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Ubeda Gutierrez AM, Remant Bahadur KC, Brandwein J, Uludağ H. Exploring the Potential of siRNA Delivery in Acute Myeloid Leukemia for Therapeutic Silencing. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:3167. [PMID: 38133064 PMCID: PMC10745893 DOI: 10.3390/nano13243167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
We investigated the feasibility of using siRNA therapy for acute myeloid leukemia (AML) by developing macromolecular carriers that facilitated intracellular delivery of siRNA. The carriers were derived from low-molecular-weight (<2 kDa) polyethyleneimine (PEI) and modified with a range of aliphatic lipids. We identified linoleic acid and lauric acid-modified PEI as optimal carriers for siRNA delivery to AML cell lines KG1 and KG1a, as well as AML patient-derived mononuclear cells. As they have been proven to be potent targets in the treatment of AML, we examined the silencing of BCL2L12 and survivin and showed how it leads to the decrease in proliferation of KG1 and stem-cell-like KG1a cells. By optimizing the transfection schedule, we were able to enhance the effect of the siRNAs on proliferation over a period of 10 days. We additionally showed that with proper modifications of PEI, other genes, including MAP2K3, CDC20, and SOD-1, could be targeted to decrease the proliferation of AML cells. Our studies demonstrated the versatility of siRNA delivery with modified PEI to elicit an effect in leukemic cells that are difficult to transfect, offering an alternative to conventional drugs for more precise and targeted treatment options.
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Affiliation(s)
- Anyeld M. Ubeda Gutierrez
- Department of Biomedical Engineering, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - K. C. Remant Bahadur
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Joseph Brandwein
- Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Hasan Uludağ
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
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2
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Valimukhametova AR, Lee BH, Topkiran UC, Gries K, Gonzalez-Rodriguez R, Coffer JL, Akkaraju G, Naumov A. Cancer Therapeutic siRNA Delivery and Imaging by Nitrogen- and Neodymium-Doped Graphene Quantum Dots. ACS Biomater Sci Eng 2023; 9:3425-3434. [PMID: 37255435 DOI: 10.1021/acsbiomaterials.3c00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
While small interfering RNA (siRNA) technology has become a powerful tool that can enable cancer-specific gene therapy, its translation to the clinic is still hampered by the inability of the genes alone to cell transfection, poor siRNA stability in blood, and the lack of delivery tracking capabilities. Recently, graphene quantum dots (GQDs) have emerged as a novel platform allowing targeted drug delivery and fluorescence image tracking in visible and near-infrared regions. These capabilities can aid in overcoming primary obstacles to siRNA therapeutics. Here, for the first time, we utilize biocompatible nitrogen- and neodymium-doped graphene quantum dots (NGQDs and Nd-NGQDs, respectively) for the delivery of Kirsten rat sarcoma virus (KRAS) and epidermal growth factor receptor (EGFR) siRNA effective against a variety of cancer types. GQDs loaded with siRNA noncovalently facilitate successful siRNA transfection into HeLa cells, confirmed by confocal fluorescence microscopy at biocompatible GQD concentrations of 375 μg/mL. While the GQD platform provides visible fluorescence tracking, Nd doping enables deeper-tissue near-infrared fluorescence imaging suitable for both in vitro and in vivo applications. The therapeutic efficacy of the GQD/siRNA complex is verified by successful protein knockdown in HeLa cells at nanomolar siEGFR and siKRAS concentrations. A range of GQD/siRNA loading ratios and payloads are tested to ultimately provide substantial inhibition of protein expression down to 31-45%, comparable with conventional Lipofectamine-mediated delivery. This demonstrates the promising potential of GQDs for the nontoxic delivery of siRNA and genes in general, complemented by multiwavelength image tracking.
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Affiliation(s)
- Alina R Valimukhametova
- Department of Physics and Astronomy, Texas Christian University, Fort Worth 76129, Texas, United States
| | - Bong Han Lee
- Department of Physics and Astronomy, Texas Christian University, Fort Worth 76129, Texas, United States
| | - Ugur C Topkiran
- Department of Physics and Astronomy, Texas Christian University, Fort Worth 76129, Texas, United States
| | - Klara Gries
- Department of Chemistry and Biochemistry, Heidelberg University, Heidelberg 69117, Germany
| | | | - Jeffery L Coffer
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth 76129, Texas, United States
| | - Giridhar Akkaraju
- Department of Biology, Texas Christian University, Fort Worth 76129, Texas, United States
| | - Anton Naumov
- Department of Physics and Astronomy, Texas Christian University, Fort Worth 76129, Texas, United States
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3
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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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4
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Jing X, Arya V, Reynolds KS, Rogers H. Clinical Pharmacology of RNA Interference-Based Therapeutics: A Summary Based on Food and Drug Administration-Approved Small Interfering RNAs. Drug Metab Dispos 2023; 51:193-198. [PMID: 36332914 PMCID: PMC9900864 DOI: 10.1124/dmd.122.001107] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-based oligonucleotide therapeutics are revolutionizing drug development for disease treatment. This class of therapeutics differs from small molecules and protein therapeutics in various ways, including both its mechanism of action and clinical pharmacology characteristics. These unique characteristics, along with evolving oligonucleotide-associated conjugates allowing specific tissue targeting, have fueled interest in the evaluation of RNA-based oligonucleotide therapeutics in a rapidly increasing number of therapeutic areas. With these unique attributes as well as growing therapeutic potential, oligonucleotide therapeutics have generated significant interest from a clinical pharmacology perspective. The Food and Drug Administration (FDA) previously published results of a survey that summarized clinical pharmacology studies supporting oligonucleotide therapies approved and in development between 2012 and 2018. Since the first approval of a small interfering RNA (siRNA) therapeutic in 2018, this class of modalities has gained momentum in various therapeutic areas. Hence, a comprehensive examination of the clinical pharmacology of FDA-approved siRNA therapeutics would benefit the path forward for many stakeholders. Thus, in this current review, we thoroughly examine and summarize clinical pharmacology data of the FDA-approved siRNA therapeutics approved from 2018 (year of first approval) to 2022, aimed at facilitating future drug development and regulatory decision making. SIGNIFICANCE STATEMENT: This review systematically summarizes the clinical pharmacology information of Food and Drug Administration (FDA)-approved small interfering RNAs (siRNA) therapeutics. SiRNAs are revolutionizing the drug development field. Unique clinical pharmacology characteristics represent a differentiating factor for this class of therapeutics. The FDArecently published a draft guidance for clinical pharmacology considerations for developing oligonucleotide therapeutics. As clinical development of this class of therapeutics is fast growing, this review will inform discovery and clinical-stage evaluation of upcoming siRNA-associated drug candidates.
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Affiliation(s)
- Xing Jing
- Divisions of Infectious Disease Pharmacology (X.J., V.A., K.S.R.) and Translational and Precision Medicine (H.R.), Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Vikram Arya
- Divisions of Infectious Disease Pharmacology (X.J., V.A., K.S.R.) and Translational and Precision Medicine (H.R.), Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Kellie Schoolar Reynolds
- Divisions of Infectious Disease Pharmacology (X.J., V.A., K.S.R.) and Translational and Precision Medicine (H.R.), Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Hobart Rogers
- Divisions of Infectious Disease Pharmacology (X.J., V.A., K.S.R.) and Translational and Precision Medicine (H.R.), Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
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5
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Bharathi JK, Anandan R, Benjamin LK, Muneer S, Prakash MAS. Recent trends and advances of RNA interference (RNAi) to improve agricultural crops and enhance their resilience to biotic and abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:600-618. [PMID: 36529010 DOI: 10.1016/j.plaphy.2022.11.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/04/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Over the last two decades, significant advances have been made using genetic engineering technology to modify genes from various exotic origins and introduce them into plants to induce favorable traits. RNA interference (RNAi) was discovered earlier as a natural process for controlling the expression of genes across all higher species. It aims to enhance precision and accuracy in pest/pathogen resistance, quality improvement, and manipulating the architecture of plants. However, it existed as a widely used technique recently. RNAi technologies could well be used to down-regulate any genes' expression without disrupting the expression of other genes. The use of RNA interference to silence genes in various organisms has become the preferred method for studying gene functions. The establishment of new approaches and applications for enhancing desirable characters is essential in crops by gene suppression and the refinement of knowledge of endogenous RNAi mechanisms in plants. RNAi technology in recent years has become an important and choicest method for controlling insects, pests, pathogens, and abiotic stresses like drought, salinity, and temperature. Although there are certain drawbacks in efficiency of this technology such as gene candidate selection, stability of trigger molecule, choice of target species and crops. Nevertheless, from past decade several target genes has been identified in numerous crops for their improvement towards biotic and abiotic stresses. The current review is aimed to emphasize the research done on crops under biotic and abiotic stress using RNAi technology. The review also highlights the gene regulatory pathways/gene silencing, RNA interference, RNAi knockdown, RNAi induced biotic and abiotic resistance and advancements in the understanding of RNAi technology and the functionality of various components of the RNAi machinery in crops for their improvement.
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Affiliation(s)
- Jothi Kanmani Bharathi
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India
| | - Ramaswamy Anandan
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India
| | - Lincy Kirubhadharsini Benjamin
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
| | - Muthu Arjuna Samy Prakash
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India.
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6
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Pascoal VDB, Marchesini RB, Athié MCP, Matos AHB, Conte FF, Pereira TC, Secolin R, Gilioli R, Malheiros JM, Polli RS, Tannús A, Covolan L, Pascoal LB, Vieira AS, Cavalheiro EA, Cendes F, Lopes-Cendes I. Modulating Expression of Endogenous Interleukin 1 Beta in the Acute Phase of the Pilocarpine Model of Epilepsy May Change Animal Survival. Cell Mol Neurobiol 2023; 43:367-380. [PMID: 35061107 DOI: 10.1007/s10571-022-01190-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/05/2022] [Indexed: 01/07/2023]
Abstract
The pilocarpine-induced (PILO) model has helped elucidate the electrophysiological and molecular aspects related to mesial temporal lobe epilepsy. It has been suggested that the extensive cell death and edema observed in the brains of these animals could be induced by increased inflammatory responses, such as the rapid release of the inflammatory cytokine interleukin 1 beta (Il1b). In this study, we investigate the role of endogenous Il1b in the acute phase of the PILO model. Our aim is twofold. First, we want to determine whether it is feasible to silence Il1b in the central nervous system using a non-invasive procedure. Second, we aim to investigate the effect of silencing endogenous Il1b and its antagonist, Il1rn.We used RNA interference applied non-invasively to knockdown Il1b and its endogenous antagonist Il1rn. We found that knocking down Il1b prior to pilocarpine injection increased the mortality rate of treated animals. Furthermore, we observed that, when exposing the animals to more Il1b by silencing its endogenous antagonist Il1rn, there was a better response to status epilepticus with decreased animal mortality in the acute phase of the PILO model. Thus, we show the feasibility of using a novel, less invasive approach to study genes involved in the inflammatory response in the central nervous system. Furthermore, our results provide suggestive evidence that modulating endogenous Il1b improves animal survival in the acute phase of the PILO model and may have effects that extend into the chronic phase.
