these modifications. However, the gene-silencing activity of conjugated siRNAs was reduced and further decreased when the number of spermine molecules was increased. Hence, this work supplies valuable information and provides scope for the further development of drug-delivery systems through non-terminal conjugation.
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Affiliation(s)
- Keisuke Koyasu
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Japan +81-58-293-2919 +81-58-293-2919
| | - Akash Chandela
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
| | - Yoshihito Ueno
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University Japan +81-58-293-2919 +81-58-293-2919
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
- United Graduate School of Agricultural Science, Gifu University 1-1 Yanagido Gifu 501-1193 Japan
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7
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Dabin A, Stirnemann G. Toward a Molecular Mechanism of Complementary RNA Duplexes Denaturation. J Phys Chem B 2023. [PMID: 37389985 DOI: 10.1021/acs.jpcb.3c00908] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
RNA duplexes are relatively rare but play very important biological roles. As an end-product of template-based RNA replication, they also have key implications for hypothetical primitive forms of life. Unless they are specifically separated by enzymes, these duplexes denature upon a temperature increase. However, mechanistic and kinetic aspects of RNA (and DNA) duplex thermal denaturation remain unclear at the microscopic level. We propose an in silico strategy that probes the thermal denaturation of RNA duplexes and allows for an extensive conformational space exploration along a wide temperature range with atomistic precision. We show that this approach first accounts for the strong sequence and length dependence of the duplexes melting temperature, reproducing the trends seen in the experiments and predicted by nearest-neighbor models. The simulations are then instrumental at providing a molecular picture of the temperature-induced strand separation. The textbook canonical "all-or-nothing" two-state model, very much inspired by the protein folding mechanism, can be nuanced. We demonstrate that a temperature increase leads to significantly distorted but stable structures with extensive base-fraying at the extremities, and that the fully formed duplexes typically do not form around melting. The duplex separation therefore appears as much more gradual than commonly thought.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
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8
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Halder K, Chaudhuri A, Abdin MZ, Datta A. Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant. Int J Mol Sci 2023; 24:ijms24043143. [PMID: 36834556 PMCID: PMC9966754 DOI: 10.3390/ijms24043143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.
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Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Correspondence: (A.C.); (A.D.); Tel.: +91-1126742750 or +91-1126735119 (A.D.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Correspondence: (A.C.); (A.D.); Tel.: +91-1126742750 or +91-1126735119 (A.D.)
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9
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Di Serio F, Owens RA, Navarro B, Serra P, Martínez de Alba ÁE, Delgado S, Carbonell A, Gago-Zachert S. Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis. Virus Res 2023; 323:198964. [PMID: 36223861 PMCID: PMC10194176 DOI: 10.1016/j.virusres.2022.198964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Viroids are small, single-stranded, non-protein coding and circular RNAs able to infect host plants in the absence of any helper virus. They may elicit symptoms in their hosts, but the underlying molecular pathways are only partially known. Here we address the role of post-transcriptional RNA silencing in plant-viroid-interplay, with major emphasis on the involvement of this sequence-specific RNA degradation mechanism in both plant antiviroid defence and viroid pathogenesis. This review is a tribute to the memory of Dr. Ricardo Flores, who largely contributed to elucidate this and other molecular mechanisms involved in plant-viroid interactions.
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Affiliation(s)
- Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Ángel Emilio Martínez de Alba
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor 37185, Salamanca, Spain
| | - Sonia Delgado
- Instituto Agroforestal Mediterráneo (IAM-UPV), Camino de Vera, s/n 46022, Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
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Tian J, Li Y, Fu H, Ren L, He Y, Zhai S, Yang B, Li Q, Liu N, Liu S. Physiological role of CYP17A1-like in cadmium detoxification and its transcriptional regulation in the Pacific oyster, Crassostrea gigas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:149039. [PMID: 34328900 DOI: 10.1016/j.scitotenv.2021.149039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) is one of the most harmful heavy metals due to its persistence and bioaccumulation through the food chains, posing health risks to human. Oysters can bioaccumulate and tolerate high concentrations of Cd, providing a great model for studying molecular mechanism of Cd detoxification. In a previous study, we identified two CYP genes, CYP17A1-like and CYP2C50, that were potentially involved in Cd detoxification in the Pacific oyster, Crassostrea gigas. In this work, we performed further investigations on their physiological roles in Cd detoxification through RNA interference (RNAi). After injection of double-stranded RNA (dsRNA) into the adductor muscle of oysters followed by Cd exposure for 7 days, we observed that the expressions of CYP17A1-like and CYP2C50 in interference group were significantly suppressed on day 3 compared with control group injected with PBS. Moreover, the mortality rate and Cd content in the CYP17A1-like dsRNA interference group (dsCYP17A1-like) was significantly higher than those of the control on day 3. Furthermore, the activities of antioxidant enzymes, including SOD, CAT, GST, were significantly increased in dsCYP17A1-like group, while were not changed in dsCYP2C50 group. More significant tissue damage was observed in gill and digestive gland of oysters in RNAi group than control group, demonstrating the critical role of CYP17A1-like in Cd detoxification. Dual luciferase reporter assay revealed three core regulatory elements of MTF-1 within promoter region of CYP17A1-like, suggesting the potential transcriptional regulation of CYP17A1-like by MTF-1 in oysters. This work demonstrated a critical role of CYP17A1-like in Cd detoxification in C. gigas and provided a new perspective toward unravelling detoxification mechanisms of bivalves under heavy metal stress.
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Affiliation(s)
- Jing Tian
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yongjing Li
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Huiru Fu
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Liting Ren
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Yameng He
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Shangyu Zhai
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Ben Yang
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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11
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Tarquini G, Pagliari L, Ermacora P, Musetti R, Firrao G. Trigger and Suppression of Antiviral Defenses by Grapevine Pinot Gris Virus (GPGV): Novel Insights into Virus-Host Interaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1010-1023. [PMID: 33983824 DOI: 10.1094/mpmi-04-21-0078-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is an emerging trichovirus that has been putatively associated with a novel grapevine disease known as grapevine leaf mottling and deformation (GLMD). Yet the role of GPGV in GLMD disease is poorly understood, since it has been detected both in symptomatic and symptomless grapevines. We exploited a recently constructed GPGV infectious clone (pRI::GPGV-vir) to induce an antiviral response in Nicotiana benthamiana plants. In silico prediction of virus-derived small interfering RNAs and gene expression analyses revealed the involvement of DCL4, AGO5, and RDR6 genes during GPGV infection, suggesting the activation of the posttranscriptional gene-silencing (PTGS) pathway as a plant antiviral defense. PTGS suppression assays in transgenic N. benthamiana 16c plants revealed the ability of the GPGV coat protein to suppress RNA silencing. This work provides novel insights on the interaction between GPGV and its host, revealing the ability of the virus to trigger and suppress antiviral RNA silencing.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Laura Pagliari
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Rita Musetti
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
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12
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Fan J, Martinez-Arguelles DB, Papadopoulos V. Genome-wide expression analysis of a new class of lncRNAs driven by SINE B2. Gene 2020; 768:145332. [PMID: 33278552 DOI: 10.1016/j.gene.2020.145332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/13/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022]
Abstract
Repetitive short interspersed elements B2 (SINE B2) have been shown to possess two promoters: polymerase III promoter for producing short B2-S RNAs and polymerase II promoter for driving the expression of long non-coding RNA (B2-AS lncRNAs). Using a B2-antisense (B2-AS) transcript sequence from the SINE B2 resident in mitochondrial translocator protein gene (Tspo) locus, we constructed a B2-AS specific RNA library and identified 96,862 sequences encoding potential B2-mediated lncRNAs, of which 55,592 lncRNAs with more than 390 nt in length possess a feature of potential genomic locus-specific effect. In addition, small RNA-Northern hybridization showed that the new B2-AS lncRNAs are constantly degraded by the Dicer1 enzyme, a finding further confirmed by in vitro Dicer1 enzyme digestion. B2-AS lncRNAs regulate the expression of target genes in a different fashion than B2-S RNAs. Genome-wide cross-comparison with mRNA mapping showed a total of 904 mRNA loci directly targeted by B2-AS lncRNAs, suggesting a locus-specific effect of the B2-AS lncRNAs and a general effect of B2-S RNAs.
