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Motamedi H, Ari MM, Alvandi A, Abiri R. Principle, application and challenges of development siRNA-based therapeutics against bacterial and viral infections: a comprehensive review. Front Microbiol 2024; 15:1393646. [PMID: 38939184 PMCID: PMC11208694 DOI: 10.3389/fmicb.2024.1393646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
While significant progress has been made in understanding and applying gene silencing mechanisms and the treatment of human diseases, there have been still several obstacles in therapeutic use. For the first time, ONPATTRO, as the first small interfering RNA (siRNA) based drug was invented in 2018 for treatment of hTTR with polyneuropathy. Additionally, four other siRNA based drugs naming Givosiran, Inclisiran, Lumasiran, and Vutrisiran have been approved by the US Food and Drug Administration and the European Medicines Agency for clinical use by hitherto. In this review, we have discussed the key and promising advances in the development of siRNA-based drugs in preclinical and clinical stages, the impact of these molecules in bacterial and viral infection diseases, delivery system issues, the impact of administration methods, limitations of siRNA application and how to overcome them and a glimpse into future developments.
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Affiliation(s)
- Hamid Motamedi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Amirhoushang Alvandi
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Do VQ, Hoang-Thi C, Pham TT, Bui NL, Kim DT, Chu DT. Computational tools supporting known miRNA identification. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:225-242. [PMID: 38360000 DOI: 10.1016/bs.pmbts.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The study of small RNAs is a field that is expanding quickly. Other functional short RNA molecules other than microRNAs, and gene expression regulators, have been found in animals and plants. MicroRNAs play a significant role in host-microbe interactions, and parasite microRNAs may affect the host's innate immunity. Furthermore, short RNAs are intriguing non-invasive biomarker possibilities because they can be found in physiological fluids. These trends suggest that for many researchers, quick and simple techniques for expression profiling and subsequent downstream analysis of miRNA-seq data are crucial. We selected sRNAtoolbox to make integrated sRNA research easier. Each tool can be used separately or to explore and analyze sRNAbench results in further depth. A special focus was placed on the tools' usability. We review available miRNA research tools to have an overview of the evaluation of the tools. Mainly we evaluate the tool sRNAtoolbox.
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Affiliation(s)
- Van-Quy Do
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Chuc Hoang-Thi
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Truong Pham
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nhat-Le Bui
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Thai Kim
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
| | - Dinh-Toi Chu
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.
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Pant P, Leese F. Probing the Nucleic Acid Flexibility to Disarm the Viral Counter-Defense Machinery: Design and Characterization of Potent p19 Inhibitors. J Phys Chem B 2023; 127:8842-8851. [PMID: 37797202 DOI: 10.1021/acs.jpcb.3c04788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Plant viruses are highly destructive and significant contributors to several global pandemics and epidemics in plants. A viral disease outbreak in plants can cause a scarcity of food supply and is a severe concern to humanity. The siRNA (small interfering RNA)-mediated RNA-induced silencing complex (RISC) formation is a primary defense mechanism in plants against viruses, where the RISC binds and degrades viral mRNAs. As a counter-defense, many viruses encode RNA-silencing suppressor proteins (e.g., the p19 protein from the Tombusviridae family) for viral proliferation in plants. The functional form of p19 (homodimer) binds to plant siRNA with high affinities, thereby interrupting the RISC formation and thus preventing the viral mRNA silencing in plants. By altering the RISC formation, the p19 protein helps the virus invasion in the plant and ultimately stunts host growth. In this study, we designed several modified siRNA-based molecules for p19 inhibition. The viral p19 protein is known to interact predominantly through H-bonds with 2'-OH and phosphates of the plant siRNA. We utilized this information and in silico-designed flexible substituents of siRNA, where we removed the C2'-C3' bond in each nucleotide unit. We performed all-atom explicit-solvent molecular dynamics simulations (400 ns, 3 replicates each) for control/modified siRNA─p19 complexes (8 in total) followed by energetic estimations. Strikingly, in a few modified complexes, the siRNA not only retained the double-helical structural integrity but also displayed remarkably enhanced p19 binding compared to the control siRNA; hence, we consider it important to perform biological and chemical in vitro and in vivo studies on proposed flexible nucleic acids as p19 inhibitors for crop protection.
