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Fu J, Dong H, Wu J, Jin Y. Emerging Progress of RNA-Based Antitumor Therapeutics. Int J Biol Sci 2023; 19:3159-3183. [PMID: 37416764 PMCID: PMC10321292 DOI: 10.7150/ijbs.83732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
RNA-based therapeutics (e.g., mRNAs, siRNAs, microRNAs, ASOs, and saRNAs) have considerable potential for tumor treatment. The development and optimization of RNA modifications and delivery systems enable the stable and efficient delivery of RNA cargos in vivo to elicit an antitumor response. Targeted RNA-based therapeutics with multiple specificities and high efficacies are now available. In this review, we discuss progress in RNA-based antitumor therapeutics, including mRNAs, siRNAs, miRNAs, ASOs, saRNAs, RNA aptamers, and CRISPR-based gene editing. We focus on the immunogenicity, stability, translation efficiency, and delivery of RNA drugs, and summarize their optimization and the development of delivery systems. In addition, we describe the mechanisms by which RNA-based therapeutics induce antitumor responses. Furthermore, we review the merits and limitations of RNA cargos and their therapeutic potential for cancers.
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Affiliation(s)
- Jiayan Fu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, 310058, Hangzhou, China
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Haiyang Dong
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, 310058, Hangzhou, China
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jian Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310006, Hangzhou, Zhejiang, China
| | - Yongfeng Jin
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, 310058, Hangzhou, China
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Department of Neurosurgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, China
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52
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Supe S, Upadhya A, Tripathi S, Dighe V, Singh K. Liposome-polyethylenimine complexes for the effective delivery of HuR siRNA in the treatment of diabetic retinopathy. Drug Deliv Transl Res 2023; 13:1675-1698. [PMID: 36630075 DOI: 10.1007/s13346-022-01281-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/12/2023]
Abstract
Diabetic retinopathy (DR) is a vision-impairing complication of diabetes, damaging the retinal microcirculatory system. Overexpression of VEGF (vascular endothelial growth factor) is implicated in the pathogenesis of DR. Human antigen R (HuR) is an RNA-binding protein that favorably regulates VEGF protein expression by binding to VEGF-encoding mRNA. Downregulating HuR via RNA interference strategies using small interfering RNAs (siRNAs) may constitute a novel therapeutic method for preventing VEGF protein overexpression in DR. Delivery of siRNAs to the cellular cytoplasm can be facilitated by cationic peptides or polymers and lipids. In this study, a cationic polymer (polyethylenimine (PEI)) and lipid nanoparticles (liposomes) were co-formulated with siRNA to form lipopolyplexes (LPPs) for the delivery of HuR siRNA. LPPs-siRNA were analyzed for size, zeta potential, serum stability, RNase stability, heparin stability, toxicity, and siRNA encapsulation efficiency. Cellular uptake, downregulation of the target HuR (mRNA and protein), and associated VEGF protein were used to demonstrate the biological efficacy of the LPPs-HuR siRNA, in vitro (human ARPE-19 cells), and in vivo (Wistar rats). In vivo efficacy study was performed by injecting LPPs-HuR siRNA formulations into the eye of streptozotocin (STZ)-induced diabetic rats after the development of retinopathy. Our findings demonstrated that high retinal HuR and VEGF levels observed in the eyes of untreated STZ rats were lowered after LPPs-HuR siRNA administration. Our observations indicate that intravitreal treatment with HuR siRNA is a promising option for DR using LPPs as delivery agents.
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Affiliation(s)
- Shibani Supe
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai, Maharashtra, 400056, India
| | - Archana Upadhya
- Humera Khan College of Pharmacy, HK College Campus, Oshiwara, Jogeshwari (West), Mumbai, Maharashtra, 400102, India
| | - Santosh Tripathi
- Bombay Veterinary College, Sindhu Nagar, Parel Village, Parel, Mumbai, Maharashtra, 400012, India
| | - Vikas Dighe
- National Centre for Preclinical Reproductive and Genetic Toxicology, ICMR-National Institute for Research in Reproductive and Child Health, J.M.Street, Parel, Mumbai, Maharashtra, 400012, India.
| | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, Mumbai, Maharashtra, 400056, India.
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53
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Xiao Y, Maeda S, Otomo T, MacRae IJ. Structural basis for RNA slicing by a plant Argonaute. Nat Struct Mol Biol 2023; 30:778-784. [PMID: 37127820 PMCID: PMC10868596 DOI: 10.1038/s41594-023-00989-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
Argonaute (AGO) proteins use small RNAs to recognize transcripts targeted for silencing in plants and animals. Many AGOs cleave target RNAs using an endoribonuclease activity termed 'slicing'. Slicing by DNA-guided prokaryotic AGOs has been studied in detail, but structural insights into RNA-guided slicing by eukaryotic AGOs are lacking. Here we present cryogenic electron microscopy structures of the Arabidopsis thaliana Argonaute10 (AtAgo10)-guide RNA complex with and without a target RNA representing a slicing substrate. The AtAgo10-guide-target complex adopts slicing-competent and slicing-incompetent conformations that are unlike known prokaryotic AGO structures. AtAgo10 slicing activity is licensed by docking target (t) nucleotides t9-t13 into a surface channel containing the AGO endoribonuclease active site. A β-hairpin in the L1 domain secures the t9-t13 segment and coordinates t9-t13 docking with extended guide-target pairing. Results show that prokaryotic and eukaryotic AGOs use distinct mechanisms for achieving target slicing and provide insights into small interfering RNA potency.
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Affiliation(s)
- Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shintaro Maeda
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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54
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Bartoszewska S, Sławski J, Collawn JF, Bartoszewski R. HIF-1-Induced hsa-miR-429: Understanding Its Direct Targets as the Key to Developing Cancer Diagnostics and Therapies. Cancers (Basel) 2023; 15:cancers15112903. [PMID: 37296866 DOI: 10.3390/cancers15112903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
MicroRNAs (miRNAs) play a critical role in the regulation of mRNA stability and translation. In spite of our present knowledge on the mechanisms of mRNA regulation by miRNAs, the utilization and translation of these ncRNAs into clinical applications have been problematic. Using hsa-miR-429 as an example, we discuss the limitations encountered in the development of efficient miRNA-related therapies and diagnostic approaches. The miR-200 family members, which include hsa-miR-429, have been shown to be dysregulated in different types of cancer. Although these miR-200 family members have been shown to function in suppressing epithelial-to-mesenchymal transition, tumor metastasis, and chemoresistance, the experimental results have often been contradictory. These complications involve not only the complex networks involving these noncoding RNAs, but also the problem of identifying false positives. To overcome these limitations, a more comprehensive research strategy is needed to increase our understanding of the mechanisms underlying their biological role in mRNA regulation. Here, we provide a literature analysis of the verified hsa-miR-429 targets in various human research models. A meta-analysis of this work is presented to provide better insights into the role of hsa-miR-429 in cancer diagnosis and any potential therapeutic approach.
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Affiliation(s)
- Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Jakub Sławski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama, Birmingham, AL 35294, USA
| | - Rafal Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
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55
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Ahmed EM, Boseila AA, Hanora AS, Solyman SM. Antiviral and protective effect of small interfering RNAs against rift valley fever virus in vitro. Mol Biol Rep 2023:10.1007/s11033-023-08455-9. [PMID: 37231214 DOI: 10.1007/s11033-023-08455-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Rift Valley Fever Virus (RVFV) is an arbovirus, a zoonotic disease that resurfaces as a potential hazard beyond geographic boundaries. Fever that can proceed to encephalitis, retinitis, hemorrhagic fever, and death is the main manifestation observed in human infections. RVFV has no authorized medication. The RNA interference (RNAi) gene silencing pathway is extremely well conserved. By targeting specific genes, small interfering RNA (siRNA) can be used to suppress viral replication. The aim of this study was to design specific siRNAs against RVFV and evaluate their prophylactic and antiviral effects on the Vero cells. METHODS AND RESULTS Various siRNAs were designed using different bioinformatics tools. Three unique candidates were tested against an Egyptian sheep cell culture-adapted strain BSL-2 that suppressed RVFV N mRNA expression. SiRNAs were transfected a day before RVFV infection (pre-transfection), and 1 h after the viral infection (post-transfection), and were evaluated to detect the silencing activity and gene expression decrease using real-time PCR and a TCID50 endpoint test. The degree of N protein expression was determined by western blot 48 h after viral infection. D2 which targets the (488-506 nucleotides), the middle region of RVFV N mRNA was the most effective siRNA at 30 nM concentration, it almost eliminates N mRNA expression when utilized as antiviral or preventive therapy. siRNAs had a stronger antiviral silencing impact when they were post-transfected into Vero cells. CONCLUSION Pre and post-transfection of siRNAs significantly reduced RVFV titer in cell lines, offering novel and potentially effective anti-RVFV epidemics and epizootics therapy.
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Affiliation(s)
- Engy M Ahmed
- Egyptian Drug Authority (EDA), Giza, Egypt
- Microbiology & Immunology Department, College of Pharmacy, Suez Canal University, Ismailia, Egypt
| | | | - Amro S Hanora
- Microbiology & Immunology Department, College of Pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Samar M Solyman
- Microbiology & Immunology Department, College of Pharmacy, Suez Canal University, Ismailia, Egypt
- Microbiology & Immunology Department, Faculty of Pharmacy, Sinai University Kantara branch, Ismailia, Egypt
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56
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Xiao Y, Liu TM, MacRae IJ. A tiny loop in the Argonaute PIWI domain tunes small RNA seed strength. EMBO Rep 2023:e55806. [PMID: 37082939 DOI: 10.15252/embr.202255806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/22/2023] Open
Abstract
Argonaute (AGO) proteins use microRNAs (miRNAs) and small interfering RNAs (siRNAs) as guides to regulate gene expression in plants and animals. AGOs that use miRNAs in bilaterian animals recognize short (6-8 nt.) elements complementary to the miRNA seed region, enabling each miRNA to interact with hundreds of otherwise unrelated targets. By contrast, AGOs that use miRNAs in plants employ longer (> 13 nt.) recognition elements such that each miRNA silences a small number of physiologically related targets. Here, we show that this major functional distinction depends on a minor structural difference between plant and animal AGO proteins: a 9-amino acid loop in the PIWI domain. Swapping the PIWI loop from human Argonaute2 (HsAGO2) into Arabidopsis Argonaute10 (AtAGO10) increases seed strength, resulting in animal-like miRNA targeting. Conversely, swapping the plant PIWI loop into HsAGO2 reduces seed strength and accelerates the turnover of cleaved targets. The loop-swapped HsAGO2 silences targets more potently, with reduced miRNA-like targeting, than wild-type HsAGO2 in mammalian cells. Thus, tiny structural differences can tune the targeting properties of AGO proteins for distinct biological roles.