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Affiliation(s)
- Jinjiang Fan
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada; Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States.
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13
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Leonetti P, Miesen P, van Rij RP, Pantaleo V. Viral and subviral derived small RNAs as pathogenic determinants in plants and insects. Adv Virus Res 2020; 107:1-36. [PMID: 32711727 DOI: 10.1016/bs.aivir.2020.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The phenotypic manifestations of disease induced by viruses and subviral infectious entities are the result of complex molecular interactions between host and viral factors. The viral determinants of the diseased phenotype have traditionally been sought at the level of structural or non-structural proteins. However, the discovery of RNA silencing mechanisms has led to speculations that determinants of the diseased phenotype are caused by viral nucleic acid sequences in addition to proteins. RNA silencing is a gene regulation mechanism conserved within eukaryotic kingdoms (with the exception of some yeast species), and in plants and insects it also functions as an antiviral mechanism. Non-coding RNAs of viral origin, ranging in size from 21 to 24 nucleotides (viral small interfering RNAs, vsiRNAs) accumulate in virus-infected tissues and organs, in some cases to comparable levels as the entire complement of host-encoded small interfering RNAs. Upon incorporation into RNA-induced silencing complexes, vsiRNAs can mediate cleavage or induce translational inhibition of nucleic acid targets in a sequence-specific manner. This review focuses on recent findings that suggest an increased complexity of small RNA-based interactions between virus and host. We mainly address plant viruses, but where applicable discuss insect viruses as well. Prominence is given to studies that have indisputably demonstrated that vsiRNAs determine diseased phenotype by either carrying sequence determinants or, indirectly, by altering host-gene regulatory pathways. Results from these studies suggest biotechnological applications, which are also discussed.
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Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food Sciences, Institute for Sustainable Plant Protection, CNR, Bari, Italy..
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14
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De Francesco A, Simeone M, Gómez C, Costa N, García ML. Transgenic Sweet Orange expressing hairpin CP-mRNA in the interstock confers tolerance to citrus psorosis virus in the non-transgenic scion. Transgenic Res 2020; 29:215-228. [PMID: 31970613 DOI: 10.1007/s11248-020-00191-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/13/2020] [Indexed: 10/25/2022]
Abstract
The lack of naturally occurring resistance to citrus psorosis virus (CPsV) necessitates a transgenic approach for the development of CPsV-resistant citrus. To evaluate the feasibility of conferring resistance to a non-transgenic scion, we have assembled citrus plants by grafting combining a non-transgenic Sweet Orange as scion, CPsV-resistant transgenic Sweet Orange lines expressing intron-hairpin (ihp) RNA derived from the viral coat protein (ihpCP) as interstock, and a non-transgenic citrus as rootstock. We demonstrated that ihpCP-transcripts translocate through the graft from interstock to scion, triggering the silencing of coat protein mRNA target. Two independent CPsV challenge assays showed that expression of ihpCP in the interstock provides resistance against CPsV in the interstock, and different levels of protection in the non-tg scion, depending of the virus delivery site. These results indicated that grafting is a promising biotechnological alternative to protect woody plants against virus infections in vegetative propagated plants.
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Affiliation(s)
- A De Francesco
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - M Simeone
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - C Gómez
- Estación Experimental Agropecuaria, INTA Concordia, Ruta Provincial 22 y vías del Ferrocarril (3200), Concordia, Entre Ríos, Argentina
| | - N Costa
- Estación Experimental Agropecuaria, INTA Concordia, Ruta Provincial 22 y vías del Ferrocarril (3200), Concordia, Entre Ríos, Argentina
| | - M L García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina.
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15
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Hornung JE, Hellwig N, Göbel MW. Peptide Nucleic Acid Conjugates of Quinone Methide Precursors Alkylate Ribonucleic Acid after Activation with Light. Bioconjug Chem 2020; 31:639-645. [PMID: 31904221 DOI: 10.1021/acs.bioconjchem.9b00796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Quinone methide precursors 2 and 3 were protected with a photoreactive 2-nitrobenzyl group and conjugated to peptide nucleic acids (PNA) using a Huisgen click reaction. After brief irradiation at 365 nm, cross-linking with complementary RNA strands started and was analyzed with an ALFexpress sequencer. When this method was used, the gel temperature had a major influence on apparent rates. Quinone methides are known to form transient as well as stable bonds with nucleotides. Although both were detected at 25 °C, analysis at 57 °C only recorded the stable types of cross-links, suggesting much slower alkylation kinetics. Linker 11 allowed us to attach quinone methides to internal positions of the PNA/RNA duplex and to capture a model of miR-20a with good efficiency.
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16
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RNA-based therapy for osteogenesis. Int J Pharm 2019; 569:118594. [DOI: 10.1016/j.ijpharm.2019.118594] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/02/2019] [Accepted: 08/03/2019] [Indexed: 02/06/2023]
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17
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Shamloo B, Usluer S. p21 in Cancer Research. Cancers (Basel) 2019; 11:cancers11081178. [PMID: 31416295 PMCID: PMC6721478 DOI: 10.3390/cancers11081178] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/21/2022] Open
Abstract
p21 functions as a cell cycle inhibitor and anti-proliferative effector in normal cells, and is dysregulated in some cancers. Earlier observations on p21 knockout models emphasized the role of this protein in cell cycle arrest under the p53 transcription factor activity. Although tumor-suppressor function of p21 is the most studied aspect of this protein in cancer, the role of p21 in phenotypic plasticity and its oncogenic/anti-apoptotic function, depending on p21 subcellular localization and p53 status, have been under scrutiny recently. Basic science and translational studies use precision gene editing to manipulate p21 itself, and proteins that interact with it; these studies have led to regulatory/functional/drug sensitivity discoveries as well as therapeutic approaches in cancer field. In this review, we will focus on targeting p21 in cancer research and its potential in providing novel therapies.
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Affiliation(s)
- Bahar Shamloo
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Sinem Usluer
- Department of Molecular Biology & Biochemistry, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8010 Graz, Austria
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18
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Chandela A, Watanabe T, Yamagishi K, Ueno Y. Synthesis and characterization of small interfering RNAs with haloalkyl groups at their 3′-dangling ends. Bioorg Med Chem 2019; 27:1341-1349. [DOI: 10.1016/j.bmc.2019.02.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/11/2022]
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19
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Chandela A, Ueno Y. Systemic Delivery of Small Interfering RNA Therapeutics: Obstacles and Advances. ACTA ACUST UNITED AC 2019. [DOI: 10.7831/ras.7.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Akash Chandela
- United Graduate School of Agricultural Science, Gifu University
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University
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20
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Abstract
Lipopolyplexes present well-established nucleic acid carriers assembled from sequence-defined cationic lipo-oligomers and DNA or RNA. They can be equipped with additional surface functionality, like shielding and targeting, in a stepwise assembly method using click chemistry. Here, we describe the synthesis of the required compounds, an azide-bearing lipo-oligomer structure and dibenzocyclooctyne (DBCO) click agents as well as the assembly of the compounds with siRNA into a surface-functionalized formulation. Both the lipo-oligomer and the DBCO-equipped shielding and targeting agents are produced by solid-phase synthesis (SPS). This enables for precise variation of all functional units, like variation in the amount of DBCO attachment sites or polyethylene glycol (PEG) length. Special cleavage conditions with only 5% trifluoroacetic acid (TFA) must be applied for the synthesis of the shielding and targeting agents due to acid lability of the DBCO unit. The two-step lipopolyplex assembly technique allows for separate optimization of the core and the shell of the formulation.