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Affiliation(s)
- Pradeep Pant
- Faculty of Biology, University of Duisburg Essen, Essen 45141, Germany
| | - Florian Leese
- Faculty of Biology, University of Duisburg Essen, Essen 45141, Germany
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Alam MS, Islam MN, Das M, Islam SF, Rabbane MG, Karim E, Roy A, Alam MS, Ahmed R, Kibria ASM. RNAi-Based Therapy: Combating Shrimp Viral Diseases. Viruses 2023; 15:2050. [PMID: 37896827 PMCID: PMC10612085 DOI: 10.3390/v15102050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Shrimp aquaculture has become a vital industry, meeting the growing global demand for seafood. Shrimp viral diseases have posed significant challenges to the aquaculture industry, causing major economic losses worldwide. Conventional treatment methods have proven to be ineffective in controlling these diseases. However, recent advances in RNA interference (RNAi) technology have opened new possibilities for combating shrimp viral diseases. This cutting-edge technology uses cellular machinery to silence specific viral genes, preventing viral replication and spread. Numerous studies have shown the effectiveness of RNAi-based therapies in various model organisms, paving the way for their use in shrimp health. By precisely targeting viral pathogens, RNAi has the potential to provide a sustainable and environmentally friendly solution to combat viral diseases in shrimp aquaculture. This review paper provides an overview of RNAi-based therapy and its potential as a game-changer for shrimp viral diseases. We discuss the principles of RNAi, its application in combating viral infections, and the current progress made in RNAi-based therapy for shrimp viral diseases. We also address the challenges and prospects of this innovative approach.
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Affiliation(s)
- Md. Shahanoor Alam
- Department of Genetics and Fish Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Mohammad Nazrul Islam
- Department of Biotechnology, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh;
| | - Mousumi Das
- Department of Aquaculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Sk. Farzana Islam
- Department of Fisheries (DoF), Government of the People’s Republic of Bangladesh, Matshya Bhaban, Ramna, Dhaka 1000, Bangladesh; (S.F.I.); (R.A.)
| | - Md. Golam Rabbane
- Department of Fisheries, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Ehsanul Karim
- Bangladesh Fisheries Research Institute, Mymensingh 2201, Bangladesh;
| | - Animesh Roy
- Department of Fisheries Biology and Aquatic Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Mohammad Shafiqul Alam
- Department of Genetics and Fish Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Raju Ahmed
- Department of Fisheries (DoF), Government of the People’s Republic of Bangladesh, Matshya Bhaban, Ramna, Dhaka 1000, Bangladesh; (S.F.I.); (R.A.)
| | - Abu Syed Md. Kibria
- Department of Aquaculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh;
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Szczesniak I, Baliga-Gil A, Jarmolowicz A, Soszynska-Jozwiak M, Kierzek E. Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors. Int J Mol Sci 2023; 24:ijms24021232. [PMID: 36674746 PMCID: PMC9860923 DOI: 10.3390/ijms24021232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic, whereas the influenza A virus (IAV) causes seasonal epidemics and occasional pandemics. Both viruses lead to widespread infection and death. SARS-CoV-2 and the influenza virus are RNA viruses. The SARS-CoV-2 genome is an approximately 30 kb, positive sense, 5' capped single-stranded RNA molecule. The influenza A virus genome possesses eight single-stranded negative-sense segments. The RNA secondary structure in the untranslated and coding regions is crucial in the viral replication cycle. The secondary structure within the RNA of SARS-CoV-2 and the influenza virus has been intensively studied. Because the whole of the SARS-CoV-2 and influenza virus replication cycles are dependent on RNA with no DNA intermediate, the RNA is a natural and promising target for the development of inhibitors. There are a lot of RNA-targeting strategies for regulating pathogenic RNA, such as small interfering RNA for RNA interference, antisense oligonucleotides, catalytic nucleic acids, and small molecules. In this review, we summarized the knowledge about the inhibition of SARS-CoV-2 and influenza A virus propagation by targeting their RNA secondary structure.