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Affiliation(s)
- Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - TingYu M Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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57
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Sequence determinant of small RNA production by DICER. Nature 2023; 615:323-330. [PMID: 36813957 DOI: 10.1038/s41586-023-05722-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 01/11/2023] [Indexed: 02/24/2023]
Abstract
RNA silencing relies on specific and efficient processing of double-stranded RNA by Dicer, which yields microRNAs (miRNAs) and small interfering RNAs (siRNAs)1,2. However, our current knowledge of the specificity of Dicer is limited to the secondary structures of its substrates: a double-stranded RNA of approximately 22 base pairs with a 2-nucleotide 3' overhang and a terminal loop3-11. Here we found evidence pointing to an additional sequence-dependent determinant beyond these structural properties. To systematically interrogate the features of precursor miRNAs (pre-miRNAs), we carried out massively parallel assays with pre-miRNA variants and human DICER (also known as DICER1). Our analyses revealed a deeply conserved cis-acting element, termed the 'GYM motif' (paired G, paired pyrimidine and mismatched C or A), near the cleavage site. The GYM motif promotes processing at a specific position and can override the previously identified 'ruler'-like counting mechanisms from the 5' and 3' ends of pre-miRNA3-6. Consistently, integrating this motif into short hairpin RNA or Dicer-substrate siRNA potentiates RNA interference. Furthermore, we find that the C-terminal double-stranded RNA-binding domain (dsRBD) of DICER recognizes the GYM motif. Alterations in the dsRBD reduce processing and change cleavage sites in a motif-dependent fashion, affecting the miRNA repertoire in cells. In particular, the cancer-associated R1855L substitution in the dsRBD strongly impairs GYM motif recognition. This study uncovers an ancient principle of substrate recognition by metazoan Dicer and implicates its potential in the design of RNA therapeutics.
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58
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Structure of the human DICER-pre-miRNA complex in a dicing state. Nature 2023; 615:331-338. [PMID: 36813958 DOI: 10.1038/s41586-023-05723-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/14/2022] [Indexed: 02/24/2023]
Abstract
Dicer has a key role in small RNA biogenesis, processing double-stranded RNAs (dsRNAs)1,2. Human DICER (hDICER, also known as DICER1) is specialized for cleaving small hairpin structures such as precursor microRNAs (pre-miRNAs) and has limited activity towards long dsRNAs-unlike its homologues in lower eukaryotes and plants, which cleave long dsRNAs. Although the mechanism by which long dsRNAs are cleaved has been well documented, our understanding of pre-miRNA processing is incomplete because structures of hDICER in a catalytic state are lacking. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state and uncover the structural basis of pre-miRNA processing. hDICER undergoes large conformational changes to attain the active state. The helicase domain becomes flexible, which allows the binding of pre-miRNA to the catalytic valley. The double-stranded RNA-binding domain relocates and anchors pre-miRNA in a specific position through both sequence-independent and sequence-specific recognition of the newly identified 'GYM motif'3. The DICER-specific PAZ helix is also reoriented to accommodate the RNA. Furthermore, our structure identifies a configuration of the 5' end of pre-miRNA inserted into a basic pocket. In this pocket, a group of arginine residues recognize the 5' terminal base (disfavouring guanine) and terminal monophosphate; this explains the specificity of hDICER and how it determines the cleavage site. We identify cancer-associated mutations in the 5' pocket residues that impair miRNA biogenesis. Our study reveals how hDICER recognizes pre-miRNAs with stringent specificity and enables a mechanistic understanding of hDICER-related diseases.
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59
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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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60
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Villa R, Renzi S, Dotti S, Lucchini F. siRNAs pools generated in Escherichia coli exhibit strong RNA-interference activity against influenza virus genomic sequences. Virology 2023; 579:38-45. [PMID: 36599198 DOI: 10.1016/j.virol.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023]
Abstract
Due to the recurrent pandemic outbreaks that occurred during the last century, Influenza A viruses are considered a serious potential danger to human health. Among the innate immune pathways in eukaryotes, RNA interference plays a significant role in the interaction between viruses and host cells. RNA interference is addressed by small dsRNA molecules produced by the host itself (miRNAs, i.e. "micro-RNAs") but can be triggered also by the administration of exogenous short RNAs (siRNAs, "short interfering RNAs"). In this work, artificial siRNA pools targeting NP and PB genomic regions of the Influenza virus were produced in engineered Escherichia coli, adapting a published protocol. In a MDCK cell in vitro model, these preparations were challenged against reporter vectors bearing viral genomic sequences. A strong and specific RNA interference activity was observed, and the details of this action were indagated.
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Affiliation(s)
- Riccardo Villa
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Laboratorio di Controllo di Prodotti Biologici, Farmaceutici e Convalida di Processi Produttivi, via A. Bianchi 9, Brescia, Italy
| | - Sabrina Renzi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Laboratorio di Controllo di Prodotti Biologici, Farmaceutici e Convalida di Processi Produttivi, via A. Bianchi 9, Brescia, Italy
| | - Silvia Dotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Laboratorio di Controllo di Prodotti Biologici, Farmaceutici e Convalida di Processi Produttivi, via A. Bianchi 9, Brescia, Italy
| | - Franco Lucchini
- Università Cattolica del Sacro Cuore, Facoltà di Scienze Agrarie, Alimentari ed Ambientali, DiSTAS - Dipartimento di Scienze e Tecnologie Alimentari per una filiera agro-alimentare sostenibile, via L. Bissolati 74, Cremona, Italy.
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61
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Iwama RE, Moran Y. Origins and diversification of animal innate immune responses against viral infections. Nat Ecol Evol 2023; 7:182-193. [PMID: 36635343 DOI: 10.1038/s41559-022-01951-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/11/2022] [Indexed: 01/14/2023]
Abstract
Immune systems are of pivotal importance to any living organism on Earth, as they protect the organism against deleterious effects of viral infections. Though the current knowledge about these systems is still biased towards the immune response in vertebrates, some studies have focused on the identification and characterization of components of invertebrate antiviral immune systems. Two classic model organisms, the insect Drosophila melanogaster and the nematode Caenorhabditis elegans, were instrumental in the discovery of several important components of the innate immune system, such as the Toll-like receptors and the RNA interference pathway. However, these two model organisms provide only a limited view of the evolutionary history of the immune system, as they both are ecdysozoan protostomes. Recent functional studies in non-classic models such as unicellular holozoans (for example, choanoflagellates), lophotrochozoans (for example, oysters) and cnidarians (for example, sea anemones) have added crucial information for understanding the evolution of antiviral systems, as they revealed unexpected ancestral complexity. This Review aims to summarize this information and present the ancestral nature of the antiviral immune response in animals. We also discuss lineage-specific adaptations and future perspectives for the comparative study of the innate immune system that are essential for understanding its evolution.
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Affiliation(s)
- Rafael E Iwama
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem, Israel.
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62
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Kim JS, Park J, Choi JH, Kang S, Park N. RNA-DNA hybrid nano-materials for highly efficient and long lasting RNA interference effect. RSC Adv 2023; 13:3139-3146. [PMID: 36756454 PMCID: PMC9854246 DOI: 10.1039/d2ra06249f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/14/2023] [Indexed: 01/21/2023] Open
Abstract
In attempts to effectively improve RNAi function, we herein report a new RNAi approach using X-shaped RDNA and Dgel (RNA interfering DNA hydrogel, Ri-Dgel). X-shaped RDNA is a 4 branched nanostructure which was composed of three dsDNA branches and one dsRNA branch, and the structure was made by annealing partially complementary ssDNAs and chimeric RNA-DNA oligonucleotides. Ri-Dgel was synthesized through the ligation of the X-shaped RDNAs using their palindromic sticky ends. In MDCK/GFP cells transfected with 1 μM of each format of siRNA, Ri-Dgel and X-RDNA, the intensity of GFP fluorescence was significantly reduced by 65% and 56%, respectively, while dsRNA which is a conventional siRNA format showed a relatively weak reduction intensity of 7% compared with a negative control. We also observed the decreased intensity of GFP fluorescence by approximately 59% in MDA-MB-231/GFP cells transfected with 5 nM Ri-Dgel. Furthermore, the Ri-Dgel showed persistent RNAi efficiency up to 6 days from the treatment. The use of Ri-Dgel to trigger RNAi resulted in enhanced efficacy and longer duration at lower concentration compared to traditional dsRNA implying the nanostructured DNA-RNA hybrid materials have great potential as a platform technology for RNAi-based therapy.