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Affiliation(s)
- V D B Pascoal
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil.,Department of Basic Science, Fluminense Federal University, Nova Friburgo, RJ, Brazil
| | - R B Marchesini
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - M C P Athié
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - A H B Matos
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - F F Conte
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - T C Pereira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil.,Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirao Preto, University of Sao Paulo (USP), Ribeirao Preto, SP, Brazil
| | - R Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil.,Department of Basic Science, Fluminense Federal University, Nova Friburgo, RJ, Brazil
| | - R Gilioli
- Multidisciplinary Centre for Biological Investigation (CEMIB), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - J M Malheiros
- Centro de Imagens e Espectroscopia por Ressonancia Magnetica (CIERMag), Institute of Physics, University of Sao Paulo (USP), Sao Carlos, SP, Brazil.,Department of Physiology, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP, Brazil
| | - R S Polli
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil
| | - A Tannús
- Centro de Imagens e Espectroscopia por Ressonancia Magnetica (CIERMag), Institute of Physics, University of Sao Paulo (USP), Sao Carlos, SP, Brazil
| | - L Covolan
- Department of Physiology, Federal University of Sao Paulo (UNIFESP), Sao Paulo, SP, Brazil
| | - L B Pascoal
- Laboratory of Cell Signaling, School of Medical Sciences, University of Campinas - (UNICAMP), Campinas, SP, Brazil
| | - A S Vieira
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas - (UNICAMP), Campinas, SP, Brazil
| | - E A Cavalheiro
- Department of Neurology and Neurosurgery, Federal University of Sao Paulo, (UNIFESP), Sao Paulo, SP, Brazil
| | - F Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas - (UNICAMP); and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - I Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Tessália Vieira de Camargo, 126, Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil.
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7
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McCann J, Sosa‐Miranda CD, Guo H, Reshke R, Savard A, Zardini Buzatto A, Taylor JA, Li L, Gibbings DJ. Contaminating transfection complexes can masquerade as small extracellular vesicles and impair their delivery of RNA. J Extracell Vesicles 2022; 11:e12220. [PMID: 36214496 PMCID: PMC9549735 DOI: 10.1002/jev2.12220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 02/02/2022] [Accepted: 03/29/2022] [Indexed: 11/06/2022] Open
Abstract
One of the functions of small extracellular vesicles (sEVs) which has received the most attention is their capacity to deliver RNA into the cytoplasm of target cells. These studies have often been performed by transfecting RNAs into sEV-producing cells, to later purify and study sEV delivery of RNA. Transfection complexes and other delivery vehicles accumulate in late endosomes where sEV are formed and over 50% of transfection complexes or delivery vehicles administered to cells are released again to the extracellular space by exocytosis. This raises the possibility that transfection complexes could alter sEVs and contaminate sEV preparations. We found that widely used transfection reagents including RNAiMax and INTERFERin accumulated in late endosomes. These transfection complexes had a size similar to sEV and were purified by ultracentrifugation like sEV. Focusing on the lipid-based transfection reagent RNAiMax, we found that preparations of sEV from transfected cells contained lipids from transfection complexes and transfected siRNA was predominantly in particles with the density of transfection complexes, rather than sEV. This suggests that transfection complexes, such as lipid-based RNAiMax, may frequently contaminate sEV preparations and could account for some reports of sEV-mediated delivery of nucleic acids. Transfection of cells also impaired the capacity of sEVs to deliver stably-expressed siRNAs, suggesting that transfection of cells may alter sEVs and prevent the study of their endogenous capacity to deliver RNA to target cells.
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Affiliation(s)
- Jenna McCann
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | | | - Huishan Guo
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | - Ryan Reshke
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | - Alexandre Savard
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | | | - James A. Taylor
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada
| | - Liang Li
- The Metabolomics Innovation CentreUniversity of AlbertaEdmontonAlbertaCanada,Department of ChemistryUniversity of AlbertaEdmontonAlbertaCanada
| | - Derrick J. Gibbings
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaOntarioCanada,Institute for Systems BiologyUniversity of OttawaOttawaOntarioCanada,Faculty of MedicineEric Poulin Centre for Neuromuscular DiseaseUniversity of OttawaOttawaOntarioCanada
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Chai H, Lei Z, Liu Y, Gong J, Cao Z, Huang Z, Yang H, Wu Z. miR-505-5p alleviates acute rejection of liver transplantation by inhibiting Myd88 and inducing M2 polarizationof Kupffer cells. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1148-1158. [PMID: 35959879 PMCID: PMC9828294 DOI: 10.3724/abbs.2022100] [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: 02/06/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022] Open
Abstract
The occurrence of acute rejection after liver transplantation seriously impairs the prognosis of patients. miRNA is involved in many physiological and pathological processes of the body, but the mechanism of miRNA action in liver transplantation is not completely clear. In this study, we discuss the role of miR-505-5p in acute rejection after liver transplantation and its putative regulating mechanism. We construct an allogeneic rat liver transplantation model, observe the morphological and pathological changes in liver tissue, detect the expression levels of Myd88, miR-505-5p, IL-10 and TNF-α, and confirm that Myd88 is one of the direct targets of miR-505. The effects of miR-505-5p on the Myd88/TRAF6/NF-κB and MAPK pathways are detected both in vitro and in vivo, and the standard markers of Kupffer cell M1/M2 polarization are also detected. The results of qRT-PCR experiments show that miR-505-5p has a downward trend in rats with acute rejection. Western blot analysis reveals that over-expression of miR-505-5p induces the reduction of NF-κB and MAPK pathways both in vitro and in vivo. The role of miR-505-5p in alleviating acute rejection after transplantation may be accomplished by inducing M2-type polarization of Kupffer cells. In conclusion, we find that miR-505-5p alleviates acute rejection of liver transplantation by inducing M2 polarization of macrophages via the Myd88/TRAF6 axis, which suggests a potential strategy based on miRNAs in the follow-up treatment of liver transplantation.
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Affiliation(s)
- Hao Chai
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Zilun Lei
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Yanyao Liu
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Junhua Gong
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Zhenrui Cao
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Zuotian Huang
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Hang Yang
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Zhongjun Wu
- Department of Hepatobiliary Surgerythe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
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9
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RNA-Based Therapy for Cryptosporidium parvum Infection: Proof-of-Concept Studies. Infect Immun 2022; 90:e0019622. [PMID: 35647663 DOI: 10.1128/iai.00196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cryptosporidium is a leading cause of moderate-to-severe diarrhea in children, which is one of the major causes of death in children under 5 years old. Nitazoxanide is the only FDA-approved treatment for cryptosporidiosis. However, it has limited efficacy in immunosuppressed patients and malnourished children. Therefore, it is urgent to develop novel therapies against this parasite. RNA interference-mediated therapies are emerging as novel approaches for the treatment of infectious diseases. We have developed a novel method to silence essential genes in Cryptosporidium using single-stranded RNA (ssRNA)/Argonaute (Ago) complexes. In this work we conducted proof-of-concept studies to test the anticryptosporidial activity of these complexes by silencing Cryptosporidium parvum nucleoside diphosphate kinase (NDK) using in vitro and in vivo models. We demonstrated that a 3-day treatment with anti-sense NDK ssRNA/Ago decreased parasite burden by ~98% on infected cells. In vivo studies showed that ssRNA/Ago complexes encapsulated in lipid nanoparticles can be delivered onto intestinal epithelial cells of mice treated orally. In addition a cryptosporidiosis-mouse model showed that treatment with NDK ssRNA/Ago complexes reduced oocyst shedding in 4/5 SCID/beige mice during the acute phase of the infection. Our findings highlight the potential use of antisense RNA-based therapy as an alternative approach to cryptosporidiosis treatment.
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10
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Zhang B, Xu S, Liu J, Xie Y, Xiaobo S. Long Noncoding RNAs: Novel Important Players in Adipocyte Lipid Metabolism and Derivative Diseases. Front Physiol 2021; 12:691824. [PMID: 34168572 PMCID: PMC8217837 DOI: 10.3389/fphys.2021.691824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 01/08/2023] Open
Abstract
Obesity, a global public health issue, is characterized by excessive adiposity and is strongly related to some chronic diseases including cardiovascular diseases and diabetes. Extra energy intake-induced adipogenesis involves various transcription factors and long noncoding RNAs (lncRNAs) that control lipogenic mRNA expression. Currently, lncRNAs draw much attention for their contribution to adipogenesis and adipose tissue function. Increasing evidence also manifests the pivotal role of lncRNAs in modulating white, brown, and beige adipose tissue development and affecting the progression of the diseases induced by adipose dysfunction. The aim of this review is to summarize the roles of lncRNAs in adipose tissue development and obesity-caused diseases to provide novel drug targets for the treatment of obesity and metabolic diseases.
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Affiliation(s)
- Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Saijun Xu
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jinyan Liu
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yong Xie
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sun Xiaobo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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11
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Kiss T, Jámbor K, Koroknai V, Szász I, Bárdos H, Mokánszki A, Ádány R, Balázs M. Silencing Osteopontin Expression Inhibits Proliferation, Invasion and Induce Altered Protein Expression in Melanoma Cells. Pathol Oncol Res 2021; 27:581395. [PMID: 34257527 PMCID: PMC8262222 DOI: 10.3389/pore.2021.581395] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/05/2021] [Indexed: 12/21/2022]
Abstract
Osteopontin (OPN) is a multifunctional phosphoprotein that is expressed in different types of cancers, including melanoma. OPN overexpression is associated with tumor progression and metastasis formation; however, the role of OPN in cell invasion and metastasis formation is not completely understood. In this study we aimed to define OPN expression in melanoma tissues and cell lines and investigate the effect of OPN expression on cell proliferation and invasion after inhibiting OPN expression with small interfering RNA (siRNA). OPN gene expression was determined by qRT-PCR, while protein expression was examined using a Proteome Profiler Oncology Array. siRNA-mediated OPN knockdown led to decreased OPN expression in melanoma cell lines, which was associated with decreased cell proliferation and invasion. Proteome profile analysis revealed significantly different protein expression between the original and transfected cell lines. The altered expression of the differently expressed proteins was validated at the mRNA level. Furthermore, OPN-specific siRNA was able to reduce OPN expression and inhibit the invasiveness of melanoma cells. Our results revealed for the first time that silencing the OPN gene influences proliferation and invasion of melanoma cells by effecting EGFR, tenascin C, survivin, galectin-3 and enolase 2 expression. To predict protein-protein interactions along with putative pathways we used STRING analysis for the differentially expressed proteins. These proteins formed multiple clusters, including extracellular matrix organization, regulation of angiogenesis, cell death and cell migration, PI3K-Akt, MAPK and focal adhesion signaling pathways. Taken together these data suggest that OPN might be an ideal target for drug development and therapies.
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Affiliation(s)
- Tímea Kiss
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztina Jámbor
- Doctoral School of Health Sciences, University of Debrecen, Debrecen, Hungary
| | - Viktória Koroknai
- MTA-DE Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - István Szász
- MTA-DE Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Helga Bárdos
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Róza Ádány
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Margit Balázs
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Public Health Research Group, University of Debrecen, Debrecen, Hungary
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12
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Chen Y, Li Z, Chen X, Zhang S. Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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13
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Rodríguez-García C, Heerman MC, Cook SC, Evans JD, DeGrandi-Hoffman G, Banmeke O, Zhang Y, Huang S, Hamilton M, Chen YP. Transferrin-mediated iron sequestration suggests a novel therapeutic strategy for controlling Nosema disease in the honey bee, Apis mellifera. PLoS Pathog 2021; 17:e1009270. [PMID: 33600478 PMCID: PMC7891791 DOI: 10.1371/journal.ppat.1009270] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 01/02/2023] Open
Abstract
Nosemosis C, a Nosema disease caused by microsporidia parasite Nosema ceranae, is a significant disease burden of the European honey bee Apis mellifera which is one of the most economically important insect pollinators. Nevertheless, there is no effective treatment currently available for Nosema disease and the disease mechanisms underlying the pathological effects of N. ceranae infection in honey bees are poorly understood. Iron is an essential nutrient for growth and survival of hosts and pathogens alike. The iron tug-of-war between host and pathogen is a central battlefield at the host-pathogen interface which determines the outcome of an infection, however, has not been explored in honey bees. To fill the gap, we conducted a study to investigate the impact of N. ceranae infection on iron homeostasis in honey bees. The expression of transferrin, an iron binding and transporting protein that is one of the key players of iron homeostasis, in response to N. ceranae infection was analysed. Furthermore, the functional roles of transferrin in iron homeostasis and honey bee host immunity were characterized using an RNA interference (RNAi)-based method. The results showed that N. ceranae infection causes iron deficiency and upregulation of the A. mellifera transferrin (AmTsf) mRNA in honey bees, implying that higher expression of AmTsf allows N. ceranae to scavenge more iron from the host for its proliferation and survival. The suppressed expression levels of AmTsf via RNAi could lead to reduced N. ceranae transcription activity, alleviated iron loss, enhanced immunity, and improved survival of the infected bees. The intriguing multifunctionality of transferrin illustrated in this study is a significant contribution to the existing body of literature concerning iron homeostasis in insects. The uncovered functional role of transferrin on iron homeostasis, pathogen growth and honey bee's ability to mount immune responses may hold the key for the development of novel strategies to treat or prevent diseases in honey bees.