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Dhotre K, Banerjee A, Dass D, Nema V, Mukherjee A. An In-silico Approach to Design and Validate siRNA against Monkeypox Virus. Curr Pharm Des 2023; 29:3060-3072. [PMID: 38062661 DOI: 10.2174/0113816128275065231103063935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION The monkeypox virus has emerged as an uncommon zoonotic infection. The recent outbreak of MPXV in Europe and abroad in 2022 presented a major threat to individuals at risk. At present, no specific MPXV vaccinations or medications are available. METHODS In this study, we predicted the most effective siRNA against the conserved region of the MPXV and validated the activity by performing molecular docking studies. RESULTS Ultimately, the most efficient siRNA molecule was shortlisted against the envelope protein gene (B6R) based on its toxicity, effectivity, thermodynamic stability, molecular interaction, and molecular dynamics simulations (MD) with the Human Argonaute 2 protein. CONCLUSION Thus, the strategy may offer a platform for the development of potential antiviral RNA therapeutics that target MPXV at the genomic level.
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Affiliation(s)
- Kishore Dhotre
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Anwesha Banerjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Debashree Dass
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
| | - Vijay Nema
- Molecular Biology, National AIDS Research Institute, Pune 411026, India
| | - Anupam Mukherjee
- Division of Virology, ICMR-National AIDS Research Institute, Pune 411026, Maharashtra, India
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Tagore R, Alagarasu K, Patil P, Pyreddy S, Polash SA, Kakade M, Shukla R, Parashar D. Targeted in vitro gene silencing of E2 and nsP1 genes of chikungunya virus by biocompatible zeolitic imidazolate framework. Front Bioeng Biotechnol 2022; 10:1003448. [PMID: 36601387 PMCID: PMC9806579 DOI: 10.3389/fbioe.2022.1003448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Chikungunya fever caused by the mosquito-transmitted chikungunya virus (CHIKV) is a major public health concern in tropical, sub-tropical and temperate climatic regions. The lack of any licensed vaccine or antiviral agents against CHIKV warrants the development of effective antiviral therapies. Small interfering RNA (siRNA) mediated gene silencing of CHIKV structural and non-structural genes serves as a potential antiviral strategy. The therapeutic efficiency of siRNA can be improved by using an efficient delivery system. Metal-organic framework biocomposits have demonstrated an exceptional capability in protecting and efficiently delivering nucleic acids into cells. In the present study, carbonated ZIF called ZIF-C has been utilized to deliver siRNAs targeted against E2 and nsP1 genes of CHIKV to achieve a reduction in viral replication and infectivity. Cellular transfection studies of E2 and nsP1 genes targeting free siRNAs and ZIF-C encapsulated siRNAs in CHIKV infected Vero CCL-81 cells were performed. Our results reveal a significant reduction of infectious virus titre, viral RNA levels and percent of infected cells in cultures transfected with ZIF-C encapsulated siRNA compared to cells transfected with free siRNA. The results suggest that delivery of siRNA through ZIF-C enhances the antiviral activity of CHIKV E2 and nsP1 genes directed siRNAs.
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Affiliation(s)
- Rajarshee Tagore
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Kalichamy Alagarasu
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Poonam Patil
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Suneela Pyreddy
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, VIC, Australia,Centre for Advanced Materials and Industrial Chemistry, RMIT University, Melbourne, VIC, Australia
| | - Shakil Ahmed Polash
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, VIC, Australia,Centre for Advanced Materials and Industrial Chemistry, RMIT University, Melbourne, VIC, Australia
| | - Mahadeo Kakade
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India
| | - Ravi Shukla
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, VIC, Australia,Centre for Advanced Materials and Industrial Chemistry, RMIT University, Melbourne, VIC, Australia,*Correspondence: Ravi Shukla, ; Deepti Parashar,
| | - Deepti Parashar
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, India,*Correspondence: Ravi Shukla, ; Deepti Parashar,
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Huynh LN, Tran LB, Nguyen HS, Ho VH, Parola P, Nguyen XQ. Mosquitoes and Mosquito-Borne Diseases in Vietnam. INSECTS 2022; 13:1076. [PMID: 36554986 PMCID: PMC9781666 DOI: 10.3390/insects13121076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Mosquito-borne diseases pose a significant threat to humans in almost every part of the world. Key factors such as global warming, climatic conditions, rapid urbanisation, frequent human relocation, and widespread deforestation significantly increase the number of mosquitoes and mosquito-borne diseases in Vietnam, and elsewhere around the world. In southeast Asia, and notably in Vietnam, national mosquito control programmes contribute to reducing the risk of mosquito-borne disease transmission, however, malaria and dengue remain a threat to public health. The aim of our review is to provide a complete checklist of all Vietnamese mosquitoes that have been recognised, as well as an overview of mosquito-borne diseases in Vietnam. A total of 281 mosquito species of 42 subgenera and 22 genera exist in Vietnam. Of those, Anopheles, Aedes, and Culex are found to be potential vectors for mosquito-borne diseases. Major mosquito-borne diseases in high-incidence areas of Vietnam include malaria, dengue, and Japanese encephalitis. This review may be useful to entomological researchers for future surveys of Vietnamese mosquitoes and to decision-makers responsible for vector control tactics.