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Affiliation(s)
- Philipp Michael Klein
- Pharmaceutical Biotechnology, Center for System-based Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Center for System-based Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
- Nanosystems Initiative Munich, Munich, Germany
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21
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Reinhard S, Wagner E. Sequence-Defined Cationic Lipo-Oligomers Containing Unsaturated Fatty Acids for Transfection. Methods Mol Biol 2019; 1943:1-25. [PMID: 30838606 DOI: 10.1007/978-1-4939-9092-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sequence-defined cationic lipo-oligomers containing unsaturated fatty acids are potent nucleic acid carriers that are produced by solid-phase supported synthesis. However, the trifluoroacetic acid (TFA)-mediated removal of acid-labile protecting groups and cleavage from the resin can be accompanied by side products caused by an addition of TFA to the double bonds of unsaturated fatty acids. These TFA adducts are converted into hydroxylated derivatives under aqueous conditions. Here we describe an optimized cleavage protocol (precooling cleavage solution to 4 °C, 20 min cleavage at 22 °C), which minimizes TFA adduct formation, retains the unsaturated hydrocarbon chain character, and ensures high yields of the synthesis.
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Affiliation(s)
- Sören Reinhard
- Department of Pharmacy, Pharmaceutical Biotechnology, Center of Nanoscience (CeNS), Ludwig-Maximilians-Universität Butenandtstr, München, Germany.
| | - Ernst Wagner
- Department of Pharmacy, Pharmaceutical Biotechnology, Center of Nanoscience (CeNS), Ludwig-Maximilians-Universität Butenandtstr, München, Germany
- Nanosystems Initiative Munich (NIM), Schellingstr, München, Germany
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22
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Chandela A, Ueno Y. Design, synthesis and evaluation of novel, branched trident small interfering RNA nanostructures for sequence-specific RNAi activity. RSC Adv 2019; 9:34166-34171. [PMID: 35529995 PMCID: PMC9073863 DOI: 10.1039/c9ra08071f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/15/2019] [Indexed: 12/21/2022] Open
Abstract
Small interfering RNAs (siRNAs) are potential candidates for gene regulation with efficient activity, but off-target effects and limited systemic delivery. Herein, we report the design and synthesis of the branched siRNA nanostructures with highly improved resistance against exonucleases. Also, these branched siRNAs showed suppression of off-target gene silencing through selection of the passenger strand as the branching unit. The physical characterization of branched siRNAs showed that they form a compact assembly with a hydrodynamic diameter of 6.9 nm against 2.8 nm of the duplex. We demonstrated that a branched siRNA synthesized with a trebling solid-support selectively exhibits RNAi activity and suppresses the off-target effect. Branched small interfering RNAs (siRNAs) are potential candidates for on-target gene silencing with enhanced serum stability. Their physical characterization also presents them as a prospective drug for systemic delivery. ![]()
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Affiliation(s)
- Akash Chandela
- The United Graduate School of Agricultural Science
- Gifu University
- Gifu
- Japan
| | - Yoshihito Ueno
- The United Graduate School of Agricultural Science
- Gifu University
- Gifu
- Japan
- Course of Applied Life Science
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23
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Arif M, Islam SU, Adnan M, Anwar M, Ali H, Wu Z. Recent progress on gene silencing/suppression by virus-derived small interfering RNAs in rice viruses especially Rice grassy stunt virus. Microb Pathog 2018; 125:210-218. [DOI: 10.1016/j.micpath.2018.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/08/2018] [Accepted: 09/11/2018] [Indexed: 12/16/2022]
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24
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McMenamin AJ, Daughenbaugh KF, Parekh F, Pizzorno MC, Flenniken ML. Honey Bee and Bumble Bee Antiviral Defense. Viruses 2018; 10:E395. [PMID: 30060518 PMCID: PMC6115922 DOI: 10.3390/v10080395] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/12/2022] Open
Abstract
Bees are important plant pollinators in both natural and agricultural ecosystems. Managed and wild bees have experienced high average annual colony losses, population declines, and local extinctions in many geographic regions. Multiple factors, including virus infections, impact bee health and longevity. The majority of bee-infecting viruses are positive-sense single-stranded RNA viruses. Bee-infecting viruses often cause asymptomatic infections but may also cause paralysis, deformity or death. The severity of infection is governed by bee host immune responses and influenced by additional biotic and abiotic factors. Herein, we highlight studies that have contributed to the current understanding of antiviral defense in bees, including the Western honey bee (Apis mellifera), the Eastern honey bee (Apis cerana) and bumble bee species (Bombus spp.). Bee antiviral defense mechanisms include RNA interference (RNAi), endocytosis, melanization, encapsulation, autophagy and conserved immune pathways including Jak/STAT (Janus kinase/signal transducer and activator of transcription), JNK (c-Jun N-terminal kinase), MAPK (mitogen-activated protein kinases) and the NF-κB mediated Toll and Imd (immune deficiency) pathways. Studies in Dipteran insects, including the model organism Drosophila melanogaster and pathogen-transmitting mosquitos, provide the framework for understanding bee antiviral defense. However, there are notable differences such as the more prominent role of a non-sequence specific, dsRNA-triggered, virus limiting response in honey bees and bumble bees. This virus-limiting response in bees is akin to pathways in a range of organisms including other invertebrates (i.e., oysters, shrimp and sand flies), as well as the mammalian interferon response. Current and future research aimed at elucidating bee antiviral defense mechanisms may lead to development of strategies that mitigate bee losses, while expanding our understanding of insect antiviral defense and the potential evolutionary relationship between sociality and immune function.
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Affiliation(s)
- Alexander J McMenamin
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Department of Microbiology and Immunology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
| | - Katie F Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
| | - Fenali Parekh
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Department of Microbiology and Immunology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
| | - Marie C Pizzorno
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA.
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Department of Microbiology and Immunology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
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25
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Zhang C, Wang S, Liu Y, Yang C. Epigenetics in myeloid derived suppressor cells: a sheathed sword towards cancer. Oncotarget 2018; 7:57452-57463. [PMID: 27458169 PMCID: PMC5303001 DOI: 10.18632/oncotarget.10767] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/10/2016] [Indexed: 12/16/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs), a heterogeneous population of cells composed of progenitors and precursors to myeloid cells, are deemed to participate in the development of tumor-favoring immunosuppressive microenvironment. Thus, the regulatory strategies targeting MDSCs' expansion, differentiation, accumulation and function could possibly be effective “weapons” in anti-tumor immunotherapies. Epigenetic mechanisms, which involve DNA modification, covalent histone modification and RNA interference, result in the heritable down-regulation or silencing of gene expression without a change in DNA sequences. Epigenetic modification of MDSC's functional plasticity leads to the remodeling of its characteristics, therefore reframing the microenvironment towards countering tumor growth and metastasis. This review summarized the pertinent findings on the DNA methylation, covalent histone modification, microRNAs and small interfering RNAs targeting MDSC in cancer genesis, progression and metastasis. The potentials as well as possible obstacles in translating into anti-cancer therapeutics were also discussed.