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Affiliation(s)
- Joung Sug Kim
- Department of Chemistry, The Natural Science Research Institute, Myongji University 116 Myongji-Ro Yongin Gyeonggi-do Republic of Korea
| | - Junghyun Park
- Department of Chemistry, The Natural Science Research Institute, Myongji University 116 Myongji-Ro Yongin Gyeonggi-do Republic of Korea
| | - Jang Hyeon Choi
- Department of Chemistry, The Natural Science Research Institute, Myongji University 116 Myongji-Ro Yongin Gyeonggi-do Republic of Korea
| | - Seungjae Kang
- Department of Chemistry, The Natural Science Research Institute, Myongji University 116 Myongji-Ro Yongin Gyeonggi-do Republic of Korea
| | - Nokyoung Park
- Department of Chemistry, The Natural Science Research Institute, Myongji University 116 Myongji-Ro Yongin Gyeonggi-do Republic of Korea
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Luo N, Shang D, Tang Z, Mai J, Huang X, Tao LZ, Liu L, Gao C, Qian Y, Xie Q, Li F. Engineered ATG8-binding motif-based selective autophagy to degrade proteins and organelles in planta. THE NEW PHYTOLOGIST 2023; 237:684-697. [PMID: 36263708 DOI: 10.1111/nph.18557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Protein-targeting technologies represent essential approaches in biological research. Protein knockdown tools developed recently in mammalian cells by exploiting natural degradation mechanisms allow for precise determination of protein function and discovery of degrader-type drugs. However, no method to directly target endogenous proteins for degradation is currently available in plants. Here, we describe a novel method for targeted protein clearance by engineering an autophagy receptor with a binder to provide target specificity and an ATG8-binding motif (AIM) to link the targets to nascent autophagosomes, thus harnessing the autophagy machinery for degradation. We demonstrate its specificity and broad potentials by degrading various fluorescence-tagged proteins, including cytosolic mCherry, the nucleus-localized bZIP transcription factor TGA5, and the plasma membrane-anchored brassinosteroid receptor BRI1, as well as fluorescence-coated peroxisomes, using a tobacco-based transient expression system. Stable expression of AIM-based autophagy receptors in Arabidopsis further confirms the feasibility of this approach in selective autophagy of endogenous proteins. With its wide substrate scope and its specificity, our concept of engineered AIM-based selective autophagy could provide a convenient and robust research tool for manipulating endogenous proteins in plants and may open an avenue toward degradation of cytoplasmic components other than proteins in plant research.
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Affiliation(s)
- Na Luo
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dandan Shang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiwei Tang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jinyan Mai
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiao Huang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Li-Zhen Tao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Linchuan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yangwen Qian
- WIMI Biotechnology Co. Ltd, Changzhou, 213000, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
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Lee YR, Tsai HP, Yeh CS, Fang CY, Chan MWY, Wu TY, Shen CH. RNA Interference Approach Is a Good Strategy against SARS-CoV-2. Viruses 2022; 15:100. [PMID: 36680140 PMCID: PMC9862891 DOI: 10.3390/v15010100] [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: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, created a devastating outbreak worldwide and consequently became a global health concern. However, no verifiable, specifically targeted treatment has been devised for COVID-19. Several emerging vaccines have been used, but protection has not been satisfactory. The complex genetic composition and high mutation frequency of SARS-CoV-2 have caused an uncertain vaccine response. Small interfering RNA (siRNA)-based therapy is an efficient strategy to control various infectious diseases employing post-transcriptional gene silencing through the silencing of target complementary mRNA. Here, we designed two highly effective shRNAs targeting the conserved region of RNA-dependent RNA polymerase (RdRP) and spike proteins capable of significant SARS-CoV-2 replication suppression. The efficacy of this approach suggested that the rapid development of an shRNA-based therapeutic strategy might prove to be highly effective in treating COVID-19. However, it needs further clinical trials.
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Affiliation(s)
- Ying-Ray Lee
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Master of Science Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Huey-Pin Tsai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Sheng Yeh
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Chiung-Yao Fang
- Department of Medical Research, Ditmanson Medical Foundation, Chiayi Christian Hospital, Chiayi 600, Taiwan
| | - Michael W. Y. Chan
- Department of Biomedical Sciences, National Chung Cheng University, Min-Hsiung, Chiayi 621, Taiwan
| | - Tzu-Yun Wu
- Department of Medical Research, Ditmanson Medical Foundation, Chiayi Christian Hospital, Chiayi 600, Taiwan
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi 600, Taiwan
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65
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Lye LF, Owens KL, Jang S, Marcus JE, Brettmann EA, Beverley SM. An RNA Interference (RNAi) Toolkit and Its Utility for Functional Genetic Analysis of Leishmania ( Viannia). Genes (Basel) 2022; 14:93. [PMID: 36672832 PMCID: PMC9858808 DOI: 10.3390/genes14010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the Leishmania subgenus Viannia, and here we describe the development, optimization, and application of RNAi tools to the study of L. (Viannia) braziliensis (Lbr). We developed vectors facilitating generation of long-hairpin or "stem-loop" (StL) RNAi knockdown constructs, using GatewayTM site-specific recombinase technology. A survey of applications of RNAi in L. braziliensis included genes interspersed within multigene tandem arrays such as quinonoid dihydropteridine reductase (QDPR), a potential target or modulator of antifolate sensitivity. Other tests include genes involved in cell differentiation and amastigote proliferation (A600), and essential genes of the intraflagellar transport (IFT) pathway. We tested a range of stem lengths targeting the L. braziliensis hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and reporter firefly luciferase (LUC) genes and found that the efficacy of RNAi increased with stem length, and fell off greatly below about 128 nt. We used the StL length dependency to establish a useful 'hypomorphic' approach not possible with other gene ablation strategies, with shorter IFT140 stems yielding viable cells with compromised flagellar morphology. We showed that co-selection for RNAi against adenine phosphoryl transferase (APRT1) using 4-aminopyrazolpyrimidine (APP) could increase the efficacy of RNAi against reporter constructs, a finding that may facilitate improvements in future work. Thus, for many genes, RNAi provides a useful tool for studying Leishmania gene function with some unique advantages.
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Affiliation(s)
| | | | | | | | | | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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66
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siRNA and targeted delivery systems in breast cancer therapy. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 25:1167-1188. [PMID: 36562927 DOI: 10.1007/s12094-022-03043-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
Recently, nucleic acid drugs have been considered as promising candidates in treatment of various diseases, especially cancer. Because of developing resistance to conventional chemotherapy, use of genetic tools in cancer therapy appears inevitable. siRNA is a RNAi tool with capacity of suppressing target gene. Owing to overexpression of oncogenic factors in cancer, siRNA can be used for suppressing those pathways. This review emphasizes the function of siRNA in treatment of breast tumor. The anti-apoptotic-related genes including Bcl-2, Bcl-xL and survivin can be down-regulated by siRNA in triggering cell death in breast cancer. STAT3, STAT8, Notch1, E2F3 and NF-κB are among the factors with overexpression in breast cancer that their silencing by siRNA paves the way for impairing tumor proliferation and invasion. The oncogenic mechanisms in drug resistance development in breast tumor such as lncRNAs can be suppressed by siRNA. Furthermore, siRNA reducing P-gp activity can increase drug internalization in tumor cells. Because of siRNA degradation at bloodstream and low accumulation at tumor site, nanoplatforms have been employed for siRNA delivery to suppress breast tumor progression via improving siRNA efficacy in gene silencing. Development of biocompatible and efficient nanostructures for siRNA delivery can make milestone progress in alleviation of breast cancer patients.
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67
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Gao L, Wang Y, Abbas M, Zhang T, Ma E, Merzendorfer H, Zhu KY, Zhang J. Both LmDicer-1 and two LmDicer-2s participate in siRNA-mediated RNAi pathway and contribute to high gene silencing efficiency in Locusta migratoria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103865. [PMID: 36336194 DOI: 10.1016/j.ibmb.2022.103865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/29/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Dicers belong to a class of large RNase III multidomain ribonucleases and are central components of the RNA interference (RNAi) pathways. In insects, Dicer-2 has been known to cleave long double-stranded RNA (dsRNA) in small interfering RNA (siRNA)-mediated-RNAi pathway. However, Dicer-1 is responsible for cleaving precursor microRNAs (pre28 miRNAs) in miRNA-mediated RNAi pathway. In this study, we identified one LmDicer-1 and two LmDicer-2 (LmDicer-2a and LmDicer-2b) genes in Locusta migratoria. The RNAi of RNAi assay showed that knockdown of each of the Dicer genes reduced RNAi efficiency against a target gene (Lmβ-Tubulin), suggesting that all these genes participated in the siRNA-mediated RNAi pathway. Sequence analyses of the siRNAs generated from dsLmβ-Tubulin after silencing each LmDicer gene showed no significant difference in the pattern of siRNAs mapped to dsLmβ-Tubulin. This result indicated that all the three LmDicers are capable of generating siRNAs from the dsRNA. We then generated recombinant proteins consisting of different domains using Escherichia coli expression system and incubated each recombinant protein with dsLmβ-Tubulin. We found that the recombinant Dicer proteins successfully cleaved dsLmβ-Tubulin. However, LmDicer-2a-R lacking dsRBD domain lost activity, suggesting that dsRBD domain is critical for Dicer function. Furthermore, overexpression of these proteins in Drosophila S2 cells improved RNAi efficiency. Our siRNA affinity chromatography and LC-MS/MS analysis identified LmDicer-2a, LmDicer-2b, LmR2D2, LmAgo2a, LmAgo1, LmStaufen and LmTARBP2 as constituents of RNA-induced silencing complex. Taken together, these data show that both LmDicer-1 and two LmDicer-2s all participate in siRNA-mediated RNAi pathway and likely contribute to high RNAi efficiency in L. migratoria.
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Affiliation(s)
- Lu Gao
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China; College of Life Science, Shanxi University, Taiyuan, China
| | - Yanli Wang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Mureed Abbas
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Tingting Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Enbo Ma
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | | | - Kun Yan Zhu
- Department of Entomology, 123 Waters Hall, Kansas State University, Manhattan, KS, 66506, USA.
| | - Jianzhen Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China.
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68
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Li BW, Xu WB, Dong WR, Zhang YM, Cheng YX, Chen DY, Xiao Y, Chen YY, Shu MA. Identification and function analysis of two fibroblast growth factor receptor (FGFR) from Scylla paramamosain: The evidence of FGFR involved in innate immunity in crustacean. FISH & SHELLFISH IMMUNOLOGY 2022; 131:602-611. [PMID: 36064005 DOI: 10.1016/j.fsi.2022.08.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The fibroblast growth factor receptor (FGFR) belongs to the tyrosine kinase family consisting of four members (FGFR1-4). This study involved identification and characterization of FGFR1 and FGFR3 from mud crab Scylla paramamosain for the first time. The obtained cDNAs of SpFGFR1 and SpFGFR3 were 2,380 bp and 2,982 bp in length with a 1,503 bp and 2,310 bp open reading frame, respectively. The predicted SpFGFR1 protein included three immunoglobulin domains and a transmembrane region, while SpFGFR3 protein possessed a typical TyrKc (Tyrosine kinase, catalytic) domain. Real-time PCR analysis showed that SpFGFR1 and SpFGFR3 were highly expressed in the hepatopancreas. Furthermore, the expression levels of SpFGFR1 and SpFGFR3 in the hepatopancreas were enhanced following challenges with Vibro alginolyticus, Staphylococcus aureus, Poly (I:C) and White spot syndrome virus, which shows the involvement of SpFGFR1 and SpFGFR3 in innate immune response to infections from bacteria and virus. There was significant suppression of six antimicrobial peptide genes (SpALF1-5 and SpCrustin) and three NF-κB members (SpDorsal, SpIKK and SpRelish) when SpFGFR1 and SpFGFR3 was interfered in vivo. Also, treatment of the hemocytes with specific inhibitor of SpFGFR for 24 h consistently down-regulated SpDorsal, SpRelish and AMPs. These results suggested that SpFGFR1 and SpFGFR3 played important roles in regulating the Toll signaling pathway and immune deficiency (IMD) pathway through NF-κB signaling pathway. These findings may provide new insights into the role of FGFRs in the innate immune function of crustaceans.