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Affiliation(s)
- Ly Na Huynh
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Institute of Malariology, Parasitology and Entomology, Quy Nhon (IMPE-QN), MoH Vietnam, Zone 8, Nhon Phu Ward, Quy Nhon City 590000, Vietnam
| | - Long Bien Tran
- Institute of Malariology, Parasitology and Entomology, Quy Nhon (IMPE-QN), MoH Vietnam, Zone 8, Nhon Phu Ward, Quy Nhon City 590000, Vietnam
| | - Hong Sang Nguyen
- Institute of Malariology, Parasitology and Entomology, Quy Nhon (IMPE-QN), MoH Vietnam, Zone 8, Nhon Phu Ward, Quy Nhon City 590000, Vietnam
| | - Van Hoang Ho
- Institute of Malariology, Parasitology and Entomology, Quy Nhon (IMPE-QN), MoH Vietnam, Zone 8, Nhon Phu Ward, Quy Nhon City 590000, Vietnam
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Xuan Quang Nguyen
- Institute of Malariology, Parasitology and Entomology, Quy Nhon (IMPE-QN), MoH Vietnam, Zone 8, Nhon Phu Ward, Quy Nhon City 590000, Vietnam
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Gul H, Habib G, Khan IM, Rahman SU, Khan NM, Wang H, Khan NU, Liu Y. Genetic resilience in chickens against bacterial, viral and protozoal pathogens. Front Vet Sci 2022; 9:1032983. [PMID: 36439341 PMCID: PMC9691405 DOI: 10.3389/fvets.2022.1032983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/28/2022] [Indexed: 06/13/2024] Open
Abstract
The genome contributes to the uniqueness of an individual breed, and enables distinctive characteristics to be passed from one generation to the next. The allelic heterogeneity of a certain breed results in a different response to a pathogen with different genomic expression. Disease resistance in chicken is a polygenic trait that involves different genes that confer resistance against pathogens. Such resistance also involves major histocompatibility (MHC) molecules, immunoglobulins, cytokines, interleukins, T and B cells, and CD4+ and CD8+ T lymphocytes, which are involved in host protection. The MHC is associated with antigen presentation, antibody production, and cytokine stimulation, which highlight its role in disease resistance. The natural resistance-associated macrophage protein 1 (Nramp-1), interferon (IFN), myxovirus-resistance gene, myeloid differentiation primary response 88 (MyD88), receptor-interacting serine/threonine kinase 2 (RIP2), and heterophile cells are involved in disease resistance and susceptibility of chicken. Studies related to disease resistance genetics, epigenetics, and quantitative trait loci would enable the identification of resistance markers and the development of disease resistance breeds. Microbial infections are responsible for significant outbreaks and have blighted the poultry industry. Breeding disease-resistant chicken strains may be helpful in tackling pathogens and increasing the current understanding on host genetics in the fight against communicable diseases. Advanced technologies, such as the CRISPR/Cas9 system, whole genome sequencing, RNA sequencing, and high-density single nucleotide polymorphism (SNP) genotyping, aid the development of resistant breeds, which would significantly decrease the use of antibiotics and vaccination in poultry. In this review, we aimed to reveal the recent genetic basis of infection and genomic modification that increase resistance against different pathogens in chickens.