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Affiliation(s)
- Chao Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Shuo Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Yufeng Liu
- General Surgery, Department of Nursing, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
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26
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Zeng G, Zhang D, Liu X, Kang Q, Fu Y, Tang B, Guo W, Zhang Y, Wei G, He D. Co-expression of Piwil2/Piwil4 in nucleus indicates poor prognosis of hepatocellular carcinoma. Oncotarget 2018; 8:4607-4617. [PMID: 27894076 PMCID: PMC5354858 DOI: 10.18632/oncotarget.13491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/28/2016] [Indexed: 01/08/2023] Open
Abstract
Purpose This study aimed to explore the localization and expression of P-element-induced wimpy testis-like 2 (piwil2)/Piwil4 in hepatocellular carcinoma (HCC) tissues, and analyze the correlation between co-expression pattern and prognosis of HCC. Results Piwil2 showed 100% positive expression in the cell nucleus, with the intensity higher than in the cytoplasm. Piwil4 showed a lower intensity of expression in the cell nucleus than in the cytoplasm. The molecular chaperone Piwil2/Piwil4 had four co-expression patterns: nuclear co-expression, nuclear and cytoplasmic co-expression, cytoplasmic co-expression, and non-coexpression. The survival rate and the overall survival sequentially increased. The prognostic phenotype of the nuclear co-expression of Piwil2/Piwil4 was worse than that of non-coexpression, and the intracellular localization and expression of Piwil2 and Piwil4 were not significantly different. Methods HCC pathological tissue samples with follow-up information (90 cases) and 2 normal control liver tissues were collected and made into a 92-site microarray. The expression of Piwil2 and Piwil4 was detected using the immunofluorescence double staining method. The differences in the expression and location of Piwil2 and Piwil4 in tumor cells were explored, and the influence of such differences on the long-term survival rate of HCC was studied using Kaplan-Meier survival curve and log-rank test. The clinical staging was analyzed according to the HCC international TNM staging criteria. Conclusions The nuclear co-expression of Piwil2/Piwil4 indicated that patients with HCC had a worse prognostic phenotype. The molecular chaperone Piwil2/Piwil4 seems promising as a molecular marker for prognosis judgment; a single marker (Piwil2/Piwil4) cannot be used for prognosis judgment.
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Affiliation(s)
- Guangping Zeng
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Deying Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Xing Liu
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Qing Kang
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Yiyao Fu
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Bo Tang
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Wenhao Guo
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27103, USA
| | - Guanghui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
| | - Dawei He
- Department of Urology, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing 400014, China
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27
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Jung J, Lee S, Cho HS, Park K, Ryu JW, Jung M, Kim J, Kim H, Kim DS. Bioinformatic analysis of regulation of natural antisense transcripts by transposable elements in human mRNA. Genomics 2018; 111:159-166. [PMID: 29366860 DOI: 10.1016/j.ygeno.2018.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/19/2022]
Abstract
Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database. Our in silico analysis identified 1079 NATs and 700 sense-antisense gene pairs. We identified 179 NATs that showed evidence of having been affected by TEs during cellular gene expression. These findings may provide an understanding of the complex regulation mechanisms of NATs. If our understanding of NATs as modulators of gene expression is further enhanced, we can develop ways to control gene expression.
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Affiliation(s)
- Jaeeun Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sugi Lee
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Department of Stem Cell Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kunhyang Park
- Department of Core Facility Management Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jea-Woon Ryu
- Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Minah Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jeongkil Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - HyeRan Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Plant Systems Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Dae-Soo Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.
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Chennareddy S, Cicak T, Clark L, Russell S, Skokut M, Beringer J, Yang X, Jia Y, Gupta M. Expression of a novel bi-directional Brassica napus promoter in soybean. Transgenic Res 2017; 26:727-738. [PMID: 28916981 DOI: 10.1007/s11248-017-0042-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The expression profile of a natural bi-directional promoter, derived from the Brassica napus EPSPS-A gene, was studied in transgenic soybean (Glycine max C.V. Maverick) lines. Two constructs, pDAB100331 and pDAB100333, were assembled to test the bi-directionality of the promoter. Two reporter genes, gfp and gusA, were employed and they were interchangeably placed in both constructs, one on each end of the promoter such that both proteins expressed divergently in each construct. In the T0 generation, GUS expression was more uniform throughout the leaf of pDAB100333 transgenic plants, where the gusA gene was expressed from the downstream or EPSPS-A end of the bi-directional promoter. Comparatively, GUS expression was more localized in the midrib and veins of the leaf of pDAB100331 transgenic plants, where the gusA gene was expressed from the upstream end of the bi-directional promoter. These observations indicated a unique expression pattern from each end of the promoter and consistently higher expression in genes expressed from the downstream end (e.g., EPSPS-A end) of the promoter in the tissues examined. The GFP expression pattern followed that of GUS when placed in the same position relative to the promoter. In the T1 generation, transcript analysis also showed higher expression of both gusA and gfp when those genes were located at the downstream end of the promoter. Accordingly, the pDAB100331 events exhibited a higher gfp/gusA transcript ratio, while pDAB100333 events produced a higher gusA/gfp transcript ratio consistent with the observations in T0 plants. These results demonstrated that the EPSPS-A gene bidirectional promoter can be effectively utilized to drive expression of two transgenes for the desired traits.
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Affiliation(s)
| | - Toby Cicak
- Dow AgroSciences, West Lafayette, IN, 47906, USA
| | | | | | | | | | - Xiaozeng Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yi Jia
- Dow AgroSciences, Indianapolis, IN, 46268, USA
| | - Manju Gupta
- Dow AgroSciences, Indianapolis, IN, 46268, USA
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Philips S, Wu HY, Li L. Using machine learning algorithms to identify genes essential for cell survival. BMC Bioinformatics 2017; 18:397. [PMID: 28984184 PMCID: PMC5629548 DOI: 10.1186/s12859-017-1799-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background With the explosion of data comes a proportional opportunity to identify novel knowledge with the potential for application in targeted therapies. In spite of this huge amounts of data, the solutions to treating complex disease is elusive. One reason being that these diseases are driven by a network of genes that need to be targeted in order to understand and treat them effectively. Part of the solution lies in mining and integrating information from various disciplines. Here we propose a machine learning method to mining through publicly available literature on RNA interference with the goal of identifying genes essential for cell survival. Results A total of 32,164 RNA interference abstracts were identified from 10.5 million pubmed abstracts (2001 - 2015). These abstracts spanned over 1467 cancer cell lines and 4373 genes representing a total of 25,891 cell gene associations. Among the 1467 cell lines 88% of them had at least 1 or up to 25 genes studied in a given cell line. Among the 4373 genes 96% of them were studied in at least 1 or up to 25 different cell lines. Conclusions Identifying genes that are crucial for cell survival can be a critical piece of information especially in treating complex diseases, such as cancer. The efficacy of a therapeutic intervention is multifactorial in nature and in many cases the source of therapeutic disruption could be from an unsuspected source. Machine learning algorithms helps to narrow down the search and provides information about essential genes in different cancer types. It also provides the building blocks to generate a network of interconnected genes and processes. The information thus gained can be used to generate hypothesis which can be experimentally validated to improve our understanding of what triggers and maintains the growth of cancerous cells. Electronic supplementary material The online version of this article (10.1186/s12859-017-1799-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santosh Philips
- Center for Computational Biology and Bioinformatics, Indiana University, 410 West 10th Street, HITS 5003 lab, Indianapolis, IN, 46202, USA
| | - Heng-Yi Wu
- Center for Computational Biology and Bioinformatics, Indiana University, 410 West 10th Street, HITS 5003 lab, Indianapolis, IN, 46202, USA
| | - Lang Li
- Center for Computational Biology and Bioinformatics, Indiana University, 410 West 10th Street, HITS 5003 lab, Indianapolis, IN, 46202, USA.
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BSMV-Induced Gene Silencing Assay for Functional Analysis of Wheat Rust Resistance. Methods Mol Biol 2017; 1659:257-264. [PMID: 28856657 DOI: 10.1007/978-1-4939-7249-4_22] [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: 03/06/2023]
Abstract
Virus-induced gene silencing (VIGS) is a widely used reverse genetics tool to knock down genes in plants transiently without transformation. The assay has been successfully used to downregulate the transcript abundance of a target gene at almost any plant developmental stages in any tissues. Here, we describe the VIGS assay using a barley stripe mosaic virus (BSMV) for functional genomics analysis in wheat with the focus on genes involved in rust resistance.