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Affiliation(s)
- Bing-Wu Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wen-Bin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Ren Dong
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan-Mei Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuan-Xin Cheng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Da-Yong Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yi Xiao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yu-Yin Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Miao-An Shu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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69
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Murcott B, Pawluk RJ, Protasio AV, Akinmusola RY, Lastik D, Hunt VL. stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences. FRONTIERS IN BIOINFORMATICS 2022; 2:994871. [DOI: 10.3389/fbinf.2022.994871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
The enzyme Dicer is a component of many small RNA (sRNA) pathways involved in RNA processing for post-transcriptional regulation, anti-viral response and control of transposable elements. Cleavage of double-stranded RNA by Dicer produces a signature overhanging sequence at the 3’ end of the sRNA sequence relative to a complementary passenger strand in a RNA duplex. There is a need for reliable tools to computationally search for Dicer cleavage signatures to help characterise families of sRNAs. This is increasingly important due to the rising popularity of sRNA sequencing, especially in non-model organisms. Here, we present stepRNA, a fast, local tool that identifies (i) overhang signatures strongly indicative of Dicer cleavage in RNA sequences, and (ii) the length of the passenger strand in sRNAs duplexes. We demonstrate the use of stepRNA with simulated and biological datasets to detect Dicer cleavage signatures in experimentally validated examples. Compared to currently available tools, stepRNA is more accurate, requires only sRNA sequence data rather than a reference genome, and provides information about other important features such as passenger strand length. stepRNA is freely available at https://github.com/Vicky-Hunt-Lab/stepRNA and is easily installable.
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70
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Cao Y, Wang J, Wu S, Yin X, Shu J, Dai X, Liu Y, Sun L, Zhu D, Deng XW, Ye K, Qian W. The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. THE PLANT CELL 2022; 34:4173-4190. [PMID: 36005862 PMCID: PMC9614442 DOI: 10.1093/plcell/koac265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs (ncRNAs) that guide chemical modifications of structural RNAs, which are essential for ribosome assembly and function in eukaryotes. Although numerous snoRNAs have been identified in plants by high-throughput sequencing, the biological functions of most of these snoRNAs remain unclear. Here, we identified box C/D SnoR28.1s as important regulators of plant growth and development by screening a CRISPR/Cas9-generated ncRNA deletion mutant library in Arabidopsis thaliana. Deletion of the SnoR28.1 locus, which contains a cluster of three genes producing SnoR28.1s, resulted in defects in root and shoot growth. SnoR28.1s guide 2'-O-ribose methylation of 25S rRNA at G2396. SnoR28.1s facilitate proper and efficient pre-rRNA processing, as the SnoR28.1 deletion mutants also showed impaired ribosome assembly and function, which may account for the growth defects. SnoR28 contains a 7-bp antisense box, which is required for 2'-O-ribose methylation of 25S rRNA at G2396, and an 8-bp extra box that is complementary to a nearby rRNA methylation site and is partially responsible for methylation of G2396. Both of these motifs are required for proper and efficient pre-rRNA processing. Finally, we show that SnoR28.1s genetically interact with HIDDEN TREASURE2 and NUCLEOLIN1. Our results advance our understanding of the roles of snoRNAs in Arabidopsis.
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Affiliation(s)
- Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jia Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
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71
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Pavan-Guimaraes J, Martins PN. Modifying organs with gene therapy and gene modulation in the age of machine perfusion. Curr Opin Organ Transplant 2022; 27:474-480. [PMID: 36102360 DOI: 10.1097/mot.0000000000001007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW This review aims to highlight current advances in gene therapy methods, describing advances in CRISPR-Cas9 gene editing and RNA interference in relevance to liver transplantation, and machine perfusion. RECENT FINDINGS In order to minimize rejection, increase the donor pool of available organs, and minimize the effects of ischemia-reperfusion injury, gene therapy and gene modification strategies are, thus, required in the context of liver transplantation. SUMMARY Gene therapy has been used successfully in a diverse array of diseases, and, more recently, this technique has gained interest in the field of organ transplantation. Biological and logistical challenges reduce the rate of successful procedures, increasing the waiting list even more. We explore the exciting future implications of customized gene therapy in livers using machine perfusion, including its potential to create a future in which organs destined for transplant are individualized to maximize both graft and recipient longevity.
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Affiliation(s)
- Juliana Pavan-Guimaraes
- Division of Transplantation, Department of Surgery, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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Arriaga-Canon C, Contreras-Espinosa L, Rebollar-Vega R, Montiel-Manríquez R, Cedro-Tanda A, García-Gordillo JA, Álvarez-Gómez RM, Jiménez-Trejo F, Castro-Hernández C, Herrera LA. Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection. Int J Mol Sci 2022; 23:11058. [PMID: 36232363 PMCID: PMC9570475 DOI: 10.3390/ijms231911058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem.
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Affiliation(s)
- Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Rosa Rebollar-Vega
- Genomics Laboratory, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan. C.P., Mexico City 14610, Mexico
| | - José Antonio García-Gordillo
- Oncología Médica, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Rosa María Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Francisco Jiménez-Trejo
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C, Coyoacán. C.P., Mexico City 04530, Mexico
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan. C.P., Mexico City 14610, Mexico
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Traube FR, Stern M, Tölke AJ, Rudelius M, Mejías‐Pérez E, Raddaoui N, Kümmerer BM, Douat C, Streshnev F, Albanese M, Wratil PR, Gärtner YV, Nainytė M, Giorgio G, Michalakis S, Schneider S, Streeck H, Müller M, Keppler OT, Carell T. Suppression of SARS‐CoV‐2 Replication with Stabilized and Click‐Chemistry Modified siRNAs. Angew Chem Int Ed Engl 2022; 61:e202204556. [PMID: 35802496 PMCID: PMC9350007 DOI: 10.1002/anie.202204556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Franziska R. Traube
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Annika J. Tölke
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Martina Rudelius
- Institute of Pathology Ludwig-Maximilians-Universität München Marchioninistr. 68 81377 Munich Germany
| | - Ernesto Mejías‐Pérez
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Nada Raddaoui
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Beate M. Kümmerer
- Institute of Virology Universitätsklinikum Bonn Venusberg-Campus 1 53127 Bonn Germany
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn 53127 Bonn Germany
| | - Céline Douat
- Department of Pharmacy Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Filipp Streshnev
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Manuel Albanese
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Paul R. Wratil
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Yasmin V. Gärtner
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Milda Nainytė
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Grazia Giorgio
- Department of Ophthalmology University Hospital Ludwig-Maximilians-Universität München 80336 Munich Germany
| | - Stylianos Michalakis
- Department of Ophthalmology University Hospital Ludwig-Maximilians-Universität München 80336 Munich Germany
| | - Sabine Schneider
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Hendrik Streeck
- Institute of Virology Universitätsklinikum Bonn Venusberg-Campus 1 53127 Bonn Germany
| | - Markus Müller
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute and Gene Center Ludwig-Maximilians-Universität München Feodor-Lynen-Straße 25 81377 Munich Germany
| | - Thomas Carell
- Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 Munich Germany
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Research progress about microRNAs involved in plant secondary metabolism. Int J Biol Macromol 2022; 216:820-829. [DOI: 10.1016/j.ijbiomac.2022.07.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022]
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Hoang T, Foquet B, Rana S, Little DW, Woller DA, Sword GA, Song H. Development of RNAi Methods for the Mormon Cricket, Anabrus simplex (Orthoptera: Tettigoniidae). INSECTS 2022; 13:739. [PMID: 36005364 PMCID: PMC9409436 DOI: 10.3390/insects13080739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/06/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Mormon crickets are a major rangeland pest in the western United States and are currently managed by targeted applications of non-specific chemical insecticides, which can potentially have negative effects on the environment. In this study, we took the first steps toward developing RNAi methods for Mormon crickets as a potential alternative to traditional broad-spectrum insecticides. To design an effective RNAi-based insecticide, we first generated a de novo transcriptome for the Mormon cricket and developed dsRNAs that could silence the expression of seven housekeeping genes. We then characterized the RNAi efficiencies and time-course of knockdown using these dsRNAs, and assessed their ability to induce mortality. We have demonstrated that it is possible to elicit RNAi responses in the Mormon cricket by injection, but knockdown efficiencies and the time course of RNAi response varied according to target genes and tissue types. We also show that one of the reasons for the poor knockdown efficiencies could be the presence of dsRNA-degrading enzymes in the hemolymph. RNAi silencing is possible in Mormon cricket, but more work needs to be done before it can be effectively used as a population management method.
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Affiliation(s)
- Toan Hoang
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Bert Foquet
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
- Department of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Seema Rana
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Drew W. Little
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Derek A. Woller
- USDA-APHIS-PPQ-Science & Technology-Insect Management and Molecular Diagnostics Laboratory (Phoenix Station), Phoenix, AZ 85040, USA
| | - Gregory A. Sword
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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76
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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Morales-Martínez M, Vega MI. Role of MicroRNA-7 (MiR-7) in Cancer Physiopathology. Int J Mol Sci 2022; 23:ijms23169091. [PMID: 36012357 PMCID: PMC9408913 DOI: 10.3390/ijms23169091] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
miRNAs are non-coding RNA sequences of approximately 22 nucleotides that interact with genes by inhibiting their translation through binding to their 3′ or 5′ UTR regions. Following their discovery, the role they play in the development of various pathologies, particularly cancer, has been studied. In this context, miR-7 is described as an important factor in the development of cancer because of its role as a tumor suppressor, regulating a large number of genes involved in the development and progression of cancer. Recent data support the function of miR-7 as a prognostic biomarker in cancer, and miR-7 has been proposed as a strategy in cancer therapy. In this work, the role of miR-7 in various types of cancer is reviewed, illustrating its regulation, direct targets, and effects, as well as its possible relationship to the clinical outcome of cancer patients.