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Affiliation(s)
| | - Matthew C. Heerman
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
| | - Steven C. Cook
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
| | | | - Olubukola Banmeke
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
| | - Yi Zhang
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
- Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong Province, China
| | - Shaokang Huang
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
- College of Animal Sciences (Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Michele Hamilton
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
| | - Yan Ping Chen
- USDA-ARS Bee Research Laboratory, Beltsville, Maryland, United States of America
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14
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Földes F, Madai M, Papp H, Kemenesi G, Zana B, Geiger L, Gombos K, Somogyi B, Bock-Marquette I, Jakab F. Small Interfering RNAs Are Highly Effective Inhibitors of Crimean-Congo Hemorrhagic Fever Virus Replication In Vitro. Molecules 2020; 25:molecules25235771. [PMID: 33297527 PMCID: PMC7731286 DOI: 10.3390/molecules25235771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 11/24/2022] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is one of the prioritized diseases of the World Health Organization, considering its potential to create a public health emergency and, more importantly, the absence of efficacious drugs and/or vaccines for treatment. The highly pathogenic characteristic of CCHFV restricts research to BSL-4 laboratories, which complicates effective research and developmental strategies. In consideration of antiviral therapies, RNA interference can be used to suppress viral replication by targeting viral genes. RNA interference uses small interfering RNAs (siRNAs) to silence genes. The aim of our study was to design and test siRNAs in vitro that inhibit CCHFV replication and can serve as a basis for further antiviral therapies. A549 cells were infected with CCHFV after transfection with the siRNAs. Following 72 h, nucleic acid from the supernatant was extracted for RT Droplet Digital PCR analysis. Among the investigated siRNAs we identified effective candidates against all three segments of the CCHF genome. Consequently, blocking any segment of CCHFV leads to changes in the virus copy number that indicates an antiviral effect of the siRNAs. In summary, we demonstrated the ability of specific siRNAs to inhibit CCHFV replication in vitro. This promising result can be integrated into future anti-CCHFV therapy developments.
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Affiliation(s)
- Fanni Földes
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Mónika Madai
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Henrietta Papp
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Brigitta Zana
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Lili Geiger
- Department of Laboratory Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary; (L.G.); (K.G.)
| | - Katalin Gombos
- Department of Laboratory Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary; (L.G.); (K.G.)
| | - Balázs Somogyi
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
| | - Ildikó Bock-Marquette
- Regenerative Science, Sport and Medicina Research Group, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary;
| | - Ferenc Jakab
- National Laboratory of Virology, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (F.F.); (M.M.); (H.P.); (G.K.); (B.Z.); (B.S.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-501-668 (ext. 29044)
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15
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Cui J, Song Y, Han X, Hu J, Chen Y, Chen X, Xu X, Xing Y, Lu H, Cai L. Targeting 14-3-3ζ Overcomes Resistance to Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in Lung Adenocarcinoma via BMP2/Smad/ID1 Signaling. Front Oncol 2020; 10:542007. [PMID: 33123465 PMCID: PMC7571474 DOI: 10.3389/fonc.2020.542007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/20/2020] [Indexed: 01/06/2023] Open
Abstract
Background: The 14-3-3ζ protein, which acts as a putative oncoprotein, has been found to promote the proliferation, metastasis, and chemoresistance of cancer cells in several cancers including lung adenocarcinoma (LUAD); however, its significance in epidermal growth factor receptor–tyrosine kinase inhibitor (EGFR-TKI) resistance remains unknown. Methods: The Cancer Genome Atlas (TCGA) database was used to determine 14-3-3ζ expression in pancancer and LUAD. 14-3-3ζ and ID1 expression was then examined in clinical LUAD samples by immunohistochemistry (IHC). Lentiviral transfection with 14-3-3ζ-specific small hairpin RNA (shRNA) was used to establish stable 14-3-3ζ knockdown gefitinib-resistant PC9 (PC9/GR) and H1975 cell lines. The effect of 14-3-3ζ knockdown on reversing EGFR-TKI resistance was determined in vitro by Cell Counting Kit-8 (CCK-8), wound healing, Transwell assays, and flow cytometry. A xenograft tumor model was established to evaluate the role of 14-3-3ζ in EGFR-TKI resistance. Microarray analysis results showed multiple pathways regulated by 14-3-3ζ-shRNA. Results: In the present study, we demonstrated that based on the TCGA, pancancer and LUAD 14-3-3ζ expression was elevated and predicted unfavorable prognosis. In addition, high 14-3-3ζ expression was associated with advanced T stage, TNM stage, presence of lymph node metastasis and, importantly, poor treatment response to EGFR-TKIs in LUAD patients with EGFR-activating mutations. 14-3-3ζ shRNA sensitized EGFR-TKI-resistant human LUAD cells to gefitinib and reversed epithelial-to-mesenchymal transition (EMT). After 14-3-3ζ depletion, bone morphogenetic protein (BMP) signaling activation was decreased in EGFR-TKI-resistant cells in microarray analysis, which was further validated by Western blot analysis. Furthermore, the expression of 14-3-3ζ positively correlates with ID1 expression in human EGFR-mutant LUAD patient samples. In vivo, there was a reduction in the tumor burden in mice treated with 14-3-3ζ shRNA and gefitinib compared to mice treated with gefitinib alone. Conclusion: Our work uncovers a hitherto unappreciated role of 14-3-3ζ in EGFR-TKI resistance. This study might provide a potential therapeutic approach for treating LUAD patients harboring EGFR mutations.
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Affiliation(s)
- Jinfang Cui
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yang Song
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuejiao Han
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jing Hu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanbo Chen
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xuesong Chen
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaomin Xu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ying Xing
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hailing Lu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
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16
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Li D, Mastaglia FL, Fletcher S, Wilton SD. Progress in the molecular pathogenesis and nucleic acid therapeutics for Parkinson's disease in the precision medicine era. Med Res Rev 2020; 40:2650-2681. [PMID: 32767426 PMCID: PMC7589267 DOI: 10.1002/med.21718] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/16/2022]
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders that manifest various motor and nonmotor symptoms. Although currently available therapies can alleviate some of the symptoms, the disease continues to progress, leading eventually to severe motor and cognitive decline and reduced life expectancy. The past two decades have witnessed rapid progress in our understanding of the molecular and genetic pathogenesis of the disease, paving the way for the development of new therapeutic approaches to arrest or delay the neurodegenerative process. As a result of these advances, biomarker‐driven subtyping is making it possible to stratify PD patients into more homogeneous subgroups that may better respond to potential genetic‐molecular pathway targeted disease‐modifying therapies. Therapeutic nucleic acid oligomers can bind to target gene sequences with very high specificity in a base‐pairing manner and precisely modulate downstream molecular events. Recently, nucleic acid therapeutics have proven effective in the treatment of a number of severe neurological and neuromuscular disorders, drawing increasing attention to the possibility of developing novel molecular therapies for PD. In this review, we update the molecular pathogenesis of PD and discuss progress in the use of antisense oligonucleotides, small interfering RNAs, short hairpin RNAs, aptamers, and microRNA‐based therapeutics to target critical elements in the pathogenesis of PD that could have the potential to modify disease progression. In addition, recent advances in the delivery of nucleic acid compounds across the blood–brain barrier and challenges facing PD clinical trials are also reviewed.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Frank L Mastaglia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
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17
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Mousavi SM, Afgar A, Mohammadi MA, Mortezaei S, Faridi A, Sadeghi B, Fasihi Harandi M. Biological and morphological consequences of dsRNA-induced suppression of tetraspanin mRNA in developmental stages of Echinococcus granulosus. Parasit Vectors 2020; 13:190. [PMID: 32276648 PMCID: PMC7146954 DOI: 10.1186/s13071-020-04052-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/28/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cystic echinococcosis, caused by the cestode Echinococcus granulosus, is a neglected tropical disease with remarkable morbidity in humans and a problem of worldwide economic importance in livestock industry. Understanding the molecular basis of the parasite growth and development is essential for the disease diagnosis, management and control. The tetraspanin (TSP) family of proteins are transmembrane proteins with a role in many physiological processes of eukaryotic organisms. TSPs present in the tegumental surface of platyhelminths play pivotal roles in host-parasite interaction. However, little is known about the role of TSPs in growth and development in the Platyhelminthes. To understand the role of TSP1 in the growth and development of E. granulosus we investigated the effect of EgTSP1-specific long dsRNA in different in vitro stages of the parasite. METHODS Different stages of E. granulosus, protoscoleces and strobilated worms, were cultivated In vitro in di-phasic media. Using long dsRNA and two delivery methods, i.e. electroporation and electro-soaking, EgTSP1 silencing was performed with an EgTSP1-specific dsRNA. The TSP1 expression profile was assessed as well as the biological and ultrastructural properties of the parasites. RESULTS After three days of dsRNA treatment, EgTSP1 expression was significantly reduced in both stages of E. granulosus as compared to irrelevant/unrelated dsRNA and untreated controls. Silencing expression of EgTSP1 in different stages of E. granulosus resulted in reduced viability and body contractions, inhibition of protoscoleces evagination and distinctive tegumental changes. Ultrastructural morphology of the strobilated worms treated with EgTSP1-specific dsRNA was indicative of the microtriches impairments and vacuolated tegument compared to the control helminths. CONCLUSIONS Results of the present study suggest that EgTSP1 plays important structural roles in tegument configuration in E. granulosus. EgTSP1 is proved to be a potential target for the development of vaccines and RNAi-based drugs.
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Affiliation(s)
- Seyed Mohammad Mousavi
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran.
| | - Mohammad Ali Mohammadi
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran
| | - Seifollah Mortezaei
- Department of Parasitology, School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Ashkan Faridi
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran
| | - Balal Sadeghi
- Department of Food Hygiene and Public Health, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran.
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18
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Le T, Winham CL, Andromidas F, Silver AC, Jellison ER, Levesque AA, Koob AO. Chimera RNA interference knockdown of γ-synuclein in human cortical astrocytes results in mitotic catastrophe. Neural Regen Res 2020; 15:1894-1902. [PMID: 32246638 PMCID: PMC7513975 DOI: 10.4103/1673-5374.280329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Elevated levels of γ-synuclein (γ-syn) expression have been noted in the progression of glioblastomas, and also in the cerebrospinal fluid of patients diagnosed with neurodegenerative diseases. γ-Syn can be either internalized from the extracellular milieu or expressed endogenously by human cortical astrocytes. Internalized γ-syn results in increased cellular proliferation, brain derived neurotrophic factor release and astroprotection. However, the function of endogenous γ-syn in primary astrocytes, and the relationship to these two opposing disease states are unknown. γ-Syn is expressed by astrocytes in the human cortex, and to gain a better understanding of the role of endogenous γ-syn, primary human cortical astrocytes were treated with chimera RNA interference (RNAi) targeting γ-syn after release from cell synchronization. Quantitative polymerase chain reaction analysis demonstrated an increase in endogenous γ-syn expression 48 hours after release from cell synchronization, while RNAi reduced γ-syn expression to control levels. Immunocytochemistry of Ki67 and 5-bromodeoxyuridine showed chimera RNAi γ-syn knockdown reduced cellular proliferation at 24 and 48 hours after release from cell synchronization. To further investigate the consequence of γ-syn knockdown on the astrocytic cell cycle, phosphorylated histone H3 pSer10 (pHH3) and phosphorylated cyclin dependent kinase-2 pTyr15 (pCDK2) levels were observed via western blot analysis. The results revealed an elevated expression of pHH3, but not pCDK2, indicating γ-syn knockdown leads to disruption of the cell cycle and chromosomal compaction after 48 hours. Subsequently, flow cytometry with propidium iodide determined that increases in apoptosis coincided with γ-syn knockdown. Therefore, γ-syn exerts its effect to allow normal astrocytic progression through the cell cycle, as evidenced by decreased proliferation marker expression, increased pHH3, and mitotic catastrophe after knockdown. In this study, we demonstrated that the knockdown of γ-syn within primary human cortical astrocytes using chimera RNAi leads to cell cycle disruption and apoptosis, indicating an essential role for γ-syn in regulating normal cell division in astrocytes. Therefore, disruption to γ-syn function would influence astrocytic proliferation, and could be an important contributor to neurological diseases.