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SiRNA-mediated in vivo gene knockdown by acid-degradable cationic nanohydrogel particles. J Control Release 2017; 248:10-23. [DOI: 10.1016/j.jconrel.2016.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 01/22/2023]
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De Francesco A, Costa N, García ML. Citrus psorosis virus coat protein-derived hairpin construct confers stable transgenic resistance in citrus against psorosis A and B syndromes. Transgenic Res 2016; 26:225-235. [PMID: 27891561 DOI: 10.1007/s11248-016-0001-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/13/2016] [Indexed: 12/18/2022]
Abstract
Citrus psorosis virus (CPsV) is the causal agent of psorosis, a serious and widespread citrus disease. Two syndromes of psorosis, PsA and PsB, have been described. PsB is the most aggressive and rampant form. Previously, we obtained Pineapple sweet orange plants transformed with a hairpin construct derived from the CPsV coat protein gene (ihpCP). Some of these plants were resistant to CPsV 90-1-1, a PsA isolate homologous to the transgene. In this study, we found that expression of the ihpCP transgene and siRNA production in lines ihpCP-10 and -15 were stable with time and propagation. In particular, line ihpCP-15 has been resistant for more than 2 years, even after re-inoculation. The ihpCP plants were also resistant against a heterologous CPsV isolate that causes severe PsB syndrome. Line ihpCP-15 manifested complete resistance while line ihpCP-10 was tolerant to the virus, although with variable behaviour, showing delay and attenuation in PsB symptoms. These lines are promising for a biotech product aimed at eradicating psorosis.
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Affiliation(s)
- A De Francesco
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - N Costa
- Estación Experimental Agropecuaria, INTA Concordia, Ruta Provincial 22 y vías del Ferrocarril, 3200, Concordia, Entre Ríos, Argentina
| | - M L García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115, 1900, La Plata, Buenos Aires, Argentina.
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Knockdown of RNA Interference Pathway Genes in Western Corn Rootworms (Diabrotica virgifera virgifera Le Conte) Demonstrates a Possible Mechanism of Resistance to Lethal dsRNA. PLoS One 2016; 11:e0157520. [PMID: 27310918 PMCID: PMC4911125 DOI: 10.1371/journal.pone.0157520] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/01/2016] [Indexed: 01/28/2023] Open
Abstract
RNA interference (RNAi) is being developed as a potential tool for insect pest management. Increased understanding of the RNAi pathway in target insect pests will provide information to use this technology effectively and to inform decisions related to resistant management strategies for RNAi based traits. Dicer 2 (Dcr2), an endonuclease responsible for formation of small interfering RNA’s and Argonaute 2 (Ago2), an essential catalytic component of the RNA-induced silencing complex (RISC) have both been associated with the RNAi pathway in a number of different insect species including the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae). We identified both genes from a transcriptome library generated from different tissues and developmental stages of the western corn rootworm, an important target pest for transgenic plants expressing dsRNA targeting essential genes. The expression of these genes was suppressed by more than 90% after injecting gene specific dsRNA into adult rootworms. The injected beetles were then fed vATPase A dsRNA which has previously been demonstrated to cause mortality in western corn rootworm adults. The suppression of both RNAi pathway genes resulted in reduced mortality after subsequent exposure to lethal concentrations of vATPase A dsRNA as well as increased vATPase A expression relative to control treatments. Injections with dsRNA for a non-lethal target sequence (Laccase 2) did not affect mortality or expression caused by vATPase A dsRNA indicating that the results observed with Argo and Dicer dsRNA were not caused by simple competition among different dsRNA’s. These results confirm that both genes play an important role in the RNAi pathway for western corn rootworms and indicate that selection pressures that potentially affect the expression of these genes may provide a basis for future studies to understand potential mechanisms of resistance.
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Omarov RT, Ciomperlik J, Scholthof HB. An in vitro reprogrammable antiviral RISC with size-preferential ribonuclease activity. Virology 2016; 490:41-8. [PMID: 26812224 DOI: 10.1016/j.virol.2015.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 01/29/2023]
Abstract
Infection of Nicotiana benthamiana plants with Tomato bushy stunt virus (TBSV) mutants compromised for silencing suppression induces formation of an antiviral RISC (vRISC) that can be isolated using chromatography procedures. The isolated vRISC sequence-specifically degrades TBSV RNA in vitro, its activity can be down-regulated by removing siRNAs, and re-stimulated by exogenous supply of siRNAs. vRISC is most effective at hydrolyzing the ~4.8kb genomic RNA, but less so for a ~2.2kb TBSV subgenomic mRNA (sgRNA1), while the 3' co-terminal sgRNA2 of ~0.9kb appears insensitive to vRISC cleavage. Moreover, experiments with in vitro generated 5' co-terminal viral transcripts show that RNAs of ~2.7kb are efficiently cleaved while those of ~1.1kb or shorter are unaffected. The isolated antiviral ribonuclease complex fails to degrade ~0.4kb defective interfering RNAs (DIs) in vitro, agreeing with findings that in plants DIs are not targeted by silencing.
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Affiliation(s)
- Rustem T Omarov
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, United States
| | - Jessica Ciomperlik
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, United States
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, United States.
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Ni JZ, Kalinava N, Chen E, Huang A, Trinh T, Gu SG. A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans. Epigenetics Chromatin 2016; 9:3. [PMID: 26779286 PMCID: PMC4714518 DOI: 10.1186/s13072-016-0052-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Background Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena are poorly understood. In C. elegans, siRNA mediates transgenerational gene
silencing through the germline nuclear RNAi pathway. This pathway is also required to maintain the germline immortality when C. elegans is under heat stress. However, the underlying molecular mechanism is unknown. In this study, we investigated the impact of heat stress on chromatin, transcription, and siRNAs at the whole-genome level, and whether any of the heat-induced effects is transgenerationally heritable in either the wild-type or the germline nuclear RNAi mutant animals. Results We performed 12-generation temperature-shift experiments using the wild-type C. elegans and a mutant strain that lacks the germline-specific nuclear Argonaute protein HRDE-1/WAGO-9. By examining the mRNA, small RNA, RNA polymerase II, and H3K9 trimethylation profiles at the whole-genome level, we revealed an epigenetic role of HRDE-1 in repressing heat stress-induced transcriptional activation of over 280 genes. Many of these genes are in or near LTR (long-terminal repeat) retrotransposons. Strikingly, for some of these genes, the heat stress-induced transcriptional activation in the hrde-1 mutant intensifies in the late generations under the heat stress and is heritable for at least two generations after the mutant animals are shifted back to lower temperature. hrde-1 mutation also leads to siRNA expression changes of many genes. This effect on siRNA is dependent on both the temperature and generation. Conclusions Our study demonstrated that a large number of the endogenous targets of the germline nuclear RNAi pathway in C. elegans are sensitive to heat-induced transcriptional activation. This effect at certain genomic loci including LTR retrotransposons is transgenerational. Germline nuclear RNAi antagonizes this temperature effect at the transcriptional level and therefore may play a key role in heat stress response in C. elegans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0052-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Alex Huang
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Thi Trinh
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA ; Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA
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Rheiner S, Bae Y. Increased poly(ethylene glycol) density decreases transfection efficacy of siRNA/poly(ethylene imine) complexes. AIMS BIOENGINEERING 2016. [DOI: 10.3934/bioeng.2016.4.454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Boyapalle S, Xu W, Raulji P, Mohapatra S, Mohapatra SS. A Multiple siRNA-Based Anti-HIV/SHIV Microbicide Shows Protection in Both In Vitro and In Vivo Models. PLoS One 2015; 10:e0135288. [PMID: 26407080 PMCID: PMC4583459 DOI: 10.1371/journal.pone.0135288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/20/2015] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus (HIV) types 1 and 2 (HIV-1 and HIV-2) are the etiologic agents of AIDS. Most HIV-1 infected individuals worldwide are women, who acquire HIV infections during sexual contact. Blocking HIV mucosal transmission and local spread in the female lower genital tract is important in preventing infection and ultimately eliminating the pandemic. Microbicides work by destroying the microbes or preventing them from establishing an infection. Thus, a number of different types of microbicides are under investigation, however, the lack of their solubility and bioavailability, and toxicity has been major hurdles. Herein, we report the development of multifunctional chitosan-lipid nanocomplexes that can effectively deliver plasmids encoding siRNA(s) as microbicides without adverse effects and provide significant protection against HIV in both in vitro and in vivo models. Chitosan or chitosan-lipid (chlipid) was complexed with a cocktail of plasmids encoding HIV-1-specific siRNAs (psiRNAs) and evaluated for their efficacy in HEK-293 cells, PBMCs derived from nonhuman primates, 3-dimensional human vaginal ectocervical tissue (3D-VEC) model and also in non-human primate model. Moreover, prophylactic administration of the chlipid to deliver a psiRNA cocktail intravaginally with a cream formulation in a non-human primate model showed substantial reduction of SHIV (simian/human immunodeficiency virus SF162) viral titers. Taken together, these studies demonstrate the potential of chlipid-siRNA nanocomplexes as a potential genetic microbicide against HIV infections.