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Affiliation(s)
- Mario Morales-Martínez
- Molecular Signal Pathway in Cancer Laboratory, UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS, Mexico City 06720, Mexico
| | - Mario I. Vega
- Molecular Signal Pathway in Cancer Laboratory, UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS, Mexico City 06720, Mexico
- Department of Medicine, Hematology-Oncology Division, Greater Los Angeles VA Healthcare Center, UCLA Medical Center, Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
- Correspondence: or
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Zhu Y, Zhu L, Wang X, Jin H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis 2022; 13:644. [PMID: 35871216 PMCID: PMC9308039 DOI: 10.1038/s41419-022-05075-2] [Citation(s) in RCA: 200] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto "undruggable" proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
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Affiliation(s)
- Yiran Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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de la Fuente J, Kocan KM. The Impact of RNA Interference in Tick Research. Pathogens 2022; 11:pathogens11080827. [PMID: 35894050 PMCID: PMC9394339 DOI: 10.3390/pathogens11080827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
Over the past two decades, RNA interference (RNAi) in ticks, in combination with omics technologies, have greatly advanced the discovery of tick gene and molecular function. While mechanisms of RNAi were initially elucidated in plants, fungi, and nematodes, the classic 2002 study by Aljamali et al. was the first to demonstrate RNAi gene silencing in ticks. Subsequently, applications of RNAi have led to the discovery of genes that impact tick function and tick-host-pathogen interactions. RNAi will continue to lead to the discovery of an array of tick genes and molecules suitable for the development of vaccines and/or pharmacologic approaches for tick control and the prevention of pathogen transmission.
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Affiliation(s)
- José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
- The Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA;
- Correspondence: or
| | - Katherine M. Kocan
- The Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA;
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Traube FR, Stern M, Tölke AJ, Rudelius M, Mejías-Pérez E, Raddaoui N, Kümmerer BM, Douat C, Streshnev F, Albanese M, Wratil PR, Gärtner YV, Nainytė M, Giorgio G, Michalakis S, Schneider S, Streeck H, Müller M, Keppler OT, Carell T. Suppression of SARS‐CoV‐2 Replication with Stabilized and Click‐Chemistry Modified siRNAs. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Franziska R. Traube
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Marcel Stern
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkopfer Institute and Gene Center, Virology GERMANY
| | - Annika J. Tölke
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Martina Rudelius
- LMU München: Ludwig-Maximilians-Universitat Munchen Institute of Pathology GERMANY
| | - Ernesto Mejías-Pérez
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Nada Raddaoui
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Beate M. Kümmerer
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Virology GERMANY
| | - Céline Douat
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Filipp Streshnev
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Manuel Albanese
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Paul R. Wratil
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Yasmin V. Gärtner
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Milda Nainytė
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Grazia Giorgio
- LMU München: Ludwig-Maximilians-Universitat Munchen Department of Ophthalmology, University Hospital GERMANY
| | - Stylianos Michalakis
- LMU München: Ludwig-Maximilians-Universitat Munchen Department of Ophthalmology, University Hospital GERMANY
| | - Sabine Schneider
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Hendrick Streeck
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Virology GERMANY
| | - Markus Müller
- LMU München: Ludwig-Maximilians-Universitat Munchen Department Chemie GERMANY
| | - Oliver T. Keppler
- LMU München: Ludwig-Maximilians-Universitat Munchen Max von Pettenkofer Institute and Gene Center, Virology GERMANY
| | - Thomas Carell
- Ludwig-Maximilians-Universitat Munchen Department of Chemistry and Biochemistry Butenandtstraße 5-13 81377 München GERMANY
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Dalaisón-Fuentes LI, Pascual A, Gazza E, Welchen E, Rivera-Pomar R, Catalano MI. Development of efficient RNAi methods in the corn leafhopper Dalbulus maidis, a promising application for pest control. PEST MANAGEMENT SCIENCE 2022; 78:3108-3116. [PMID: 35442515 DOI: 10.1002/ps.6937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The corn leafhopper Dalbulus maidis is the main vector of important stunting pathogens that affect maize production. Currently, there are no effective methods available to manage this pest without adverse impact on the environment. In this context, genomic-based technologies such as RNA interference (RNAi) provide a more environmentally friendly pest control strategy. Therefore, we aimed to assess the application of RNAi in D. maidis and determine the function of a candidate gene related to insect reproduction and propagation. RESULTS We have characterized the core RNAi genes and evaluated the functionality of the RNAi machinery. We assessed the potential of RNAi technology in D. maidis via injection or ingestion of double-stranded RNA (dsRNA) to adult females. We chose Bicaudal C (BicC) as a target gene due to its important role during insect oogenesis. Administration of dsRNABicC caused significant reductions in the transcript levels (fold changes up to 170 times) and ovipositions. Phenotypic analysis of the ovaries revealed alterations in oocyte development, providing additional confirmation for our results and supporting the idea that Dmai-BicC is a key player of D. maidis oogenesis. CONCLUSION This is, to our knowledge, the first report of efficient RNAi in D. maidis. We believe our findings provide a starting point for future control strategies against one of the most important maize pests in the Americas. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Lucía Inés Dalaisón-Fuentes
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
| | - Agustina Pascual
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
| | - Elías Gazza
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Rolando Rivera-Pomar
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
- Centro Regional de Estudios Genómicos (Facultad de Ciencias Exactas, Universidad Nacional de La Plata), La Plata, Argentina
| | - María Inés Catalano
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
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Knockdown of 15-bp Deletion-Type v-raf Murine Sarcoma Viral Oncogene Homolog B1 mRNA in Pancreatic Ductal Adenocarcinoma Cells Repressed Cell Growth In Vitro and Tumor Volume In Vivo. Cancers (Basel) 2022; 14:cancers14133162. [PMID: 35804932 PMCID: PMC9264874 DOI: 10.3390/cancers14133162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The v-raf murine sarcoma viral oncogene homolog B1 (BRAF) gene containing a 15-base pair (bp) deletion at L485-P490 is the cause of several cancers. We generated siRNA to specifically knock down BRAF mRNA containing the 15-bp deletion. This siRNA suppressed the expression of BRAF, harboring the deletion without affecting wild-type BRAF expression in BxPC-3 pancreatic ductal adenocarcinoma cells in vitro and in vivo. Cell growth and phosphorylation of downstream extracellular-signal-regulated kinase proteins were also repressed. An off-target effect is the most common side effect of siRNA therapy. In this study, we reveal that siRNA with a 2′-O-methyl chemical modification in the seed region of the siRNA guide strand reduced seed-dependent off-target effects. Abstract Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second-most common cause of death within the next 10 years. Due to the limited efficacy of available therapies, the survival rate of PDAC patients is very low. Oncogenic BRAF mutations are one of the major causes of PDAC, specifically the missense V600E and L485–P490 15-bp deletion mutations. Drugs targeting the V600E mutation have already been approved by the United States Food and Drug Administration. However, a drug targeting the deletion mutation at L485–P490 of the BRAF gene has not been developed to date. The BxPC-3 cell line is a PDAC-derived cell line harboring wild-type KRAS and L485–P490 deleted BRAF genes. These cells are heterozygous for BRAF, harboring both wild-type BRAF and BRAF with the 15-bp deletion. In this study, siRNA was designed for the targeted knockdown of 15-bp deletion-type BRAF mRNA. This siRNA repressed the phosphorylation of extracellular-signal-regulated kinase proteins downstream of BRAF and suppressed cell growth in vitro and in vivo. Furthermore, siRNAs with 2′-O-methyl modifications at positions 2–5 reduce the seed-dependent off-target effects, as confirmed by reporter and microarray analyses. Thus, such siRNA is a promising candidate therapy for 15-bp deletion-type BRAF-induced tumorigenesis.
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83
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Li Z, Li X, Ai S, Liu S, Guan W. Glucose Metabolism Intervention-Facilitated Nanomedicine Therapy. Int J Nanomedicine 2022; 17:2707-2731. [PMID: 35747168 PMCID: PMC9213040 DOI: 10.2147/ijn.s364840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
Ordinarily, cancer cells possess features of abnormally increased nutrient intake and metabolic pathways. The disorder of glucose metabolism is the most important among them. Therefore, starvation therapy targeting glucose metabolism specifically, which results in metabolic disorders, restricted synthesis, and inhibition of tumor growth, has been developed for cancer therapy. However, issues such as inadequate targeting effectiveness and drug tolerance impede their clinical transformation. In recent years, nanomaterial-assisted starvation treatment has made significant progress in addressing these challenges, whether as a monotherapy or in combination with other medications. Herein, representative researches on the construction of nanosystems conducting starvation therapy are introduced. Elaborate designs and interactions between different treatment mechanisms are meticulously mentioned. Not only are traditional treatments based on glucose oxidase involved, but also newly sprung small molecule agents targeting glucose metabolism. The obstacles and potential for advancing these anticancer therapies were also highlighted in this review.