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Affiliation(s)
- Haji Gul
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Gul Habib
- Department of Microbiology, Abbottabad University of Science and Technology, Abbottabad, Pakistan
| | - Ibrar Muhammad Khan
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Sajid Ur Rahman
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Laboratory of Quality and Safety Risk Assessment for Animal Products on Biohazards (Shanghai) of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Nazir Muhammad Khan
- Department of Zoology, University of Science and Technology, Bannu, Pakistan
| | - Hongcheng Wang
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Najeeb Ullah Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
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Dhanya CR, Mary AS, Madhavan M. Aptamer-siRNA chimeras: Promising tools for targeting HER2 signaling in cancer. Chem Biol Drug Des 2022; 101:1162-1180. [PMID: 36099164 DOI: 10.1111/cbdd.14143] [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: 12/19/2021] [Revised: 08/28/2022] [Accepted: 09/11/2022] [Indexed: 11/30/2022]
Abstract
RNA interference is a transformative approach and has great potential in the development of novel and more efficient cancer therapeutics. Immense prospects exist in the silencing of HER2 and its downstream genes which are overexpressed in many cancers, through exogenously delivered siRNA. However, there is still a long way to exploit the full potential and versatility of siRNA therapeutics due to the challenges associated with the stability and delivery of siRNA targeted to specific sites. Aptamers offer several advantages as a vehicle for siRNA delivery, over other carriers such as antibodies. In this review, we discuss the progress made in the development and applications of aptamer-siRNA chimeras in HER2 targeting and gene silencing. A schematic workflow is also provided which will provide ample insight for all those researchers who are new to this field. Also, we think that a mechanistic understanding of the HER2 signaling pathway is crucial in designing extensive investigations aimed at the silencing of a wider array of genes. This review is expected to stimulate more research on aptamer-siRNA chimeras targeted against HER2 which might arm us with potential effective therapeutic interventions for the management of cancer.
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Affiliation(s)
- C R Dhanya
- Department of Biochemistry, Government College Kariavattom, Thiruvananthapuram, Kerala, India
| | - Aarcha Shanmugha Mary
- Department of Microbiology, Central University of Tamil Nadu, Thiruvarur, Tamil Nadu, India
| | - Maya Madhavan
- Department of Biochemistry, Government College for Women, Thiruvananthapuram, Kerala, India
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Ali LMA, Gary-Bobo M. Photochemical Internalization of siRNA for Cancer Therapy. Cancers (Basel) 2022; 14:cancers14153597. [PMID: 35892854 PMCID: PMC9331967 DOI: 10.3390/cancers14153597] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary The objective of this review is to focus on the different nanovectors capable of transporting genetic material such as small-interfering RNA (siRNA) in order to block the expression of genes responsible for the development of cancer. Usually, these nanovectors are internalized by cancer cells via the endo-lysosomal pathway. To increase the lysosomal cargo escape, excitation using a lamp or a laser, can be applied to induce a more efficient leakage of siRNA to the cytoplasm, which is the site of action of the siRNA to block the translation of RNA into proteins. This is the mechanism of photochemical internalization. Abstract In the race to design ever more effective therapy with ever more focused and controlled actions, nanomedicine and phototherapy seem to be two allies of choice. Indeed, the use of nanovectors making it possible to transport and protect genetic material is becoming increasingly important. In addition, the use of a method allowing the release of genetic material in a controlled way in space and time is also a strategy increasingly studied thanks to the use of lasers. In parallel, the use of interfering RNA and, more particularly, of small-interfering RNA (siRNA) has demonstrated significant potential for gene therapy. In this review, we focused on the design of the different nanovectors capable of transporting siRNAs and releasing them so that they can turn off the expression of deregulated genes in cancers through controlled photoexcitation with high precision. This mechanism, called photochemical internalization (PCI), corresponds to the lysosomal leakage of the cargo (siRNA in this case) after destabilization of the lysosomal membrane under light excitation.