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Affiliation(s)
- Sandhya Boyapalle
- Department of Internal Medicine -Division of Translational Medicine and Nanomedicine Research Center, University of South Florida, Tampa, Florida, United States of America
- Transgenex Nanobiotech Inc, Tampa, Florida, United States of America
| | - Weidong Xu
- Department of Internal Medicine -Division of Translational Medicine and Nanomedicine Research Center, University of South Florida, Tampa, Florida, United States of America
- Transgenex Nanobiotech Inc, Tampa, Florida, United States of America
| | - Payal Raulji
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Transgenex Nanobiotech Inc, Tampa, Florida, United States of America
| | - Subhra Mohapatra
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- James A Haley VA Hospital, Tampa, Florida, United States of America
| | - Shyam S Mohapatra
- Department of Internal Medicine -Division of Translational Medicine and Nanomedicine Research Center, University of South Florida, Tampa, Florida, United States of America
- James A Haley VA Hospital, Tampa, Florida, United States of America
- * E-mail:
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RNAi in murine hepatocytes: the agony of choice--a study of the influence of lipid-based transfection reagents on hepatocyte metabolism. Arch Toxicol 2015; 89:1579-88. [PMID: 26233687 DOI: 10.1007/s00204-015-1571-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/15/2015] [Indexed: 10/23/2022]
Abstract
Primary hepatocyte cell cultures are widely used for studying hepatic diseases with alterations in hepatic glucose and lipid metabolism, such as diabetes and non-alcoholic fatty liver disease. Therefore, small interfering RNAs (siRNAs) provide a potent and specific tool to elucidate the signaling pathways and gene functions involved in these pathologies. Although RNA interference (RNAi) in vitro is frequently used in these investigations, the metabolic alterations elucidated by different siRNA delivery strategies have hardly been investigated in transfected hepatocytes. To elucidate the influence of the most commonly used lipid-based transfection reagents on cultured primary hepatocytes, we studied the cytotoxic effects and transfection efficiencies of INTERFERin(®), Lipofectamine(®)RNAiMAX, and HiPerFect(®). All of these transfection agents displayed low cytotoxicity (5.6-9.0 ± 1.3-3.4%), normal cell viability, and high transfection efficiency (fold change 0.08-0.13 ± 0.03-0.05), and they also favored the satisfactory down-regulation of target gene expression. However, when effects on the metabolome and lipidome were studied, considerable differences were observed among the transfection reagents. Cellular triacylglycerides levels were either up- or down-regulated [maximum fold change: INTERFERin(®) (48 h) 2.55 ± 0.34, HiPerFect(®) (24 h) 0.79 ± 0.08, Lipofectamine(®)RNAiMAX (48 h) 1.48 ± 0.21], and mRNA levels of genes associated with lipid metabolism were differentially affected. Likewise, metabolic functions such as amino acid utilization from were perturbed (alanine, arginine, glycine, ornithine, and pyruvate). In conclusion, these findings demonstrate that the choice of non-viral siRNA delivery agent is critical in hepatocytes. This should be remembered, especially if RNA silencing is used for studying hepatic lipid homeostasis and its regulation.
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Zhu L, Bao L, Zhang X, Xia X, Sun H. Inhibition of porcine reproductive and respiratory syndrome virus replication with exosome-transferred artificial microRNA targeting the 3' untranslated region. J Virol Methods 2015; 223:61-8. [PMID: 26238924 DOI: 10.1016/j.jviromet.2015.07.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/05/2015] [Accepted: 07/29/2015] [Indexed: 12/30/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is an economically important swine disease. As part of the development of RNA interference (RNAi) strategy against the disease, in this study a recombinant adenovirus (rAd) expressing the artificial microRNA (amiRNA) targeting the 3' untranslated region (UTR) was used to investigate the exosome-mediated amiRNA transfer from different pig cell types to porcine alveolar macrophages (PAMs). Quantitative RT-PCR showed that the sequence-specific amiRNA was expressed in and secreted via exosomes from the rAd-transduced pig kidney cell line PK-15, PAM cell line 3D4/163, kidney fibroblast cells (PFCs) and endometrial endothelial cells (PEECs) with different secretion efficiencies. Fluorescent microscopy revealed that the dye-labeled amiRNA-containing exosomes of different cell origins were efficiently taken up by all of the five types of pig cells tested, including primary PAMs. Quantitative RT-PCR showed that the amiRNA-containing exosomes of different cell origins were taken up by primary PAMs in both time- and dose-dependent manners. Both quantitative RT-PCR and viral titration assays showed that the exosome-delivered amiRNA had potent anti-viral effects against three different PRRSV strains. These data suggest that the exosomes derived from pig cells could serve as an efficient miRNA transfer vehicle, and that the exosome-delivered amiRNA had potent anti-viral effects against different PRRSV strains.
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Affiliation(s)
- Li Zhu
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Liping Bao
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xinyu Zhang
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiaoli Xia
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Huaichang Sun
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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Huang L, Kong Y, Wang J, Sun J, Shi Q, Qiu YH. Reducing progression of experimental lupus nephritis via inhibition of the B7/CD28 signaling pathway. Mol Med Rep 2015; 12:4187-4195. [PMID: 26096149 PMCID: PMC4526067 DOI: 10.3892/mmr.2015.3953] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 02/26/2015] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to evaluate the effects of the B7/cluster of differentiation (CD)28 signaling pathway on experimental lupus nephritis and examine the molecular mechanism involved by inhibiting the B7/CD28 signaling pathway. A lupus nephritis model in C57BL/6 J mice was induced via intraperitoneal injection of pristane. A recombinant B7-1 short hairpin RNA (shRNA) lentivirus vector was constructed by synthesis and splicing. A neutralizing mouse anti-human B7-1 antibody termed 4E5 was also prepared. The mouse model of lupus nephritis was treated with B7-1 shRNA and 4E5 via injection through the tail vein. The silencing effects of B7-1 shRNA lentiviral infection on target molecules were evaluated using immunofluorescence and flow cytometry. The levels of protein in the urine were detected using Albustix test paper each month over 10 months. The concentration of interleukin (IL)-4 and interferon-γ in the serum was determined using an ELISA. The immune complex (IC) deposits in the kidney were analyzed using direct immunofluorescence. The results demonstrated that the C57BL/6 J mouse lupus nephritis model was successfully constructed with immune cells activated in the spleen of the mice, increases in the concentration of anti-nuclear antibody (ANA) and anti-double stranded DNA antibodies as well as positive IC formation. Following B7-1 shRNA lentivirus or 4E5 treatment, CD11b+B7-1+, CD11c+B7-1+ and CD21+B7-1+ cells in the spleen of the mice were significantly reduced. The concentration of ANA and IL-4 in the serum was also decreased. The concentration of urine protein was reduced and it was at its lowest level in the 4E5 early intervention group. It was also revealed that the immunofluorescence intensity of the IC deposits was weak in the 4E5 early intervention group. In conclusion, inhibiting the B7-1/CD28 signaling pathway is able to alleviate experimental lupus nephritis and provides an experimental basis for the therapeutic use of blocking the B7-1/CD28 signaling pathway in human lupus nephritis and other autoimmune disorders.