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Affiliation(s)
- Zhiyan Li
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Xianghui Li
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Shichao Ai
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Song Liu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, People's Republic of China
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84
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Dhandapani RK, Gurusamy D, Palli SR. Protamine-Lipid-dsRNA Nanoparticles Improve RNAi Efficiency in the Fall Armyworm, Spodoptera frugiperda. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6634-6643. [PMID: 35612305 DOI: 10.1021/acs.jafc.2c00901] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Developing safe and effective double-stranded RNA (dsRNA) delivery systems remains a major challenge for gene silencing, especially in lepidopteran insects. This study evaluated the protamine sulfate (PS)/lipid/dsRNA nanoparticle (NP) delivery system for RNA interference (RNAi) in cells and larvae of the fall armyworm (FAW), Spodoptera frugiperda, a major worldwide pest. A highly efficient gene delivery formulation was prepared using a cationic biopolymer, PS, and a cationic lipid, Cellfectin (CF), complexed with dsRNA. The NPs were prepared by a two-step self-assembly method. The formation of NPs was revealed by dynamic light scattering and transmission electron microscopy. The formation of CF/dsRNA/PS NPs was spherical in shape and size, ranging from 20 to 100 nm with a positive charge (+23.3 mV). Interestingly, prepared CF/dsRNA/PS NPs could protect dsRNA (95%) from nuclease degradation and thus significantly improve the stability of dsRNA. Formulations prepared by combining EGFP DNA with CF/PS increased transfection efficiency in Sf9 cells compared to PS/EGFP and CF/EGFP NPs. Also, the PS/CF/dsRNA NPs enhanced the endosomal escape for the intracellular delivery of dsRNA. The gene knockdown efficiency was assessed in Sf9 Luciferase (Luc) stable cells after a 72 h incubation with CF/dsRNA/PS, PS/dsRNA, CF/dsRNA, or naked dsRNA. Knockdown of the Luc gene was detected in CF/dsRNA/PS (76%) and PS/dsRNA (42.4%) not CF/dsRNA (19.5%) and naked dsRNA (10.3%) in Sf9 Luc cells. Moreover, CF/dsIAP/PS (25 μg of dsRNA targeting the inhibitor of apoptosis, IAP, gene of FAW) NPs showed knockdown of the IAP gene (39.5%) and mortality (55%) in FAW larvae. These results highlight the potential application of PS/lipid/dsRNA NPs for RNA-mediated control of insect pests.
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Affiliation(s)
| | - Dhandapani Gurusamy
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Subba Reddy Palli
- Department of Entomology, University of Kentucky, Lexington, Kentucky 40546, United States
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85
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Habib S, Singh M. Carbon-based Nanomaterials for delivery of small RNA molecules: a focus on potential cancer treatment applications. Pharm Nanotechnol 2022; 10:PNT-EPUB-124198. [PMID: 35670355 DOI: 10.2174/2211738510666220606102906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/17/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleic acid-mediated therapy holds immense potential in the treatment of recalcitrant human diseases such as cancer. This is underscored by advances in understanding the mechanisms of gene regulation. In particular, the endogenous protective mechanism of gene silencing known as RNA interference (RNAi) has been extensively exploited. METHODS We review here the developments from 2011 to 2021, in the use of nanographene oxide, carbon nanotubes, fullerenes, carbon nanohorns, carbon nanodots and nanodiamonds for the delivery of therapeutic small RNA molecules. RESULTS Appropriately designed effector molecules such as small interfering RNA (siRNA), can, in theory, silence the expression of any disease-causing gene. Alternatively, siRNA can be generated in vivo through the introduction of plasmid-based short hairpin RNA (shRNA) expression vectors. Other small RNAs such as micro RNA (miRNA) also function in post-transcriptional gene regulation and are aberrantly expressed under disease conditions. The miRNA-based therapy involves either restoration of miRNA function through the introduction of miRNA mimics; or the inhibition of miRNA function by delivering anti-miRNA oligomers. However, the large size, hydrophilicity, negative charge and nuclease-sensitivity of nucleic acids necessitate an appropriate carrier for their introduction as medicine into cells. CONCLUSION While numerous organic and inorganic materials have been investigated for this purpose, the perfect carrier agent remains elusive. In recent years, carbon-based nanomaterials have received widespread attention in biotechnology due to their tunable surface characteristics, mechanical, electrical, optical and chemical properties.
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Affiliation(s)
- Saffiya Habib
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Moganavelli Singh
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
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86
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Valiunas V, Gordon C, Valiuniene L, Devine D, Lin RZ, Cohen IS, Brink PR. Intercellular delivery of therapeutic oligonucleotides. J Drug Deliv Sci Technol 2022; 72:103404. [PMID: 36721641 PMCID: PMC9886232 DOI: 10.1016/j.jddst.2022.103404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
One promising approach to cancer therapeutics is to induce changes in gene expression that either reduce cancer cell proliferation or induce cancer cell death. Therefore, delivering oligonucleotides (siRNA/miRNA) that target specific genes or gene programs might have a potential therapeutic benefit. The aim of this study was to examine the potential of cell-based delivery of oligonucleotides to cancer cells via two naturally occurring intercellular pathways: gap junctions and vesicular/exosomal traffic. We utilized human mesenchymal stem cells (hMSCs) as delivery cells and chose to deliver in vitro two synthetic oligonucleotides, AllStars HS Cell Death siRNA and miR-16 mimic, as toxic (therapeutic) oligonucleotides targeting three cancer cell lines: prostate (PC3), pancreatic (PANC1) and cervical (HeLa). Both oligonucleotides dramatically reduced cell proliferation and/or induced cell death when transfected directly into target cells and delivery hMSCs. The delivery and target cells we chose express gap junction connexin 43 (Cx43) endogenously (PC3, PANC1, hMSC) or via stable transfection (HeLaCx43). Co-culture of hMSCs (transfected with either toxic oligonucleotide) with any of Cx43 expressing cancer cells induced target cell death (~20% surviving) or senescence (~85% proliferation reduction) over 96 hours. We eliminated gap junction-mediated delivery by using connexin deficient HeLaWT cells or knocking out endogenous Cx43 in PANC1 and PC3 cells via CRISPR/Cas9. Subsequently, all Cx43 deficient target cells co-cultured with the same toxic oligonucleotide loaded hMSCs proliferated, albeit at significantly slower rates, with cell number increasing on average ~2.2-fold (30% of control cells) over 96 hours. Our results show that both gap junction and vesicular/exosomal intercellular delivery pathways from hMSCs to target cancer cells deliver oligonucleotides and function to either induce cell death or significantly reduce their proliferation. Thus, hMSC-based cellular delivery is an effective method of delivering synthetic oligonucleotides that can significantly reduce tumor cell growth and should be further investigated as a possible approach to cancer therapy.
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Affiliation(s)
- Virginijus Valiunas
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Chris Gordon
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Laima Valiuniene
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Daniel Devine
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Richard Z Lin
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Ira S Cohen
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Peter R Brink
- Department of Physiology and Biophysics and the Institute for Molecular Cardiology Stony Brook University, Stony Brook, NY 11794-8661, USA
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87
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He W, Xu W, Fu K, Guo W, Kim DS, Zhang J. Positional effects of double-stranded RNAs targeting β-Actin gene affect RNA interference efficiency in Colorado potato beetle. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 184:105121. [PMID: 35715059 DOI: 10.1016/j.pestbp.2022.105121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Pesticide resistance in pests drives the development of RNA interference (RNAi)-based technology as a novel approach for pest control. To investigate the effects of the positional dependency of double-stranded RNAs (dsRNAs), we newly designed four different 200 bp dsRNAs targeting Colorado potato beetle (CPB) β-Actin gene, termed as dsACT200-1 to dsACT200-4, to compare their insecticidal activity to CPB larvae together with our previously used 200 bp and 700 bp dsRNAs (dsACT200 and dsACT700), respectively (He et al., 2020a). Each of dsRNAs harbors different numbers of expected siRNAs predicted by sequence-based prediction platform, dsACT200 and dsACT200-2 have a relatively higher number of siRNA than other 200 bps dsRNAs. When CPB larvae were fed with in vitro synthesized dsRNA-painted potato leaves, all the tested dsRNAs showed significant effects to protect against CPB larvae. Combined with the survival rate of CPB larvae, β-Actin gene expression level and the surviving CPB larvae weight, various positional dsRNAs from the same allele showed different plant protection activity against CPB larvae and partially correlated with the predicted siRNA numbers and distribution on the target sequence. This study suggests the specific allelic locus for rational dsRNA design triggering RNAi efficiency for target gene silencing is an essential factor in enhancing the insecticidal activity.
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Affiliation(s)
- Wanwan He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; Wuhan Academy of Agricultural Sciences, Wuhan 430070, China
| | - Wenbo Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Kaiyun Fu
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Wenchao Guo
- Institute of Microbial Application, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
| | - Dae Sung Kim
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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88
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Akbar S, Wei Y, Zhang MQ. RNA Interference: Promising Approach to Combat Plant Viruses. Int J Mol Sci 2022; 23:ijms23105312. [PMID: 35628126 PMCID: PMC9142109 DOI: 10.3390/ijms23105312] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/16/2022] Open
Abstract
Plant viruses are devastating plant pathogens that severely affect crop yield and quality. Plants have developed multiple lines of defense systems to combat viral infection. Gene silencing/RNA interference is the key defense system in plants that inhibits the virulence and multiplication of pathogens. The general mechanism of RNAi involves (i) the transcription and cleavage of dsRNA into small RNA molecules, such as microRNA (miRNA), or small interfering RNA (siRNA), (ii) the loading of siRNA/miRNA into an RNA Induced Silencing Complex (RISC), (iii) complementary base pairing between siRNA/miRNA with a targeted gene, and (iv) the cleavage or repression of a target gene with an Argonaute (AGO) protein. This natural RNAi pathway could introduce transgenes targeting various viral genes to induce gene silencing. Different RNAi pathways are reported for the artificial silencing of viral genes. These include Host-Induced Gene Silencing (HIGS), Virus-Induced Gene Silencing (VIGS), and Spray-Induced Gene Silencing (SIGS). There are significant limitations in HIGS and VIGS technology, such as lengthy and time-consuming processes, off-target effects, and public concerns regarding genetically modified (GM) transgenic plants. Here, we provide in-depth knowledge regarding SIGS, which efficiently provides RNAi resistance development against targeted genes without the need for GM transgenic plants. We give an overview of the defense system of plants against viral infection, including a detailed mechanism of RNAi, small RNA molecules and their types, and various kinds of RNAi pathways. This review will describe how RNA interference provides the antiviral defense, recent improvements, and their limitations.
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Affiliation(s)
- Sehrish Akbar
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China; (S.A.); (Y.W.)
| | - Yao Wei
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China; (S.A.); (Y.W.)
| | - Mu-Qing Zhang
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China; (S.A.); (Y.W.)