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Affiliation(s)
- Timmy Le
- Graduate Program in Neuroscience, Biology Department, University of Hartford, West Hartford, CT, USA
| | - Cynthia L Winham
- Graduate Program in Neuroscience, Biology Department, University of Hartford, West Hartford, CT, USA
| | - Fotis Andromidas
- Graduate Program in Neuroscience, Biology Department, University of Hartford, West Hartford, CT, USA
| | - Adam C Silver
- Graduate Program in Neuroscience, Biology Department, University of Hartford, West Hartford, CT, USA
| | - Evan R Jellison
- Department of Immunology, UCONN Health Center, Farmington, CT, USA
| | - Aime A Levesque
- Graduate Program in Neuroscience, Biology Department, University of Hartford, West Hartford, CT, USA
| | - Andrew O Koob
- Graduate Program in Neuroscience, Biology Department, University of Hartford, West Hartford, CT, USA
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Lloret-Llinares M, Jensen TH. Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing. Methods Mol Biol 2020; 2062:127-145. [PMID: 31768975 DOI: 10.1007/978-1-4939-9822-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The RNA exosome is involved in RNA processing and quality control. In humans, it consists of an enzymatically inactive nine-subunit core, with ribonucleolytic activity contributed by one or two additional components. Moreover, several protein cofactors interact with the exosome to enable and specify its recruitment to a wide range of substrates. A common strategy to identify these substrates has been to deplete an exosome subunit or a cofactor and subsequently interrogate which transcripts become stabilized. Here, we describe an experimental pipeline including siRNA-mediated depletion of the RNA exosome or its cofactors in HeLa cells, confirmation of the knockdown efficiencies, and the manual or high-throughput identification of exosome targets.
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Affiliation(s)
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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20
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Hueso M, Casas A, Mallén A, de Ramón L, Bolaños N, Varela C, Cruzado JM, Torras J, Navarro E. The double edge of anti-CD40 siRNA therapy: It increases renal microcapillar density but favours the generation of an inflammatory milieu in the kidneys of ApoE -/- mice. JOURNAL OF INFLAMMATION-LONDON 2019; 16:25. [PMID: 31889910 PMCID: PMC6916081 DOI: 10.1186/s12950-019-0228-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
Background Chronic kidney disease (CKD) is associated with endothelial dysfunctions thus prompting links between microcirculation (MC), inflammation and major cardiovascular risk factors. Purpose of the study We have previously reported that siRNA-silencing of CD40 (siCD40) reduced atherosclerosis (ATH) progression. Here, we have deepened on the effects of the siCD40 treatment by evaluating retrospectively, in stored kidneys from the siCD40 treated ApoE−/− mice, the renal microcirculation (measured as the density of peritubular capillaries), macrophage infiltration and NF-κB activation. Methods Kidneys were isolated after 16 weeks of treatment with the anti-CD40 siRNA (siCD40), with a scrambled control siRNA (siSC) or with PBS (Veh. group). Renal endothelium, infiltrating macrophages and activated NF-κB in endothelium were identified by immunohistochemistry, while the density of stained peritubular capillaries was quantified by image analysis. Results ATH was associated with a reduction in renal MC, an effect reversed by the anti-CD40 siRNA treatment (3.8 ± 2.7% in siCD40; vs. 1.8 ± 0.1% in siSC; or 1.9 ± 1.6% in Veh.; p < 0.0001). Furthermore, siCD40 treatment reduced the number of infiltrating macrophages compared to the SC group (14.1 ± 5.9 cells/field in siCD40; vs. 37.1 ± 17.8 cells/field in siSC; and 1.3 ± 1.7 cells/field in Veh.; p = 0.001). NF-κB activation also peaked in the siSC group, showing lower levels in the siCD40 and Veh. groups (63 ± 60 positive cells/section in siCD40; vs. 152 ± 44 positive cells/section in siSC; or 26 ± 29 positive cells/section in veh.; p = 0.014). Lastly, serum creatinine was also increased in the siCD40 (3.4 ± 3.3 mg/dL) and siSC (4.6 ± 3.0 mg/dL) groups when compared with Veh. (1.1 ± 0.9 mg/dL, p = 0.1). Conclusions Anti-CD40 siRNA therapy significantly increased the density of peritubular capillaries and decreased renal inflammation in the ATH model. These data provide a physiological basis for the development of renal diseases in patients with ATH. Furthermore, our results also highligth renal off-target effects of the siRNA treatment which are discussed. Graphical abstract ![]()
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Affiliation(s)
- Miguel Hueso
- 1Department of Nephrology, Hospital Universitari Bellvitge, and Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Angela Casas
- 1Department of Nephrology, Hospital Universitari Bellvitge, and Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Adrian Mallén
- 2Laboratori de Nefrología Experimental, Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura de Ramón
- 2Laboratori de Nefrología Experimental, Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, Spain
| | - Nuria Bolaños
- 2Laboratori de Nefrología Experimental, Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristian Varela
- 2Laboratori de Nefrología Experimental, Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep M Cruzado
- 1Department of Nephrology, Hospital Universitari Bellvitge, and Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Joan Torras
- 1Department of Nephrology, Hospital Universitari Bellvitge, and Bellvitge Research Institute (IDIBELL). L'Hospitalet de Llobregat, 08907 Barcelona, Spain
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21
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Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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22
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Vu AL, Leesutthiphonchai W, Ah-Fong AMV, Judelson HS. Defining Transgene Insertion Sites and Off-Target Effects of Homology-Based Gene Silencing Informs the Application of Functional Genomics Tools in Phytophthora infestans. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:915-927. [PMID: 30811313 DOI: 10.1094/mpmi-09-18-0265-ta] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA transformation and homology-based transcriptional silencing are frequently used to assess gene function in Phytophthora spp. Since unplanned side-effects of these tools are not well-characterized, we used P. infestans to study plasmid integration sites and whether knockdowns caused by homology-dependent silencing spread to other genes. Insertions occurred both in gene-dense and gene-sparse regions but disproportionately near the 5' ends of genes, which disrupted native coding sequences. Microhomology at the recombination site between plasmid and chromosome was common. Studies of transformants silenced for 12 different gene targets indicated that neighbors within 500 nt were often cosilenced, regardless of whether hairpin or sense constructs were employed and the direction of transcription of the target. However, this cis spreading of silencing did not occur in all transformants obtained with the same plasmid. Genome-wide studies indicated that unlinked genes with partial complementarity with the silencing-inducing transgene were not usually down-regulated. We learned that hairpin or sense transgenes were not cosilenced with the target in all transformants, which informs how screens for silencing should be performed. We conclude that transformation and gene silencing can be reliable tools for functional genomics in Phytophthora spp. but must be used carefully, especially by testing for the spread of silencing to genes flanking the target.
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Affiliation(s)
- Andrea L Vu
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | | | - Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
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23
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Ervin EH, Pook M, Teino I, Kasuk V, Trei A, Pooga M, Maimets T. Targeted gene silencing in human embryonic stem cells using cell-penetrating peptide PepFect 14. Stem Cell Res Ther 2019; 10:43. [PMID: 30678718 PMCID: PMC6345057 DOI: 10.1186/s13287-019-1144-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/29/2018] [Accepted: 01/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background Human embryonic stem (hES) cells serve as an invaluable tool for research and future medicine, but their transfection often leads to unwanted side effects as the method itself may induce differentiation. On the other hand, RNA interference (RNAi)-based targeted gene silencing is a quick, cost-effective, and easy-to-perform method to address questions regarding the function of genes, especially when hypomorphic knockdowns are needed. Therefore, effective transfection method with minimal side effects is essential for applying RNAi to hES cells. Here, we report a highly promising approach for targeted gene silencing in hES cells with siRNA complexed with cell-penetrating peptide PepFect 14 (PF14). This strategy provides researchers with efficient tool for unraveling the functions of genes or addressing the differentiation of pluripotent stem cells. Methods We present a method for delivery of siRNA into hES cells with cell-penetrating peptide PF14. Accordingly, hES cells were transfected in ROCK inhibitor containing medium for 24 h right after EDTA passaging as small cell clumps. Fluorescently labeled siRNA and siRNAs targeting OCT4 or beta-2-microglobulin (B2M) mRNA sequences were used to evaluate the efficiency of transfection and silencing. Analyses were performed at various time points by flow cytometry, RT-qPCR, and immunofluorescence microscopy. Results Effective downregulation of OCT4 in 70% of treated hES cells at protein level was achieved, along with 90% reduction at mRNA level in bulk population of cells. The applicability of this low-cost and easy-to-perform method was confirmed by inducing silencing of another target not associated with hES cell pluripotency (B2M). Furthermore, we discovered that downregulation of OCT4 induces neuroectodermal differentiation accompanied by reduced expression of B2M during early stage of this lineage. Conclusions The results demonstrate PF14 as a promising tool for studying gene function and regulatory networks in hES cells by using RNAi. Electronic supplementary material The online version of this article (10.1186/s13287-019-1144-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Egle-Helene Ervin
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Martin Pook
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Indrek Teino
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Valmar Kasuk
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Annika Trei
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Margus Pooga
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.,Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Toivo Maimets
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
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24
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Angart PA, Adu-Berchie K, Carlson RJ, Vocelle DB, Chan C, Walton SP. Relative Quantification of siRNA Strand Loading into Ago2 for Design of Highly Active siRNAs. Methods Mol Biol 2019; 1974:41-56. [PMID: 31098994 DOI: 10.1007/978-1-4939-9220-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In RNA interference (RNAi), silencing is achieved through the interaction of double-stranded small interfering RNAs (siRNAs) with essential RNAi pathway proteins, including Argonaute 2 (Ago2). Based on these interactions, one strand of the siRNA is loaded into Ago2 forming the active RNA-induced silencing complex (RISC). Optimal siRNAs maximize RISC activity against the intended target and minimize off-target silencing. To achieve the desired activity and specificity, selection of the appropriate siRNA strand for loading into Ago2 is essential. Here, we provide a protocol to quantify the relative loading of individual siRNA strands into Ago2, one factor in determining the capacity of a siRNA to achieve silencing activity and target specificity.