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Affiliation(s)
- Li Huang
- Department of Internal Medicine, Children's Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Yong Kong
- Department of Immunology, Medical College, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Jing Wang
- Laboratory Animal Center of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Jie Sun
- Division of Nano Biomedicine, Suzhou Institute of Nano‑Tech and Nano‑Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215000, P.R. China
| | - Qin Shi
- Department of Orthopedics, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Yu-Hua Qiu
- Department of Immunology, Medical College, Soochow University, Suzhou, Jiangsu 215123, P.R. China
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Jiang XH, Xie YT, Jiang B, Tang MY, Ma T, Peng H. Inhibition of expression of hepatitis C virus 1b genotype core and NS4B genes in HepG2 cells using artificial microRNAs. Mol Med Rep 2015; 12:1905-13. [PMID: 25847260 DOI: 10.3892/mmr.2015.3571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 02/05/2015] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to evaluate the silencing effect of artificial microRNAs (amiRNAs) against the hepatitis C virus (HCV) 1b (HCV1b) genotype core (C) and non-structural protein 4B (NS4B) genes. pDsRed-monomer-Core and pDsRed-monomer-NS4B plasmids, containing the target genes were constructed. A total of eight artificial micro RNA (amiRNA)-expressing plasmids, namely, pmiRE-C-mi1 to -mi4 and pmiRE-NS4B-mi1 to -mi4, were designed and constructed to interfere with various sites of the core and NS4B genes, and the amiRNA interfering plasmid and the corresponding target gene-expressing plasmid were co-transfected into HepG2 cells. At 48 h after transfection, HCV core and NS4B gene expression levels were detected using fluorescence microscopy, flow cytometry, reverse transcription quantitative polymerase chain reaction and western blot analysis. Fluorescence microscopy revealed that the target gene-transfected cells expressed red fluorescent protein, whereas the interfering plasmid-transfected cells exhibited expression of green fluorescent protein. The percentage of red fluorescent proteins and mean fluorescence intensity, as well as protein expression levels of the core and NS4B genes within the cells, which were co-transfected by the amiRNA interfering plasmid and the target gene, were significantly decreased. The results of the present study confirmed that amiRNAs may effectively and specifically inhibit the expression of HCV1b core and NS4B genes in HepG2 cells, potentially providing a novel therapeutic strategy for the treatment of HCV.
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Affiliation(s)
- Xiao-Hua Jiang
- Department of Infectious Diseases, Xiangya Hospital of Central South University, Changsha, Hunan 410087, P.R. China
| | - Yu-Tao Xie
- Department of Infectious Diseases, Xiangya Hospital of Central South University, Changsha, Hunan 410087, P.R. China
| | - Bo Jiang
- Department of Infectious Diseases, The First Affiliated Hospital of The University of South China, Hengyang, Hunan 421001, P.R. China
| | - Meng-Ying Tang
- Department of Infectious Diseases, The First Affiliated Hospital of The University of South China, Hengyang, Hunan 421001, P.R. China
| | - Tao Ma
- Department of Infectious Diseases, The First Affiliated Hospital of The University of South China, Hengyang, Hunan 421001, P.R. China
| | - Hua Peng
- Department of Infectious Diseases, The First Affiliated Hospital of The University of South China, Hengyang, Hunan 421001, P.R. China
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42
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RNAi: antiviral therapy against dengue virus. Asian Pac J Trop Biomed 2015; 3:232-6. [PMID: 23620845 DOI: 10.1016/s2221-1691(13)60057-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 02/25/2013] [Indexed: 01/01/2023] Open
Abstract
Dengue virus infection has become a global threat affecting around 100 countries in the world. Currently, there is no licensed antiviral agent available against dengue. Thus, there is a strong need to develop therapeutic strategies that can tackle this life threatening disease. RNA interference is an important and effective gene silencing process which degrades targeted RNA by a sequence specific process. Several studies have been conducted during the last decade to evaluate the efficiency of siRNA in inhibiting dengue virus replication. This review summarizes siRNAs as a therapeutic approach against dengue virus serotypes and concludes that siRNAs against virus and host genes can be next generation treatment of dengue virus infection.
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43
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Wolniak SM, Boothby TC, van der Weele CM. Posttranscriptional control over rapid development and ciliogenesis in Marsilea. Methods Cell Biol 2015; 127:403-44. [PMID: 25837402 DOI: 10.1016/bs.mcb.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Marsilea vestita is a semiaquatic fern that produces its spores (meiotic products) as it undergoes a process of natural desiccation. During the period of desiccation, the spores mature, and produce large quantities of pre-mRNA, which is partially processed and stored in nuclear speckles and can remain stable during a period of extended quiescence in the dry spore. Rehydration of the spores initiates a highly coordinated developmental program, featuring nine successive mitotic division cycles that occur at precise times and in precise planes within the spore wall to produce 39 cells, 32 of which are spermatids. The spermatids then undergo de novo basal body formation, the assembly of a massive cytoskeleton, nuclear and cell elongation, and finally ciliogenesis, before being released from the spore wall. The entire developmental program requires only 11 h to reach completion, and is synchronous in a population of spores rehydrated at the same time. Rapid development in this endosporic gametophyte is controlled posttranscriptionally, where stored pre-mRNAs, many of which are intron-retaining transcripts, are unmasked, processed, and translated under tight spatial and temporal control. Here, we describe posttranscriptional mechanisms that exert temporal and spatial control over this developmental program, which culminates in the production of ∼140 ciliary axonemes in each spermatozoid.
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Affiliation(s)
- Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Thomas C Boothby
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
| | - Corine M van der Weele
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park MD 20742, USA
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Sato S, Morita K, Nakamura H. Regulation of Target Protein Knockdown and Labeling Using Ligand-Directed Ru(bpy)3 Photocatalyst. Bioconjug Chem 2015; 26:250-6. [DOI: 10.1021/bc500518t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shinichi Sato
- Chemical
Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Kohei Morita
- Department
of Chemistry, Faculty of Science, Gakushuin University, Mejiro, Tokyo 171-8588, Japan
| | - Hiroyuki Nakamura
- Chemical
Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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45
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Rheiner S, Rychahou P, Bae Y. Effects of the Lipophilic Core of Polymer Nanoassemblies on Intracellular Delivery and Transfection of siRNA. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.3.284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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46
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Abstract
Viruses are obligate intracellular entities that infect all forms of life. In plants, invading viral nucleic acids trigger RNA silencing machinery and it results in the accumulation of viral short interfering RNAs (v-siRNAs). The study of v-siRNAs population in biological samples has become a major part of many research projects aiming to identify viruses infecting them, including unknown viruses, even at extremely low titer. Currently, siRNA populations are investigated by high-throughput sequencing approaches, which generate very large data sets. The major difficulty in these studies is to properly analyze such huge amount of data. In this regard, easy-to-use bioinformatics tools to groom and decipher siRNA libraries and to draw out v-siRNAs are needed. Here we describe a workflow, which permit users with little experience in bioinformatics to draw out v-siRNAs from raw data sequences obtained by Illumina technology. Such pipeline has been released in the context of Galaxy, an open source Web-based platform for bioinformatics analyses.