- IRREC-IFAS, University of Florida, Fort Pierce, FL 34945, USA
- Correspondence: or
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89
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Karannagoda N, Spokevicius A, Hussey S, Cassan-Wang H, Grima-Pettenati J, Bossinger G. Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PLANT MOLECULAR BIOLOGY 2022; 109:51-65. [PMID: 35292886 PMCID: PMC9072461 DOI: 10.1007/s11103-022-01255-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Our Induced Somatic Sector Analysis and protein-protein interaction experiments demonstrate that Eucalyptus grandis IAA13 regulates xylem fibre and vessel development, potentially via EgrIAA13 modules involving ARF2, ARF5, ARF6 and ARF19. Auxin is a crucial phytohormone regulating multiple aspects of plant growth and differentiation, including regulation of vascular cambium activity, xylogenesis and its responsiveness towards gravitropic stress. Although the regulation of these biological processes greatly depends on auxin and regulators of the auxin signalling pathway, many of their specific functions remain unclear. Therefore, the present study aims to functionally characterise Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13), a member of the auxin signalling pathway. In Eucalyptus and Populus, EgrIAA13 and its orthologs are preferentially expressed in the xylogenic tissues and downregulated in tension wood. Therefore, to further investigate EgrIAA13 and its function during xylogenesis, we conducted subcellular localisation and Induced Somatic Sector Analysis experiments using overexpression and RNAi knockdown constructs of EgrIAA13 to create transgenic tissue sectors on growing stems of Eucalyptus and Populus. Since Aux/IAAs interact with Auxin Responsive Factors (ARFs), in silico predictions of IAA13-ARF interactions were explored and experimentally validated via yeast-2-hybrid experiments. Our results demonstrate that EgrIAA13 localises to the nucleus and that downregulation of EgrIAA13 impedes Eucalyptus xylem fibre and vessel development. We also observed that EgrIAA13 interacts with Eucalyptus ARF2, ARF5, ARF6 and ARF19A. Based on these results, we conclude that EgrIAA13 is a regulator of Eucalyptus xylogenesis and postulate that the observed phenotypes are likely to result from alterations in the auxin-responsive transcriptome via IAA13-ARF modules such as EgrIAA13-EgrARF5. Our results provide the first insights into the regulatory role of EgrIAA13 during xylogenesis.
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Affiliation(s)
- Nadeeshani Karannagoda
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia.
- Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, Victoria, 3083, Australia.
| | - Antanas Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia
| | - Steven Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Hua Cassan-Wang
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia
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90
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Design of siRNA molecules for silencing of membrane glycoprotein, nucleocapsid phosphoprotein, and surface glycoprotein genes of SARS-CoV2. J Genet Eng Biotechnol 2022; 20:65. [PMID: 35482116 PMCID: PMC9047631 DOI: 10.1186/s43141-022-00346-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/18/2022] [Indexed: 12/24/2022]
Abstract
The global COVID-19 pandemic caused by SARS-CoV2 infected millions of people and resulted in more than 4 million deaths worldwide. Apart from vaccines and drugs, RNA silencing is a novel approach for treating COVID-19. In the present study, siRNAs were designed for the conserved regions targeting three structural genes, M, N, and S, from forty whole-genome sequences of SARS-CoV2 using four different software, RNAxs, siDirect, i-Score Designer, and OligoWalk. Only siRNAs which were predicted in common by all the four servers were considered for further shortlisting. A multistep filtering approach has been adopted in the present study for the final selection of siRNAs by the usage of different online tools, viz., siRNA scales, MaxExpect, DuplexFold, and SMEpred. All these web-based tools consider several important parameters for designing functional siRNAs, e.g., target-site accessibility, duplex stability, position-specific nucleotide preference, inhibitory score, thermodynamic parameters, GC content, and efficacy in cleaving the target. In addition, a few parameters like GC content and dG value of the entire siRNA were also considered for shortlisting of the siRNAs. Antisense strands were subjected to check for any off-target similarities using BLAST. Molecular docking was carried out to study the interactions of guide strands with AGO2 protein. A total of six functional siRNAs (two for each gene) have been finally selected for targeting M, N, and S genes of SARS-CoV2. The siRNAs have not shown any off-target effects, interacted with the domain(s) of AGO2 protein, and were efficacious in cleaving the target mRNA. However, the siRNAs designed in the present study need to be tested in vitro and in vivo in the future.
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91
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Kajino R, Sakamoto S, Ueno Y. Synthesis, gene silencing activity, thermal stability, and serum stability of siRNA containing four ( S)-5'- C-aminopropyl-2'- O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine). RSC Adv 2022; 12:11454-11476. [PMID: 35425057 PMCID: PMC9002251 DOI: 10.1039/d2ra00705c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Herein, we report the synthesis of (S)-5'-C-aminopropyl-2'-O-methyladenosine and (S)-5'-C-aminopropyl-2'-O-methylguanosine phosphoramidites and the properties of small interfering RNAs (siRNAs) containing four (S)-5'-C-aminopropyl-2'-O-methylnucleosides (A, adenosine; U, uridine; G, guanosine; and C, cytidine). The siRNAs containing (S)-5'-C-aminopropyl-nucleosides at the 3'- and 5'-regions of the passenger strand were well tolerated for RNA interference (RNAi) activity. Conversely, the (S)-5'-C-aminopropyl modification in the central region of the passenger strand decreased the RNAi activity. Furthermore, the siRNAs containing three or four consecutive (S)-5'-C-aminopropyl-2'-O-methylnucleosides at the 3'- and 5'-regions of the passenger strand exhibited RNAi activity similar to that of the corresponding 2'-O-methyl-modified siRNAs. Finally, it was observed that (S)-5'-C-aminopropyl modifications effectively improved the serum stability of the siRNAs, compared with 2'-O-methyl modifications. Therefore, (S)-5'-C-aminopropyl-2'-O-methylnucleosides would be useful for improving the serum stability of therapeutic siRNA molecules without affecting their RNAi activities.
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Affiliation(s)
- Ryohei Kajino
- United Graduate School of Agricultural Science, Gifu University Japan +81-58-293-2919 +81-58-293-2919
| | - Shuichi Sakamoto
- Institute of Microbial Chemistry (BIKAKEN) Numazu Branch, Microbial Chemistry Research Foundation 18-24 Miyamoto Numazu Shizuoka 410-0301 Japan
| | - Yoshihito Ueno
- United Graduate School of Agricultural Science, Gifu University Japan +81-58-293-2919 +81-58-293-2919
- Department of Life Science and Chemistry, The Graduate School of Natural Science and Technology, Gifu University Japan
- Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University 1-1 Yanagido Gifu 501-1193 Japan
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92
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Zhao X, Yang J, Zhang J, Wang X, Chen L, Zhang C, Shen Z. Inhibitory Effect of Aptamer-Carbon Dot Nanomaterial-siRNA Complex on the Metastasis of Hepatocellular Carcinoma Cells by Interfering with FMRP. Eur J Pharm Biopharm 2022; 174:47-55. [PMID: 35364257 DOI: 10.1016/j.ejpb.2022.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/23/2022] [Accepted: 03/27/2022] [Indexed: 11/04/2022]
Abstract
Using small interfering RNA (siRNA) for the specific gene-silencing has been a novel therapeutic method for the treatment of incurable diseases such as malignancies. However, it remains a challenge whether siRNA can be safely and effectively delivered into target cells. Therefore, we synthesized fluorescent carbon dots (CDs) as a gene vector at the siRNA delivery system that induced efficient gene knockdown in vitro while binding aptamer AS1411 to resolve the difficulty in cell targeting. We found that CDs with adequate biocompatibility can improve the efficiency of cellular uptake of siRNA. CLSM and FCM results showed that CDs were mainly localized in the cytoplasm and emitted bright green fluorescence. In addition, the CD/siRNA delivery system mediated by the aptamer AS1411 effectively silenced the expression of Fragile X mental retardation protein (FMRP) and successfully inhibited the migration and invasive propensity of hepatocellular carcinoma (HCC) cells. In summary, we have synthesized a valuable siRNA delivery vector enabling not only bioimaging but also effective downregulation of gene expression, which is indicative of an efficient potential for gene delivery and therapy.
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Affiliation(s)
- Xiaoliang Zhao
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, and School of Basic Medicine, Xinxiang Medical University, Xinxiang, 453003, China; these authors contributed equally to this work
| | - Jie Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, 321000, China; these authors contributed equally to this work
| | - Jing Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiangyun Wang
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, and School of Basic Medicine, Xinxiang Medical University, Xinxiang, 453003, China
| | - Lulu Chen
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, and School of Basic Medicine, Xinxiang Medical University, Xinxiang, 453003, China
| | - Chao Zhang
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, and School of Basic Medicine, Xinxiang Medical University, Xinxiang, 453003, China
| | - Zhifa Shen
- Research Center for Molecular Oncology and Functional Nucleic Acids, School of Laboratory Medicine, and School of Basic Medicine, Xinxiang Medical University, Xinxiang, 453003, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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93
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Saadat KASM. RNAi-mediated siRNA sequences to combat the COVID-19 pandemic with the inhibition of SARS-CoV2. GENE REPORTS 2022; 26:101512. [PMID: 35071824 PMCID: PMC8760737 DOI: 10.1016/j.genrep.2022.101512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Khandakar A S M Saadat
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep 27310, Turkey
- Department of Medical Biology and Genetics, Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey
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94
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Harnessing Intronic microRNA Structures to Improve Tolerance and Expression of shRNAs in Animal Cells. Methods Protoc 2022; 5:mps5010018. [PMID: 35200534 PMCID: PMC8879667 DOI: 10.3390/mps5010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/01/2022] Open
Abstract
Exogenous RNA polymerase III (pol III) promoters are commonly used to express short hairpin RNA (shRNA). Previous studies have indicated that expression of shRNAs using standard pol III promoters can cause toxicity in vivo due to saturation of the native miRNA pathway. A potential way of mitigating shRNA-associated toxicity is by utilising native miRNA processing enzymes to attain tolerable shRNA expression levels. Here, we examined parallel processing of exogenous shRNAs by harnessing the natural miRNA processing enzymes and positioning a shRNA adjacent to microRNA107 (miR107), located in the intron 5 of the Pantothenate Kinase 1 (PANK1) gene. We developed a vector encoding the PANK1 intron containing miR107 and examined the expression of a single shRNA or multiple shRNAs. Using qRT-PCR analysis and luciferase assay-based knockdown assay, we confirmed that miR30-structured shRNAs have resulted in the highest expression and subsequent transcript knockdown. Next, we injected Hamburger and Hamilton stage 14–15 chicken embryos with a vector encoding multiple shRNAs and confirmed that the parallel processing was not toxic. Taken together, this data provides a novel strategy to harness the native miRNA processing pathways for shRNA expression. This enables new opportunities for RNAi based applications in animal species such as chickens.