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Affiliation(s)
- Phillip A Angart
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Office of Biotechnology Products, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Rebecca J Carlson
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - Daniel B Vocelle
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
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25
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Wang J, Thomas M, Lin P, Cheng JX, Matei DE, Wei A. siRNA Delivery Using Dithiocarbamate-Anchored Oligonucleotides on Gold Nanorods. Bioconjug Chem 2018; 30:443-453. [PMID: 30395447 DOI: 10.1021/acs.bioconjchem.8b00723] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We present a robust method for loading small interfering RNA (siRNA) duplexes onto the surfaces of gold nanorods (GNRs) at high density, using near-infrared laser irradiation to trigger their intracellular release with subsequent knockdown activity. Citrate-stabilized GNRs were first coated with oleylsulfobetaine, a zwitterionic amphiphile with low cytotoxicity, which produced stable dispersions at high ionic strength. Amine-modified siRNA duplexes were converted into dithiocarbamate (DTC) ligands and adsorbed onto GNR surfaces in a single incubation step at 0.5 M NaCl, simplifying the charge screening process. The DTC anchors were effective at minimizing premature siRNA desorption and release, a common but often overlooked problem in the use of gold nanoparticles as oligonucleotide carriers. The activity of GNR-siRNA complexes was evaluated systematically against an eGFP-producing ovarian cancer cell line (SKOV-3) using folate receptor-mediated uptake. Efficient knockdown was achieved by using a femtosecond-pulsed laser source to release DTC-anchored siRNA, with essentially no contributions from spontaneous (dark) RNA desorption. GNRs coated with thiol-anchored siRNA duplexes were less effective and also permitted low levels of knockdown activity without photothermal activation. Optimized siRNA delivery conditions were applied toward the targeted knockdown of transglutaminase 2, whose expression is associated with the progression of recurrent ovarian cancer, with a reduction in activity of >80% achieved after a single pulsed laser treatment.
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Affiliation(s)
- Jianxin Wang
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Mini Thomas
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States
| | - Peng Lin
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States.,Department of Biomedical Engineering , Purdue University , 206 South Martin Jischke Drive , West Lafayette , Indiana 47907 , United States
| | - Ji-Xin Cheng
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States.,Department of Biomedical Engineering , Purdue University , 206 South Martin Jischke Drive , West Lafayette , Indiana 47907 , United States
| | - Daniela E Matei
- Department of Obstetrics and Gynecology , Northwestern University Feinberg School of Medicine , 250 East Superior Street , Chicago , Illinois 60611 , United States.,Robert H. Lurie Comprehensive Cancer Center , Chicago , Illinois 60611 , United States
| | - Alexander Wei
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States.,Department of Materials Science and Engineering , Purdue University , 701 West Stadium Avenue , West Lafayette , Indiana 47907 , United States
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26
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Guidi LG, Velayos‐Baeza A, Martinez‐Garay I, Monaco AP, Paracchini S, Bishop DVM, Molnár Z. The neuronal migration hypothesis of dyslexia: A critical evaluation 30 years on. Eur J Neurosci 2018; 48:3212-3233. [PMID: 30218584 PMCID: PMC6282621 DOI: 10.1111/ejn.14149] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022]
Abstract
The capacity for language is one of the key features underlying the complexity of human cognition and its evolution. However, little is known about the neurobiological mechanisms that mediate normal or impaired linguistic ability. For developmental dyslexia, early postmortem studies conducted in the 1980s linked the disorder to subtle defects in the migration of neurons in the developing neocortex. These early studies were reinforced by human genetic analyses that identified dyslexia susceptibility genes and subsequent evidence of their involvement in neuronal migration. In this review, we examine recent experimental evidence that does not support the link between dyslexia and neuronal migration. We critically evaluate gene function studies conducted in rodent models and draw attention to the lack of robust evidence from histopathological and imaging studies in humans. Our review suggests that the neuronal migration hypothesis of dyslexia should be reconsidered, and the neurobiological basis of dyslexia should be approached with a fresh start.
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Affiliation(s)
- Luiz G. Guidi
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Antonio Velayos‐Baeza
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Isabel Martinez‐Garay
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
- Division of NeuroscienceSchool of BiosciencesCardiff UniversityCardiffUK
| | | | | | | | - Zoltán Molnár
- Department of Physiology, Anatomy, and GeneticsUniversity of OxfordOxfordUK
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27
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CARM1 (PRMT4) Acts as a Transcriptional Coactivator during Retinoic Acid-Induced Embryonic Stem Cell Differentiation. J Mol Biol 2018; 430:4168-4182. [PMID: 30153436 PMCID: PMC6186513 DOI: 10.1016/j.jmb.2018.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/25/2018] [Accepted: 08/12/2018] [Indexed: 02/07/2023]
Abstract
Activation of the retinoic acid (RA) signaling pathway is important for controlling embryonic stem cell differentiation and development. Modulation of this pathway occurs through the recruitment of different epigenetic regulators at the retinoic acid receptors (RARs) located at RA-responsive elements and/or RA-responsive regions of RA-regulated genes. Coactivator-associated arginine methyltransferase 1 (CARM1, PRMT4) is a protein arginine methyltransferase that also functions as a transcriptional coactivator. Previous studies highlight CARM1's importance in the differentiation of different cell types. We address CARM1 function during RA-induced differentiation of murine embryonic stem cells (mESCs) using shRNA lentiviral transduction and CRISPR/Cas9 technology to deplete CARM1 in mESCs. We identify CARM1 as a novel transcriptional coactivator required for the RA-associated decrease in Rex1 (Zfp42) and for the RA induction of a subset of RA-regulated genes, including CRABP2 and NR2F1 (Coup-TF1). Furthermore, CARM1 is required for mESCs to differentiate into extraembryonic endoderm in response to RA. We next characterize the epigenetic mechanisms that contribute to RA-induced transcriptional activation of CRABP2 and NR2F1 in mESCs and show for the first time that CARM1 is required for this activation. Collectively, our data demonstrate that CARM1 is required for transcriptional activation of a subset of RA target genes, and we uncover changes in the recruitment of Suz12 and the epigenetic H3K27me3 and H3K27ac marks at gene regulatory regions for CRABP2 and NR2F1 during RA-induced differentiation.
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van Gastel J, Boddaert J, Jushaj A, Premont RT, Luttrell LM, Janssens J, Martin B, Maudsley S. GIT2-A keystone in ageing and age-related disease. Ageing Res Rev 2018; 43:46-63. [PMID: 29452267 DOI: 10.1016/j.arr.2018.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/15/2022]
Abstract
Since its discovery, G protein-coupled receptor kinase-interacting protein 2, GIT2, and its family member, GIT1, have received considerable interest concerning their potential key roles in regulating multiple inter-connected physiological and pathophysiological processes. GIT2 was first identified as a multifunctional protein that is recruited to G protein-coupled receptors (GPCRs) during the process of receptor internalization. Recent findings have demonstrated that perhaps one of the most important effects of GIT2 in physiology concerns its role in controlling multiple aspects of the complex ageing process. Ageing can be considered the most prevalent pathophysiological condition in humans, affecting all tissue systems and acting as a driving force for many common and intractable disorders. The ageing process involves a complex interplay among various deleterious activities that profoundly disrupt the body's ability to cope with damage, thus increasing susceptibility to pathophysiologies such as neurodegeneration, central obesity, osteoporosis, type 2 diabetes mellitus and atherosclerosis. The biological systems that control ageing appear to function as a series of interconnected complex networks. The inter-communication among multiple lower-complexity signaling systems within the global ageing networks is likely coordinated internally by keystones or hubs, which regulate responses to dynamic molecular events through protein-protein interactions with multiple distinct partners. Multiple lines of research have suggested that GIT2 may act as one of these network coordinators in the ageing process. Identifying and targeting keystones, such as GIT2, is thus an important approach in our understanding of, and eventual ability to, medically ameliorate or interdict age-related progressive cellular and tissue damage.
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29
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Allan KJ, Mahoney DJ, Baird SD, Lefebvre CA, Stojdl DF. Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy. J Vis Exp 2018. [PMID: 29683442 DOI: 10.3791/56913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High-throughput genome-wide RNAi (RNA interference) screening technology has been widely used for discovering host factors that impact virus replication. Here we present the application of this technology to uncovering host targets that specifically modulate the replication of Maraba virus, an oncolytic rhabdovirus, and vaccinia virus with the goal of enhancing therapy. While the protocol has been tested for use with oncolytic Maraba virus and oncolytic vaccinia virus, this approach is applicable to other oncolytic viruses and can also be utilized for identifying host targets that modulate virus replication in mammalian cells in general. This protocol describes the development and validation of an assay for high-throughput RNAi screening in mammalian cells, the key considerations and preparation steps important for conducting a primary high-throughput RNAi screen, and a step-by-step guide for conducting a primary high-throughput RNAi screen; in addition, it broadly outlines the methods for conducting secondary screen validation and tertiary validation studies. The benefit of high-throughput RNAi screening is that it allows one to catalogue, in an extensive and unbiased fashion, host factors that modulate any aspect of virus replication for which one can develop an in vitro assay such as infectivity, burst size, and cytotoxicity. It has the power to uncover biotherapeutic targets unforeseen based on current knowledge.
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Affiliation(s)
- Kristina J Allan
- Children's Hospital of Eastern Ontario (CHEO) Research Institute; Department of Biology, Microbiology and Immunology, University of Ottawa
| | - Douglas J Mahoney
- Children's Hospital of Eastern Ontario (CHEO) Research Institute; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary
| | - Stephen D Baird
- Children's Hospital of Eastern Ontario (CHEO) Research Institute
| | | | - David F Stojdl
- Children's Hospital of Eastern Ontario (CHEO) Research Institute; Department of Biology, Microbiology and Immunology, University of Ottawa; Department of Pediatrics, University of Ottawa;
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Combined shRNA over CRISPR/cas9 as a methodology to detect off-target effects and a potential compensatory mechanism. Sci Rep 2018; 8:93. [PMID: 29311693 PMCID: PMC5758708 DOI: 10.1038/s41598-017-18551-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/13/2017] [Indexed: 11/25/2022] Open
Abstract
Inhibition of genes is a powerful approach to study their function. While RNA interference is a widely used method to achieve this goal, mounting evidence indicates that such an approach is prone to off-target effects. An alternative approach to gene function inhibition is genetic mutation, such as the CRISPR/cas9 method. A recent report, however, demonstrated that genetic mutation and inhibition of gene expression do not always give corresponding results. This can be explained by off-target effects, but it was recently shown, at least in one case, that these differences are the result of a compensatory mechanism induced only by genetic mutation. We present here a combination of RNA inhibition and CRISPR/cas9 methods to identify possible off targets as well as potential compensatory effects. This approach is demonstrated by testing a possible role for Sema4B in glioma biology, in which our results implicate Sema4B as having a critical function. In stark contrast, by using shRNA over CRISPR/cas9 combined methodology, we clearly demonstrate that the Sema4B targeted shRNA effects on cell proliferation is the result of off-target effects. Nevertheless, it also revealed that certain splice variants of Sema4B are important for the ability of glioma cells to grow as individual clones.
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31
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Höti N, Yang S, Aiyetan P, Kumar B, Hu Y, Clark D, Eroglu AU, Shah P, Johnson T, Chowdery WH, Zhang H, Rodriguez R. Overexpression of Exportin-5 Overrides the Inhibitory Effect of miRNAs Regulation Control and Stabilize Proteins via Posttranslation Modifications in Prostate Cancer. Neoplasia 2017; 19:817-829. [PMID: 28881308 PMCID: PMC5587889 DOI: 10.1016/j.neo.2017.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 01/21/2023] Open
Abstract
Although XPO5 has been characterized to have tumor-suppressor features in the miRNA biogenesis pathway, the impact of altered expression of XPO5 in cancers is unexplored. Here we report a novel "oncogenic" role of XPO5 in advanced prostate cancer. Using prostate cancer models, we found that excess levels of XPO5 override the inhibitory effect of the canoncial miRNA-mRNA regulation, resulting in a global increase in proteins expression. Importantly, we found that decreased expression of XPO5 could promote an increase in proteasome degradation, whereas overexpression of XPO5 leads to altered protein posttranslational modification via hyperglycosylation, resulting in cellular protein stability. We evaluated the therapeutic advantage of targeting XPO5 in prostate cancer and found that knocking down XPO5 in prostate cancer cells suppressed cellular proliferation and tumor development without significantly impacting normal fibroblast cells survival. To our knowledge, this is the first report describing the oncogenic role of XPO5 in overriding the miRNAs regulation control. Furthermore, we believe that these findings will provide an explanation as to why, in some cancers that express higher abundance of mature miRNAs, fail to suppress their potential protein targets.