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Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection of CNR, Strada delle Cacce 73, Turin, Italy
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47
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Zhu L, Song H, Zhang X, Xia X, Sun H. Inhibition of porcine reproductive and respiratory syndrome virus infection by recombinant adenovirus- and/or exosome-delivered the artificial microRNAs targeting sialoadhesin and CD163 receptors. Virol J 2014; 11:225. [PMID: 25522782 PMCID: PMC4279792 DOI: 10.1186/s12985-014-0225-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/10/2014] [Indexed: 01/24/2023] Open
Abstract
Background The current vaccines failed to provide substantial protection against porcine reproductive and respiratory syndrome (PRRS) and the new vaccine development faces great challenges. Sialoadhesin (Sn) and CD163 are the two key receptors for PRRS virus (PRRSV) infection of porcine alveolar macrophages (PAMs), but the artificial microRNA (amiRNA) strategy targeting two viral receptors has not been described. Methods The candidate miRNAs targeting Sn or CD163 receptor were predicted using a web-based miRNA design tool and validated by transfection of cells with each amiRNA expression vector plus the reporter vector. The amiRNA-expressing recombinant adenoviruses (rAds) were generated using AdEasy Adenoviral Vector System. The rAd transduction efficiencies for pig cells were measured by flow cytometry and fluorescent microscopy. The expression and exosome-mediated secretion of amiRNAs were detected by RT-PCR. The knock-down of Sn or CD163 receptor by rAd- and/or exosome-delivered amiRNA was detected by quantitative RT-PCR and flow cytometry. The additive anti-PRRSV effect between the two amiRNAs was detected by quantitative RT-PCR and viral titration. Results All 18 amiRNAs validated were effective against Sn or CD163 receptor mRNA expression. Two rAds expressing Sn- or CD163-targeted amiRNA were generated for further study. The maximal rAd transduction efficiency was 62% for PAMs at MOI 800 or 100% for PK-15 cells at MOI 100. The sequence-specific amiRNAs were expressed efficiently in and secreted from the rAd-transduced cells via exosomes. The expression of Sn and CD163 receptors was inhibited significantly by rAd transduction and/or amiRNA-containing exosome treatment at mRNA and protein levels. Both PRRSV ORF7 copy number and viral titer were reduced significantly by transduction of PAMs with the two rAds and/or by treatment with the two amiRNA-containing exosomes. The additive anti-PRRSV effect between the two amiRNAs was relatively long-lasting (96 h) and effective against three different viral strains. Conclusion These results suggested that Sn- and CD163-targeted amiRNAs had an additive anti-PRRSV effect against different viral strains. Our findings provide new evidence supporting the hypothesis that exosomes can also serve as an efficient small RNA transfer vehicle for pig cells.
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Affiliation(s)
- Li Zhu
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
| | - Hongqin Song
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
| | - Xinyu Zhang
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
| | - Xiaoli Xia
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
| | - Huaichang Sun
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
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48
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Sinha S, Medhi B, Sehgal R. Challenges of drug-resistant malaria. ACTA ACUST UNITED AC 2014; 21:61. [PMID: 25402734 PMCID: PMC4234044 DOI: 10.1051/parasite/2014059] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/23/2014] [Indexed: 01/09/2023]
Abstract
Over the past six decades, the drug resistance of Plasmodium falciparum has become an issue of utmost concern. Despite the remarkable progress that has been made in recent years in reducing the mortality rate to about 30% with the scaling-up of vector control, introduction of artemisinin-based combination therapies and other malaria control strategies, the confirmation of artemisinin resistance on the Cambodia–Thailand border threatened all the previous success. This review addresses the global scenario of antimalarial resistance and factors associated with it, with the main emphasis on futuristic approaches like nanotechnology and stem cell therapy that may impede resistant malaria, along with novel medications which are preparing to enter the global antimalarial market. These novel studies are likely to escalate over the coming years and will hopefully help to reduce the burden of malaria.
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Affiliation(s)
- Shweta Sinha
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Bikash Medhi
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
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Zhang W, Cai L, Geng HJ, Su CF, Yan L, Wang JH, Gao Q, Luo HM. Methyl 3,4-dihydroxybenzoate extends the lifespan of Caenorhabditis elegans, partly via W06A7.4 gene. Exp Gerontol 2014; 60:108-16. [PMID: 25456844 DOI: 10.1016/j.exger.2014.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/27/2014] [Accepted: 10/14/2014] [Indexed: 02/07/2023]
Abstract
To identify and analyze the compounds that delay aging and extend the lifespan is an important aspect of the gerontology research. A number of compounds, including the ones with the antioxidant properties, have been shown to extend the lifespan of Caenorhabditis elegans. Here, we report that methyl 3,4-dihydroxybenzoate (MDHB), a small antioxidant molecule, prolongs the C. elegans' lifespan under normal as well as stress conditions, delays the age-associated decline in the pharyngeal pumping rate, and obviously enhances the abilities of scavenging intracellular reactive oxygen species (ROS). To further investigate the mechanism underlying the anti-aging action of MDHB, microarray analyses were performed, which demonstrated that 13 genes were differentially expressed in worms treated with MDHB for 48 and 144 h in common. RNA interference of W06A7.4 (NM_001269697.1), the most significantly up-regulated gene, shortened the lifespan of worms by 14%, compared with the L4440 control. Our findings demonstrate that W06A7.4 is a potentially positive determinant of the MDHB induced C. elegans' lifespan extension effect.
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Affiliation(s)
- Wei Zhang
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China; Department of Pathogen Biology and Medical Immunology, School of Basic Medicine, Ningxia Medical University, Yinchuan, China; Discipline of Pathology and Pathophysiology, School of Medicine, Jinan University, Guangzhou, China
| | - Liang Cai
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China
| | - Hai-Ju Geng
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China
| | - Chao-Fen Su
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China
| | - Li Yan
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China
| | - Jia-Hui Wang
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China
| | - Qin Gao
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China
| | - Huan-Min Luo
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou, China; Institute of Brain Sciences, Jinan University, Guangzhou, China.
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A target repurposing approach identifies N-myristoyltransferase as a new candidate drug target in filarial nematodes. PLoS Negl Trop Dis 2014; 8:e3145. [PMID: 25188325 PMCID: PMC4154664 DOI: 10.1371/journal.pntd.0003145] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/25/2014] [Indexed: 11/19/2022] Open
Abstract
Myristoylation is a lipid modification involving the addition of a 14-carbon unsaturated fatty acid, myristic acid, to the N-terminal glycine of a subset of proteins, a modification that promotes their binding to cell membranes for varied biological functions. The process is catalyzed by myristoyl-CoA:protein N-myristoyltransferase (NMT), an enzyme which has been validated as a drug target in human cancers, and for infectious diseases caused by fungi, viruses and protozoan parasites. We purified Caenorhabditis elegans and Brugia malayi NMTs as active recombinant proteins and carried out kinetic analyses with their essential fatty acid donor, myristoyl-CoA and peptide substrates. Biochemical and structural analyses both revealed that the nematode enzymes are canonical NMTs, sharing a high degree of conservation with protozoan NMT enzymes. Inhibitory compounds that target NMT in protozoan species inhibited the nematode NMTs with IC50 values of 2.5–10 nM, and were active against B. malayi microfilariae and adult worms at 12.5 µM and 50 µM respectively, and C. elegans (25 µM) in culture. RNA interference and gene deletion in C. elegans further showed that NMT is essential for nematode viability. The effects observed are likely due to disruption of the function of several downstream target proteins. Potential substrates of NMT in B. malayi are predicted using bioinformatic analysis. Our genetic and chemical studies highlight the importance of myristoylation in the synthesis of functional proteins in nematodes and have shown for the first time that NMT is required for viability in parasitic nematodes. These results suggest that targeting NMT could be a valid approach for the development of chemotherapeutic agents against nematode diseases including filariasis. Lymphatic filariasis and onchocerciasis are neglected tropical diseases caused by filarial nematodes. The limitations of existing drugs to treat these infections highlight the need for new drugs. In the present study, we investigated myristoylation, a lipid modification of a subset of proteins that promotes their binding to cell membranes for varied biological functions. The process is catalyzed by N-myristoyltransferase (NMT), an enzyme which has been validated as a drug target in protozoan parasites. We performed kinetic analyses on Caenorhabditis elegans and Brugia malayi NMTs. NMT inhibitors were active against B. malayi microfilariae and adult worms, and C. elegans in culture. RNA interference and gene deletion in C. elegans further demonstrated that NMT is essential for nematode viability. Our genetic and chemical studies indicate the importance of myristoylation in the synthesis of functional proteins in nematodes and have shown for the first time that NMT is required for viability in parasitic nematodes. These results suggest that targeting NMT could be a valid approach for the development of new therapies against nematode infection including filarial diseases.
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