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95
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The siRNA Off-Target Effect Is Determined by Base-Pairing Stabilities of Two Different Regions with Opposite Effects. Genes (Basel) 2022; 13:genes13020319. [PMID: 35205363 PMCID: PMC8872465 DOI: 10.3390/genes13020319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
In RNA interference (RNAi), small interfering RNA (siRNA) suppresses the expression of its target mRNA with a perfect complementary sequence. In addition, siRNA also suppresses the expression of unintended mRNAs with partially complementary sequences mainly within the siRNA seed region (nucleotides 2–8). This mechanism is highly similar to microRNA (miRNA)-mediated RNA silencing, and known as the siRNA-mediated off-target effect. Previously, we revealed that the off-target effect is induced through stable base-pairing between the siRNA seed region and off-target mRNAs, but not induced through unstable base-pairing. However, in our recent study, we found that the siRNA seed region consists of two functionally different domains: nucleotides 2–5, essential for off-target effects, and nucleotides 6–8, involved in both RNAi and off-target effects. In this study, we investigated the most responsible region for the off-target effect by conducting a comprehensive analysis of the thermodynamic properties of all possible siRNA subregions that involved a machine learning technique using a random sampling procedure. As a result, the thermodynamic stability of nucleotides 2–5 showed the highest positive correlation with the off-target effect, and nucleotides 8–14 showed the most negative correlation. Thus, it is revealed that the siRNA off-target effect is determined by the base-pairing stabilities of two different subregions with opposite effects.
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96
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Kobayashi Y, Fukuhara D, Akase D, Aida M, Ui-Tei K. siRNA Seed Region Is Divided into Two Functionally Different Domains in RNA Interference in Response to 2'-OMe Modifications. ACS OMEGA 2022; 7:2398-2410. [PMID: 35071927 PMCID: PMC8771963 DOI: 10.1021/acsomega.1c06455] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/24/2021] [Indexed: 05/04/2023]
Abstract
In RNA interference (RNAi), small interfering RNA (siRNA) functions to suppress the expression of its target mRNA with perfect sequence complementarity. In a mechanism different from above, siRNA also suppresses unintended mRNAs with partial sequence complementarities, mainly to the siRNA seed region (nucleotides 2-8). This mechanism is largely utilized by microRNAs (miRNAs) and results in siRNA-mediated off-target effects. Thus, the siRNA seed region is considered to be involved in both RNAi and off-target effects. In this study, we revealed that the impact of 2'-O-methyl (2'-OMe) modification is different according to the nucleotide positions. The 2'-OMe modifications of nucleotides 2-5 inhibited off-target effects without affecting on-target RNAi activities. In contrast, 2'-OMe modifications of nucleotides 6-8 increased both RNAi and off-target activities. The computational simulation revealed that the structural change induced by 2'-OMe modifications interrupts base pairing between siRNA and target/off-target mRNAs at nucleotides 2-5 but enhances at nucleotides 6-8. Thus, our results suggest that siRNA seed region consists of two functionally different domains in response to 2'-OMe modifications: nucleotides 2-5 are essential for avoiding off-target effects, and nucleotides 6-8 are involved in the enhancement of both RNAi and off-target activities.
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Affiliation(s)
- Yoshiaki Kobayashi
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Daiki Fukuhara
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Dai Akase
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Misako Aida
- Center
for Quantum Life Sciences and Department of Chemistry, Graduate School
of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kumiko Ui-Tei
- Department
of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department
of Computational Biology and Medical Sciences, Graduate School of
Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
- . Phone: +81-3-5841-3044. Fax: +81-3-5841-3044
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97
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Sobrero M, Montecucco F, Carbone F. Circulating MicroRNAs for Diagnosis of Acute Pulmonary Embolism: Still a Long Way to Go. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4180215. [PMID: 35047634 PMCID: PMC8763471 DOI: 10.1155/2022/4180215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/14/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022]
Abstract
Venous thromboembolism (VTE) represents the third most frequent cause of acute cardiovascular syndrome. Among VTE, acute pulmonary embolism (APE) is the most life-threatening complication. Due to the low specificity of symptoms clinical diagnosis of APE may be sometimes very difficult. Accordingly, the latest European guidelines only suggest clinical prediction tests for diagnosis of APE, eventually associated with D-dimer, a biomarker burdened by a very low specificity. A growing body of evidence is highlighting the role of miRNAs in hemostasis and thrombosis. Due to their partial inheritance and susceptibility to the environmental factors, miRNAs are increasingly described as active modifiers of the classical Virchow's triad. Clinical evidence on deep venous thrombosis reported specific miRNA signatures associated to thrombosis development, organization, recanalization, and resolution. Conversely, data of miRNA profiling as a predictor/diagnostic marker of APE are still preliminary. Here, we have summarized clinical evidence on the potential role of miRNA in diagnosis of APE. Despite some intriguing insight, miRNA assay is still far from any potential clinical application. Especially, the small sample size of cohorts likely represents the major limitation of published studies, so that extensive analysis of miRNA profiles with a machine learning approach are warranted in the next future. In addition, the cost-benefit ratio of miRNA assay still has a negative impact on their clinical application and routinely test.
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Affiliation(s)
- Matteo Sobrero
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132 Genoa, Italy
| | - Fabrizio Montecucco
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa-Italian Cardiovascular Network, 10 Largo Benzi, 16132 Genoa, Italy
| | - Federico Carbone
- First Clinic of Internal Medicine, Department of Internal Medicine, University of Genoa, 6 Viale Benedetto XV, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa-Italian Cardiovascular Network, 10 Largo Benzi, 16132 Genoa, Italy
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98
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Darlington M, Reinders JD, Sethi A, Lu AL, Ramaseshadri P, Fischer JR, Boeckman CJ, Petrick JS, Roper JM, Narva KE, Vélez AM. RNAi for Western Corn Rootworm Management: Lessons Learned, Challenges, and Future Directions. INSECTS 2022; 13:57. [PMID: 35055900 PMCID: PMC8779393 DOI: 10.3390/insects13010057] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 02/06/2023]
Abstract
The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is considered one of the most economically important pests of maize (Zea mays L.) in the United States (U.S.) Corn Belt with costs of management and yield losses exceeding USD ~1-2 billion annually. WCR management has proven challenging given the ability of this insect to evolve resistance to multiple management strategies including synthetic insecticides, cultural practices, and plant-incorporated protectants, generating a constant need to develop new management tools. One of the most recent developments is maize expressing double-stranded hairpin RNA structures targeting housekeeping genes, which triggers an RNA interference (RNAi) response and eventually leads to insect death. Following the first description of in planta RNAi in 2007, traits targeting multiple genes have been explored. In June 2017, the U.S. Environmental Protection Agency approved the first in planta RNAi product against insects for commercial use. This product expresses a dsRNA targeting the WCR snf7 gene in combination with Bt proteins (Cry3Bb1 and Cry34Ab1/Cry35Ab1) to improve trait durability and will be introduced for commercial use in 2022.
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Affiliation(s)
- Molly Darlington
- Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA; (M.D.); (J.D.R.)
| | - Jordan D. Reinders
- Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA; (M.D.); (J.D.R.)
| | - Amit Sethi
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | - Albert L. Lu
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | | | - Joshua R. Fischer
- Bayer Crop Science, Chesterfield, MO 63017, USA; (P.R.); (J.R.F.); (J.S.P.)
| | - Chad J. Boeckman
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | - Jay S. Petrick
- Bayer Crop Science, Chesterfield, MO 63017, USA; (P.R.); (J.R.F.); (J.S.P.)
| | - Jason M. Roper
- Corteva Agriscience, Johnston, IA 50131, USA; (A.S.); (A.L.L.); (C.J.B.); (J.M.R.)
| | | | - Ana M. Vélez
- Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA; (M.D.); (J.D.R.)
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99
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Narayanaswami P, Živković S. Molecular and Genetic Therapies. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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100
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Ben Youssef M, Christelle Ouédraogo B, Bastarache P, Dumas P, Moffat CE, Vickruck JL, Morin PJ. Exposure to Temperature and Insecticides Modulates the Expression of Small Noncoding RNA-Associated Transcripts in the Colorado Potato Beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:23. [PMID: 35172010 PMCID: PMC8849280 DOI: 10.1093/jisesa/ieac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 06/14/2023]
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata (Say)) is an insect that can adapt to various challenges, including temperature fluctuations or select insecticide treatments. This pest is also an ongoing threat to the potato industry. Small noncoding RNAs such as miRNAs, which can control posttranscriptionally the expression of various genes, and piRNAs, which can notably impact mRNA turnover, are modulated in insects under different conditions. Unfortunately, information regarding the expression status of key players involved in their synthesis and function is for the most part lacking. The current study thus aims at assessing the levels of such targets in L. decemlineata exposed to hot and cold temperatures as well as treated to the insecticides chlorantraniliprole, clothianidin, imidacloprid, and spinosad. Transcript expression levels of Ago1, Ago2, Ago3, Dcr2a, Dcr2b, Expo-5, Siwi-1, and Siwi-2, components of pathways associated with small noncoding RNA production or function, were measured by qRT-PCR and revealed modulation of select transcripts in response to temperature challenges and to select insecticides. RNAi-mediated reduction of Ago2 transcript levels in L. decemlineata injected with Ago2-targeting dsRNA and exposed to cold and warm temperatures was also conducted. Changes in survival rates were observed for the latter condition in dsRNA- versus saline-injected insects. These results showcase the differential expression of select targets involved in small noncoding RNA homeostasis and provide leads for the subsequent assessment of their involvement during stress response in L. decemlineata using RNAi-based approaches.
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Affiliation(s)
- Mariem Ben Youssef
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Brigitte Christelle Ouédraogo
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Pierre Bastarache
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Pascal Dumas
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Chandra E Moffat
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Jessica L Vickruck
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
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