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Affiliation(s)
- Naseruddin Höti
- Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD; Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD.
| | - Shuang Yang
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Paul Aiyetan
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Binod Kumar
- Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Yingwei Hu
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - David Clark
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Arife Unal Eroglu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Punit Shah
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Tamara Johnson
- Brady Urological Institute, Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Wasim H Chowdery
- Department of Urology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Hui Zhang
- Department of Pathology, Division of Clinical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD
| | - Ronald Rodriguez
- Department of Urology, The University of Texas Health Science Center at San Antonio, San Antonio, TX
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Seiler J, Breinig M, Caudron-Herger M, Polycarpou-Schwarz M, Boutros M, Diederichs S. The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its extremely low abundance. Nucleic Acids Res 2017; 45:5458-5469. [PMID: 28160600 PMCID: PMC5435915 DOI: 10.1093/nar/gkx076] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 01/22/2023] Open
Abstract
Little is known about the function of most non-coding RNAs (ncRNAs). The majority of long ncRNAs (lncRNAs) is expressed at very low levels and it is a matter of intense debate whether these can be of functional relevance. Here, we identified lncRNAs regulating the viability of lung cancer cells in a high-throughput RNA interference screen. Based on our previous expression profiling, we designed an siRNA library targeting 638 lncRNAs upregulated in human cancer. In a functional siRNA screen analyzing the viability of lung cancer cells, the most prominent hit was a novel lncRNA which we called Viability Enhancing LUng Cancer Transcript (VELUCT). In silico analyses confirmed the non-coding properties of the transcript. Surprisingly, VELUCT was below the detection limit in total RNA from NCI-H460 cells by RT-qPCR as well as RNA-Seq, but was robustly detected in the chromatin-associated RNA fraction. It is an extremely low abundant lncRNA with an RNA copy number of less than one copy per cell. Blocking transcription with actinomycin D revealed that VELUCT RNA was highly unstable which may partially explain its low steady-state concentration. Despite its extremely low abundance, loss-of-function of VELUCT with three independent experimental approaches in three different lung cancer cell lines led to a significant reduction of cell viability: Next to four individual siRNAs, also two complex siPOOLs as well as two antisense oligonucleotides confirmed the strong and specific phenotype. In summary, the extremely low abundant lncRNA VELUCT is essential for regulation of cell viability in several lung cancer cell lines. Hence, VELUCT is the first example for a lncRNA that is expressed at a very low level, but has a strong loss-of-function phenotype. Thus, our study proves that at least individual low-abundant lncRNAs can play an important functional role.
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Affiliation(s)
- Jana Seiler
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marco Breinig
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maïwen Caudron-Herger
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center – University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
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Adeola OA. Treatment of Influenza: Prospects of Post-Transcriptional Gene Silencing Through Synthetic siRNAs. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2017; 2:1-2. [DOI: 10.14218/erhm.2016.00013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Braga ACS, Carneiro BM, Batista MN, Akinaga MM, Rahal P. Inhibition of hepatitis C virus using siRNA targeted to the virus and Hsp90. Cell Stress Chaperones 2017; 22:113-122. [PMID: 27858224 PMCID: PMC5225065 DOI: 10.1007/s12192-016-0747-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/24/2016] [Accepted: 11/08/2016] [Indexed: 01/19/2023] Open
Abstract
Hepatitis C (HCV) is a viral disease affecting millions of people worldwide, and persistent HCV infection can lead to progressive liver disease with the development of liver cirrhosis and hepatocellular carcinoma. During treatment for hepatitis C, the occurrence of viral resistance is common. To reduce the occurrence of resistance, new viral treatments should target both viral and cellular factors. Many interactions occur between viral and host proteins during the HCV replication cycle and might be used for the development of new therapies against hepatitis C. Heat shock protein 90 (Hsp90) plays a role in the folding of cellular and viral proteins and also interacts with HCV proteins. In the present study, we knocked down the expression of the Hsp90 gene and inhibited viral replication using siRNA molecules. Reducing the expression of Hsp90 successfully decreased HCV replication. All siRNA molecules specific to the viral genome showed the efficient inhibition of viral replication, particularly siRNA targeted to the 5'UTR region. The combination of siRNAs targeting the viral genome and Hsp90 mRNA also successfully reduced HCV replication and reduced the occurrence of viral resistance. Moreover, these results suggest that an approach based on the combination of cellular and viral siRNAs can be used as an effective alternative for hepatitis C viral suppression.
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Affiliation(s)
- Ana Claudia Silva Braga
- Institute of Biosciences, Letters and Exact Sciences, UNESP, Rua Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP: 15054-000, Brazil
| | - Bruno Moreira Carneiro
- Institute of Biosciences, Letters and Exact Sciences, UNESP, Rua Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP: 15054-000, Brazil
- Institute of Exact and Natural Sciences, Mato Grosso Federal University, Rondonópolis, Brazil
| | - Mariana Nogueira Batista
- Institute of Biosciences, Letters and Exact Sciences, UNESP, Rua Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP: 15054-000, Brazil
| | - Mônica Mayumi Akinaga
- Institute of Biosciences, Letters and Exact Sciences, UNESP, Rua Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP: 15054-000, Brazil
| | - Paula Rahal
- Institute of Biosciences, Letters and Exact Sciences, UNESP, Rua Cristóvão Colombo, 2265, São José do Rio Preto, SP, CEP: 15054-000, Brazil.
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Zhao T, Zhao H, Li G, Zheng S, Liu M, Gu C, Wang Y. Role of the PKCα-c-Src tyrosine kinase pathway in the mediation of p120-catenin degradation in ventilator-induced lung injury. Respirology 2016; 21:1404-1410. [PMID: 27459952 DOI: 10.1111/resp.12858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/08/2016] [Accepted: 04/23/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVE Ventilator-induced lung injury (VILI) is commonly associated with respiratory barrier dysfunction; however, the mechanisms have not been fully elucidated. This study aimed to determine the order and components of the signalling pathway that mediates the degradation of adherin junction of p120-catenin in VILI. METHODS For the in vivo study, C57BL/6 mice were pre-treated with inhibitors for 60 min prior to 4 h of mechanical ventilation. For the in vitro study, mouse lung epithelial 12 (MLE-12) cells were pre-treated with inhibitors for 60 min or small interfering RNA (siRNA) for 48 h prior to cyclic stretch at 20% for 4 h. The protein levels of protein kinase Cα (PKCα), activated c-Src and p120-catenin were determined via western blot analysis. Lung injury was determined via HE staining, immunofluorescence, wet/dry ratio and lung injury scores. RESULTS High tidal volume mechanical ventilation and 20% cyclic stretch resulted in the degradation of p120-catenin. Inhibitors of PKCα blocked c-Src kinase activation and p120-catenin degradation in VILI. Inhibitors of c-Src kinase or PP2 or siRNA blocked p120-catenin degradation but not PKCα activation. CONCLUSION The current findings demonstrates that PKCα and c-Src kinase participate in VILI. PKCα activation phosphorylates c-Src kinase and further decreases p120-catenin in VILI.
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Affiliation(s)
- Tao Zhao
- Department of Anesthesiology, Rizhao People's Hospital, Rizhao, China.,Department of Anesthesiology, Qianfoshan Hospital, Shandong University, Jinan, China
| | - Hongwei Zhao
- Department of Anesthesiology, Rizhao People's Hospital, Rizhao, China
| | - Gang Li
- Department of Anesthesiology, Rizhao People's Hospital, Rizhao, China
| | - Shengfa Zheng
- Department of Anesthesiology, Rizhao People's Hospital, Rizhao, China
| | - Mengjie Liu
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, Jinan, China
| | - Changping Gu
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, Jinan, China
| | - Yuelan Wang
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, Jinan, China.
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Nair BG, Hagiwara K, Ueda M, Yu HH, Tseng HR, Ito Y. High Density of Aligned Nanowire Treated with Polydopamine for Efficient Gene Silencing by siRNA According to Cell Membrane Perturbation. ACS APPLIED MATERIALS & INTERFACES 2016; 8:18693-18700. [PMID: 27420034 DOI: 10.1021/acsami.6b04913] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
High aspect ratio nanomaterials, such as vertically aligned silicon nanowire (SiNW) substrates, are three-dimensional topological features for cell manipulations. A high density of SiNWs significantly affects not only cell adhesion and proliferation but also the delivery of biomolecules to cells. Here, we used polydopamine (PD) that simply formed a thin coating on various material surfaces by the action of dopamine as a bioinspired approach. The PD coating not only enhanced cell adhesion, spreading, and growth but also anchored more siRNA by adsorption and provided more surface concentration for substrate-mediated delivery. By comparing plain and SiNW surfaces with the same amount of loaded siRNA, we quantitatively found that PD coating efficiently anchored siRNA on the surface, which knocked down the expression of a specific gene by RNA interference. It was also found that the interaction of SiNWs with the cell membrane perturbed the lateral diffusion of lipids in the membrane by fluorescence recovery after photobleaching. The perturbation was considered to induce the effective delivery of siRNA into cells and allow the cells to carry out their biological functions. These results suggest promising applications of PD-coated, high-density SiNWs as simple, fast, and versatile platforms for transmembrane delivery of biomolecules.
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Affiliation(s)
- Baiju G Nair
- Nano Medical Engineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
| | - Kyoji Hagiwara
- Emergent Bioengineering Material Research Team, RIKEN Centre for Emergent Matter Science , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
- Laboratory of Human Science and Engineering , 1-3-1 Minaminagasaki, Toshima-ku, Tokyo 1710052, Japan
| | - Motoki Ueda
- Nano Medical Engineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
- Emergent Bioengineering Material Research Team, RIKEN Centre for Emergent Matter Science , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
| | - Hsiao-Hua Yu
- Nano Medical Engineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
- Institute of Chemistry, Academia Sinica , 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, University of California , Los Angeles CNSI, 570 Westwood Plaza, Los Angeles, California 90095, United States
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
- Emergent Bioengineering Material Research Team, RIKEN Centre for Emergent Matter Science , 2-1 Hirosawa, Wako, Saitama 3510198, Japan
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37
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Bégin-Lavallée V, Midavaine É, Dansereau MA, Tétreault P, Longpré JM, Jacobi AM, Rose SD, Behlke MA, Beaudet N, Sarret P. Functional inhibition of chemokine receptor CCR2 by dicer-substrate-siRNA prevents pain development. Mol Pain 2016; 12:12/0/1744806916653969. [PMID: 27306408 PMCID: PMC4956154 DOI: 10.1177/1744806916653969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/16/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Accumulating evidence suggests that the C-C chemokine ligand 2 (CCL2, or monocyte chemoattractant protein 1) acts as a neuromodulator in the central nervous system through its binding to the C-C chemokine receptor 2 (CCR2). Notably, it is well established that the CCL2/CCR2 axis plays a key role in neuron-glia communication as well as in spinal nociceptive transmission. Gene silencing through RNA interference has recently emerged as a promising avenue in research and drug development, including therapeutic management of chronic pain. In the present study, we used 27-mer Dicer-substrate small interfering RNA (DsiRNA) targeting CCR2 and assessed their ability to reverse the nociceptive behaviors induced by spinal CCL2 injection or following intraplantar injection of complete Freund's adjuvant. RESULTS To this end, we first developed high-potency DsiRNAs designed to target different sequences distributed across the rat CCR2 (rCCR2) messenger RNA. For optimization, methyl groups were added to the two most potent DsiRNA candidates (Evader and M7 2'-O-methyl modified duplexes) in order to improve in vivo duplex stability and to reduce potential immunostimulatory activity. Our results demonstrated that all modified candidates formulated with the cell-penetrating peptide reagent Transductin showed strong RNAi activity following intrathecal delivery, exhibiting >50% rCCR2 knockdown in lumbar dorsal root ganglia. Accordingly, we found that these DsiRNA duplexes were able to reduce spinal microglia activation and were effective at blocking CCL2-induced mechanical hypersensitivity. Along with similar reductions of rCCR2 messenger RNA, both sequences and methylation patterns were similarly effective in inhibiting the CCL2 nociceptive action for the whole seven days testing period, compared to mismatch DsiRNA. DsiRNAs against CCR2 also reversed the hypernociceptive responses observed in the complete Freund's adjuvant-induced inflammatory chronic pain model. CONCLUSION Altogether, these results validate CCR2 as a an appropriate molecular target for pain control and demonstrate that RNAi-based gene therapy represent an highly specific alternative to classical pharmacological approaches to treat central pathologies such as chronic pain.
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Affiliation(s)
- Valérie Bégin-Lavallée
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Philippe Sarret, Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, Canada.
| | - Élora Midavaine
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Marc-André Dansereau
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pascal Tétreault
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Michel Longpré
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | - Scott D Rose
- Integrated DNA Technologies Inc, Coralville, IA, USA
| | - Mark A Behlke
- Integrated DNA Technologies Inc, Coralville, IA, USA
| | - Nicolas Beaudet
- Department of Anesthesiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe Sarret
- Department of Pharmacology and Physiology, Institut de Pharmacologie de Sherbrooke, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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Ghadakzadeh S, Mekhail M, Aoude A, Hamdy R, Tabrizian M. Small Players Ruling the Hard Game: siRNA in Bone Regeneration. J Bone Miner Res 2016; 31:475-87. [PMID: 26890411 DOI: 10.1002/jbmr.2816] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/02/2016] [Accepted: 02/16/2016] [Indexed: 12/17/2022]
Abstract
Silencing gene expression through a sequence-specific manner can be achieved by small interfering RNAs (siRNAs). The discovery of this process has opened the doors to the development of siRNA therapeutics. Although several preclinical and clinical studies have shown great promise in the treatment of neurological disorders, cancers, dominant disorders, and viral infections with siRNA, siRNA therapy is still gaining ground in musculoskeletal tissue repair and bone regeneration. Here we present a comprehensive review of the literature to summarize different siRNA delivery strategies utilized to enhance bone regeneration. With advancement in understanding the targetable biological pathways involved in bone regeneration and also the rapid progress in siRNA technologies, application of siRNA for bone regeneration has great therapeutic potential. High rates of musculoskeletal injuries and diseases, and their inevitable consequences, impose a huge financial burden on individuals and healthcare systems worldwide.
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Affiliation(s)
- Saber Ghadakzadeh
- Experimental Surgery, Department of Surgery, Faculty of Medicine, McGill University, Montreal, Canada.,Division of Orthopaedic Surgery, Shriners Hospital for Children, McGill University, Montreal, Canada
| | - Mina Mekhail
- Division of Orthopaedic Surgery, Shriners Hospital for Children, McGill University, Montreal, Canada
| | - Ahmed Aoude
- Division of Orthopaedic Surgery, Shriners Hospital for Children, McGill University, Montreal, Canada
| | - Reggie Hamdy
- Experimental Surgery, Department of Surgery, Faculty of Medicine, McGill University, Montreal, Canada.,Division of Orthopaedic Surgery, Shriners Hospital for Children, McGill University, Montreal, Canada
| | - Maryam Tabrizian
- Department of Biomedical Engineering, McGill University, Montreal, Canada
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Yu-Wai-Man C, Tagalakis AD, Manunta MD, Hart SL, Khaw PT. Receptor-targeted liposome-peptide-siRNA nanoparticles represent an efficient delivery system for MRTF silencing in conjunctival fibrosis. Sci Rep 2016; 6:21881. [PMID: 26905457 PMCID: PMC4764806 DOI: 10.1038/srep21881] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/03/2016] [Indexed: 12/22/2022] Open
Abstract
There is increasing evidence that the Myocardin-related transcription factor/Serum response factor (MRTF/SRF) pathway plays a key role in fibroblast activation and that knocking down MRTF can lead to reduced scarring and fibrosis. Here, we have developed a receptor-targeted liposome-peptide-siRNA nanoparticle as a non-viral delivery system for MRTF-B siRNA in conjunctival fibrosis. Using 50 nM siRNA, the MRTF-B gene was efficiently silenced by 76% and 72% with LYR and LER nanoparticles, respectively. The silencing efficiency was low when non-targeting peptides or siRNA alone or liposome-siRNA alone were used. LYR and LER nanoparticles also showed higher silencing efficiency than PEGylated LYR-P and LER-P nanoparticles. The nanoparticles were not cytotoxic using different liposomes, targeting peptides, and 50 nM siRNA. Three-dimensional fibroblast-populated collagen matrices were also used as a functional assay to measure contraction in vitro, and showed that MRTF-B LYR nanoparticles completely blocked matrix contraction after a single transfection treatment. In conclusion, this is the first study to develop and show that receptor-targeted liposome-peptide-siRNA nanoparticles represent an efficient and safe non-viral siRNA delivery system that could be used to prevent fibrosis after glaucoma filtration surgery and other contractile scarring conditions in the eye.
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Affiliation(s)
- Cynthia Yu-Wai-Man
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Aristides D Tagalakis
- Wolfson Centre for Gene Therapy of Childhood Disease, UCL Institute of Child Health, London, United Kingdom
| | - Maria D Manunta
- Wolfson Centre for Gene Therapy of Childhood Disease, UCL Institute of Child Health, London, United Kingdom
| | - Stephen L Hart
- Wolfson Centre for Gene Therapy of Childhood Disease, UCL Institute of Child Health, London, United Kingdom
| | - Peng T Khaw
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
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40
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Kamola PJ, Nakano Y, Takahashi T, Wilson PA, Ui-Tei K. The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. PLoS Comput Biol 2015; 11:e1004656. [PMID: 26657993 PMCID: PMC4676691 DOI: 10.1371/journal.pcbi.1004656] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA ‘specificity’ design rules. Small interfering RNAs (siRNAs) are double stranded RNA molecules designed to perfectly match the sequence of a target gene and silence its expression. The function is exerted through the RNA interference (RNAi) pathway and has revolutionised biological research due to its ease-of-use and high potency. While siRNAs were initially believed to be highly specific, they have subsequently been observed to interact with other, unintended messenger RNAs. However, the mechanistic details of this process remain poorly understood, and there is a paucity of strategies and guidelines directed toward mitigating this issue. To address this potential safety liability, we performed a comprehensive analysis of sequence characteristics of siRNA duplexes and their target regions. Results from luciferase-reporter assays and global expression data confirmed previous observations that the siRNA seed region is the primary determinant for off-target gene recognition and binding. Furthermore, our analysis revealed the important contribution of siRNA non-seed region, and its corresponding target sequences, to the potency of off-target knockdown. Similar results were observed in an equivalent evaluation of the miRNA-targeting mechanism, suggesting that the correlating features arise through an evolutionary conserved mechanistic factor.
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Affiliation(s)
- Piotr J. Kamola
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Safety Assessment, GlaxoSmithKline R&D, Ware, Hertfordshire, United Kingdom
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Harwell Science and Innovation Campus, United Kingdom
| | - Yuko Nakano
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Tomoko Takahashi
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Paul A. Wilson
- Computational Biology, GlaxoSmithKline R&D, Stevenage, Hertfordshire, United Kingdom
| | - Kumiko Ui-Tei
- Department of Biological Sciences, University of Tokyo, Bunkyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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Bobbin ML, Burnett JC, Rossi JJ. RNA interference approaches for treatment of HIV-1 infection. Genome Med 2015; 7:50. [PMID: 26019725 PMCID: PMC4445287 DOI: 10.1186/s13073-015-0174-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/13/2015] [Indexed: 01/05/2023] Open
Abstract
HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the onset of AIDS, viral mutagenesis often leads to viral escape from multiple drugs. In addition to the pharmacological agents that comprise cART drug cocktails, new biological therapeutics are reaching the clinic. These include gene-based therapies that utilize RNA interference (RNAi) to silence the expression of viral or host mRNA targets that are required for HIV-1 infection and/or replication. RNAi allows sequence-specific design to compensate for viral mutants and natural variants, thereby drastically expanding the number of therapeutic targets beyond the capabilities of cART. Recent advances in clinical and preclinical studies have demonstrated the promise of RNAi therapeutics, reinforcing the concept that RNAi-based agents might offer a safe, effective, and more durable approach for the treatment of HIV/AIDS. Nevertheless, there are challenges that must be overcome in order for RNAi therapeutics to reach their clinical potential. These include the refinement of strategies for delivery and to reduce the risk of mutational escape. In this review, we provide an overview of RNAi-based therapies for HIV-1, examine a variety of combinatorial RNAi strategies, and discuss approaches for ex vivo delivery and in vivo delivery.
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Affiliation(s)
- Maggie L Bobbin
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA
| | - John C Burnett
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
| | - John J Rossi
- Irell & Manella School of Biological Sciences, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 91010 USA ; Department of Molecular and Cell Biology, Beckman Research Institute of City of Hope, East Duarte Road, Duarte, CA 9101 USA
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42
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Modulation of the RNA Interference Activity Using Central Mismatched siRNAs and Acyclic Threoninol Nucleic Acids (aTNA) Units. Molecules 2015; 20:7602-19. [PMID: 25919280 PMCID: PMC6272285 DOI: 10.3390/molecules20057602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 02/06/2023] Open
Abstract
The understanding of the mechanisms behind nucleotide recognition by Argonaute 2, core protein of the RNA-induced silencing complex, is a key aspect in the optimization of small interfering RNAs (siRNAs) activity. To date, great efforts have been focused on the modification of certain regions of siRNA, such as the 3'/5'-termini and the seed region. Only a few reports have described the roles of central positions flanking the cleavage site during the silence process. In this study, we investigate the potential correlations between the thermodynamic and silencing properties of siRNA molecules carrying, at internal positions, an acyclic L-threoninol nucleic acid (aTNA) modification. Depending on position, the silencing is weakened or impaired. Furthermore, we evaluate the contribution of mismatches facing either a natural nucleotide or an aTNA modification to the siRNA potency. The position 11 of the antisense strand is more permissive to mismatches and aTNA modification, in respect to the position 10. Additionally, comparing the ON-/OFF-target silencing of central mismatched siRNAs with 5'-terminal modified siRNA, we concluded: (i) central perturbation of duplex pairing features weights more on potency rather than silencing asymmetry; (ii) complete bias for the ON-target silencing can be achieved with single L-threoninol modification near the 5'-end of the sense strand.
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Ollitrault D, Legendre F, Drougard C, Briand M, Benateau H, Goux D, Chajra H, Poulain L, Hartmann D, Vivien D, Shridhar V, Baldi A, Mallein-Gerin F, Boumediene K, Demoor M, Galera P. BMP-2, hypoxia, and COL1A1/HtrA1 siRNAs favor neo-cartilage hyaline matrix formation in chondrocytes. Tissue Eng Part C Methods 2015; 21:133-47. [PMID: 24957638 PMCID: PMC4313417 DOI: 10.1089/ten.tec.2013.0724] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Osteoarthritis (OA) is an irreversible pathology that causes a decrease in articular cartilage thickness, leading finally to the complete degradation of the affected joint. The low spontaneous repair capacity of cartilage prevents any restoration of the joint surface, making OA a major public health issue. Here, we developed an innovative combination of treatment conditions to improve the human chondrocyte phenotype before autologous chondrocyte implantation. First, we seeded human dedifferentiated chondrocytes into a collagen sponge as a scaffold, cultured them in hypoxia in the presence of a bone morphogenetic protein (BMP), BMP-2, and transfected them with small interfering RNAs targeting two markers overexpressed in OA dedifferentiated chondrocytes, that is, type I collagen and/or HtrA1 serine protease. This strategy significantly decreased mRNA and protein expression of type I collagen and HtrA1, and led to an improvement in the chondrocyte phenotype index of differentiation. The effectiveness of our in vitro culture process was also demonstrated in the nude mouse model in vivo after subcutaneous implantation. We, thus, provide here a new protocol able to favor human hyaline chondrocyte phenotype in primarily dedifferentiated cells, both in vitro and in vivo. Our study also offers an innovative strategy for chondrocyte redifferentiation and opens new opportunities for developing therapeutic targets.
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Affiliation(s)
- David Ollitrault
- 1 Microenvironnement Cellulaire et Pathologies Laboratory (MILPAT) EA 4652, Federative Research Structure (FRS) 146 ICORE, Faculty of Medicine, IBFA, University of Caen/Lower-Normandy (UCLN) , Caen, France
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Abstract
Insults to nuclear DNA induce multiple response pathways to mitigate the deleterious effects of damage and mediate effective DNA repair. G-protein-coupled receptor kinase-interacting protein 2 (GIT2) regulates receptor internalization, focal adhesion dynamics, cell migration, and responses to oxidative stress. Here we demonstrate that GIT2 coordinates the levels of proteins in the DNA damage response (DDR). Cellular sensitivity to irradiation-induced DNA damage was highly associated with GIT2 expression levels. GIT2 is phosphorylated by ATM kinase and forms complexes with multiple DDR-associated factors in response to DNA damage. The targeting of GIT2 to DNA double-strand breaks was rapid and, in part, dependent upon the presence of H2AX, ATM, and MRE11 but was independent of MDC1 and RNF8. GIT2 likely promotes DNA repair through multiple mechanisms, including stabilization of BRCA1 in repair complexes; upregulation of repair proteins, including HMGN1 and RFC1; and regulation of poly(ADP-ribose) polymerase activity. Furthermore, GIT2-knockout mice demonstrated a greater susceptibility to DNA damage than their wild-type littermates. These results suggest that GIT2 plays an important role in MRE11/ATM/H2AX-mediated DNA damage responses.
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Abstract
RNA interference (RNAi) is one of the most popular and effective molecular technologies for knocking down the expression of an individual gene of interest in living organisms. Yet the technology still faces the major issue of nonspecific gene silencing, which can compromise gene functional characterization and the interpretation of phenotypes associated with individual gene knockdown. Designing an effective and target-specific small interfering RNA (siRNA) for induction of RNAi is therefore the major challenge in RNAi-based gene silencing. A 'good' siRNA molecule must possess three key features: (a) the ability to specifically silence an individual gene of interest, (b) little or no effect on the expressions of unintended siRNA gene targets (off-target genes), and (c) no cell toxicity. Although several siRNA design and analysis algorithms have been developed, only a few of them are specifically focused on gene silencing in plants. Furthermore, current algorithms lack a comprehensive consideration of siRNA specificity, efficacy, and nontoxicity in siRNA design, mainly due to lack of integration of all known rules that govern different steps in the RNAi pathway. In this review, we first describe popular RNAi methods that have been used for gene silencing in plants and their serious limitations regarding gene-silencing potency and specificity. We then present novel, rationale-based strategies in combination with computational and experimental approaches to induce potent, specific, and nontoxic gene silencing in plants.
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Affiliation(s)
- Firoz Ahmed
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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A multicolor panel of TALE-KRAB based transcriptional repressor vectors enabling knockdown of multiple gene targets. Sci Rep 2014; 4:7338. [PMID: 25475013 PMCID: PMC4256643 DOI: 10.1038/srep07338] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/14/2014] [Indexed: 02/06/2023] Open
Abstract
Stable and efficient knockdown of multiple gene targets is highly desirable for dissection of molecular pathways. Because it allows sequence-specific DNA binding, transcription activator-like effector (TALE) offers a new genetic perturbation technique that allows for gene-specific repression. Here, we constructed a multicolor lentiviral TALE-Kruppel-associated box (KRAB) expression vector platform that enables knockdown of multiple gene targets. This platform is fully compatible with the Golden Gate TALEN and TAL Effector Kit 2.0, a widely used and efficient method for TALE assembly. We showed that this multicolor TALE-KRAB vector system when combined together with bone marrow transplantation could quickly knock down c-kit and PU.1 genes in hematopoietic stem and progenitor cells of recipient mice. Furthermore, our data demonstrated that this platform simultaneously knocked down both c-Kit and PU.1 genes in the same primary cell populations. Together, our results suggest that this multicolor TALE-KRAB vector platform is a promising and versatile tool for knockdown of multiple gene targets and could greatly facilitate dissection of molecular pathways.
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Zhao T, Liu M, Gu C, Wang X, Wang Y. Activation of c-Src tyrosine kinase mediated the degradation of occludin in ventilator-induced lung injury. Respir Res 2014; 15:158. [PMID: 25471013 PMCID: PMC4262993 DOI: 10.1186/s12931-014-0158-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/25/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Ventilator-induced lung injury (VILI) is characterized by increased alveolar permeability, pulmonary edema. The tyrosine kinase, c-Src, is involved in VILI but its role has not been fully elucidated. This study examined the relationship between c-Src activation and occludin levels in VILI both in vitro and in vivo. METHODS For the in vivo study, Wistar rats were randomly divided into five groups: control (group C); normal tidal volume (group M); normal tidal volume + c-Src inhibitor (PP2) (group M + P); high tidal volume (group H); and high tidal volume + c-Src inhibitor (PP2) (group H + P). Rats in all groups but group C underwent mechanical ventilation for 4 h. For the in vitro study, MLE-12 cells pretreated with PP2 and siRNA underwent cyclic stretching at 8% or 20% for 0, 1, 2 and 4 h. The expressions of occludin, c-Src, and p-c-Src were analyzed by western blotting, hematoxylin and eosin (HE) staining, and immunofluorescence. RESULTS For the in vivo study, rats in group H showed decreased occludin expression and activated c-Src compared with group C. HE staining and lung injury score showed more severe lung injury and alveolar edema in group H compared with group M and group C. Group H + P had less pulmonary edema induced by the high tidal volume ventilation. For the in vitro study, occludin expression decreased and c-Src activation increased as indicated by the phosphorylation of c-Src over time. Consistently, PP2 could restore occludin levels. CONCLUSIONS Mechanical ventilation can activate c-Src by phosphorylation and increase the degradation of occludin. c-Src inhibitor can ameliorate barrier function and lung injury by up-regulating occludin.
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Affiliation(s)
- Tao Zhao
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, No. 16766 Jingshi Road, Jinan, 250014, Shandong Province, China.
| | - Mengjie Liu
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, No. 16766 Jingshi Road, Jinan, 250014, Shandong Province, China.
| | - Changping Gu
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, No. 16766 Jingshi Road, Jinan, 250014, Shandong Province, China.
| | - Xin Wang
- Department of Anesthesiology, Jinan Fifth People's Hospital, Ji'nan, Shandong, China.
| | - Yuelan Wang
- Department of Anesthesiology, Qianfoshan Hospital, Shandong University, No. 16766 Jingshi Road, Jinan, 250014, Shandong Province, China.
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Ren YJ, Zhang Y. An update on RNA interference-mediated gene silencing in cancer therapy. Expert Opin Biol Ther 2014; 14:1581-92. [PMID: 25010067 DOI: 10.1517/14712598.2014.935334] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Based on our previous review, this article presents the new progress in RNA interference (RNAi)-mediated gene silencing in cancer therapy, and reviews the hurdles and how they might be overcome. AREAS COVERED RNAi-mediated gene silencing approaches have been demonstrated in humans, and ongoing clinical trials hold promise for treating cancer or providing alternatives to traditional chemotherapies. Here we describe the broad range of approaches to achieve targeted gene silencing for cancer therapy, discuss the progress made in developing RNAi as therapeutics for cancer and highlight challenges and emerging solutions associated with its clinical development. EXPERT OPINION Although the field of RNAi-based cancer therapy is still an emerging one, we have yet to get solutions for overcoming all obstacles associated with its clinical development. The current rapid advances in development of new targeted delivery strategies and noninvasive imaging methods will be big steps to explore RNAi as a new and potent clinical modality in humans.
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Affiliation(s)
- Yi-Jie Ren
- Soochow University, College of Pharmaceutical Sciences, Department of Pharmacology , Suzhou, Jiangsu , China
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Guo Y, Feng Y, Li Z, Lin X. Drosophila heparan sulfate 3-O sulfotransferase B null mutant is viable and exhibits no defects in Notch signaling. J Genet Genomics 2014; 41:369-78. [PMID: 25064676 DOI: 10.1016/j.jgg.2014.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/18/2014] [Accepted: 04/24/2014] [Indexed: 11/26/2022]
Abstract
Heparan sulfate proteoglycans (HSPGs) are critically involved in a variety of biological events. The functions of HSPGs are determined by the nature of the core proteins and modifications of heparan sulfate (HS) glycosaminoglycan (GAG) chains. The distinct O-sulfotransferases are important for nonrandom modifications at specific positions. Two HS 3-O sulfotransferase (Hs3st) genes, Hs3st-A and Hs3st-B, were identified in Drosophila. Previous experiments using RNA interference (RNAi) suggested that Hs3st-B was required for Notch signaling. Here, we generated a null mutant of Hs3st-B via ends-out gene targeting and examined its role(s) in development. We found that homozygous Hs3st-B mutants have no neurogenic defects or alterations in the expression of Notch signaling target gene. Thus, our results strongly argue against an essential role for Hs3st-B in Notch signaling. Moreover, we have generated two independent Hs3st-A RNAi lines which worked to deplete Hs3st-A. Importantly, Hs3st-A RNAi combined with Hs3st-B mutant flies did not alter the expression of Notch signaling components, arguing that both Hs3st-A and Hs3st-B were not essential for Notch signaling. The establishment of Hs3st-B mutant and effective Hs3st-A RNAi lines provides essential tools for further studies of the physiological roles of Hs3st-A and Hs3st-B in development and homeostasis.
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Affiliation(s)
- Yueqin Guo
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Feng
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou 325000, China; State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhouhua Li
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Xinhua Lin
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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Zhou ZX, Zhang J, Sun L. C7: a CpG oligodeoxynucleotide that induces protective immune response against megalocytivirus in Japanese flounder (Paralichthys olivaceus) via Toll-like receptor 9-mediated signaling pathway. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:124-132. [PMID: 24333437 DOI: 10.1016/j.dci.2013.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 12/06/2013] [Accepted: 12/06/2013] [Indexed: 06/03/2023]
Abstract
Megalocytivirus is the causative agent of severe disease outbreaks in farmed fish. Currently there is no effective control against megalocytivirus in aquaculture. Synthetic oligodeoxynucleotides (ODNs) containing unmethylated CpG motifs are known to possess marked immunostimulatory properties. In this study, we investigated the potentials of ten CpG ODNs as antiviral agents in a model of Japanese flounder (Paralichthys olivaceus). We found that, when administered into flounder, three of the ten CpG ODNs inhibited viral replication in kidney, spleen, and liver. ODN C7, which exhibited the strongest inhibitory activity, was able to promote proliferation of peripheral blood leukocytes and enhance activation of head kidney mononuclear adherent phagocytes. When the expression of toll-like receptor 9 (TLR9) was knocked down in vivo by small interfering RNA, C7-mediated immune response and antiviral activity were significantly blocked. Moreover, when C7 was co-administered with pCN86, a DNA vaccine against megalocytivirus, a significant increase in vaccine-induced protection was observed compared to administration with pCN86 alone. Further analysis showed that compared to fish immunized with pCN86, fish immunized with pCN86 plus C7 exhibited significantly upregulated expression of a wide range of genes involved in innate and adaptive immunity. Taken together, these results indicate that ODN C7 activates TLR9-mediated immune response and possesses antiviral and adjuvant potentials that may be exploited for the control of megalocytivirus infection in farmed flounder.
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Affiliation(s)
- Zhi-xia Zhou
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Jian Zhang
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Sun
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
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