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Affiliation(s)
- Lamiaa Mohamed Ahmed Ali
- IBMM, University Montpellier, CNRS, ENSCM, 34093 Montpellier, France;
- Department of Biochemistry, Medical Research Institute, University of Alexandria, Alexandria 21561, Egypt
- Correspondence:
| | - Magali Gary-Bobo
- IBMM, University Montpellier, CNRS, ENSCM, 34093 Montpellier, France;
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Agarwal A, Sarma DK, Chaurasia D, Maan HS. Novel molecular approaches to combat vectors and vector-borne viruses: Special focus on RNA interference (RNAi) mechanisms. Acta Trop 2022; 233:106539. [PMID: 35623398 DOI: 10.1016/j.actatropica.2022.106539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Vector-borne diseases, such as dengue, chikungunya, zika, yellow fever etc pose significant burden among the infectious diseases globally, especially in tropical and sub-tropical regions. Globalization, deforestation, urbanization, climate change, uncontrolled population growth, inadequate waste management and poor vector-management infrastructure have all contributed to the expansion of vector habitats and subsequent increase in vector-borne diseases throughout the world. Conventional vector control methods, such as use of insecticides, have significant negative environmental repercussions in addition to developing resistance in vectors. Till date, a very few vaccines or antiviral therapies have been approved for the treatment of vector borne diseases. In this review, we have discussed emerging molecular approaches like CRISPR (clustered regularly interspaced short palindromic repeats)/Cas-9, sterile insect technique (SIT), release of insects carrying a dominant lethal (RIDL), Wolbachia (virus transmission blocking) and RNA interference (RNAi) to combat vector and vector-borne viruses. Due to the extensive advancements in RNAi research, a special focus has been given on its types, biogenesis, mechanism of action, delivery and experimental studies evaluating their application as anti-mosquito and anti-viral agent. These technologies appear to be highly promising in terms of contributing to vector control and antiviral drug development, and hence can be used to reduce global vector and vector-borne disease burden.
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Affiliation(s)
- Ankita Agarwal
- State Virology Laboratory, Department of Microbiology, Gandhi Medical College, Bhopal 462001, Madhya Pradesh, India.
| | - Devojit Kumar Sarma
- ICMR-National Institute for Research in Environmental Health, Bhopal 462030, Madhya Pradesh, India
| | - Deepti Chaurasia
- State Virology Laboratory, Department of Microbiology, Gandhi Medical College, Bhopal 462001, Madhya Pradesh, India
| | - Harjeet Singh Maan
- State Virology Laboratory, Department of Microbiology, Gandhi Medical College, Bhopal 462001, Madhya Pradesh, India
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Amjadimanesh E, Mokhtari A, Saffar B. RNA interference targeting UL25 gene as a gene therapy approach against BHV-1. Res Vet Sci 2022; 145:109-115. [DOI: 10.1016/j.rvsc.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/01/2022] [Accepted: 02/02/2022] [Indexed: 10/19/2022]
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14
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Mousavi SR, Sajjadi MS, Khosravian F, Feizbakhshan S, Salmanizadeh S, Esfahani ZT, Beni FA, Arab A, Kazemi M, Shahzamani K, Sami R, Hosseinzadeh M, Salehi M, Lotfi H. Dysregulation of RNA interference components in COVID-19 patients. BMC Res Notes 2021; 14:401. [PMID: 34715923 PMCID: PMC8554738 DOI: 10.1186/s13104-021-05816-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the novel coronavirus causing severe respiratory illness (COVID-19). This virus was initially identified in Wuhan city, a populated area of the Hubei province in China, and still remains one of the major global health challenges. RNA interference (RNAi) is a mechanism of post-transcriptional gene silencing that plays a crucial role in innate viral defense mechanisms by inhibiting the virus replication as well as expression of various viral proteins. Dicer, Drosha, Ago2, and DGCR8 are essential components of the RNAi system, which is supposed to be dysregulated in COVID-19 patients. This study aimed to assess the expression level of the mentioned mRNAs in COVID-19patients compared to healthy individuals. RESULTS Our findings demonstrated that the expression of Dicer, Drosha, and Ago2 was statistically altered in COVID-19 patients compared to healthy subjects. Ultimately, the RNA interference mechanism as a crucial antiviral defense system was suggested to be dysregulated in COVID-19 patients.
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Affiliation(s)
- Seyyed Reza Mousavi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Sadat Sajjadi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farinaz Khosravian
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sara Feizbakhshan
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sharareh Salmanizadeh
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Taherian Esfahani
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Faeze Ahmadi Beni
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ameneh Arab
- Noor Educational and Medical Center،Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Kiana Shahzamani
- Isfahan Gastroenterology and Hepatology Research Center (lGHRC), Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ramin Sami
- Department of Pulmonology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Hosseinzadeh
- Craniofacial and Cleft Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, 8175954319, Isfahan, Iran.
- Medical Genetics Research Center of Genome, Isfahan University of Medical Sciences, Isfahan, Iran.
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hajie Lotfi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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16
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Arani MJH, Mokhtari A, Saffar B, Asadi Samani L. In vitro Inhibition of Border Disease Virus Replication With Lentivirus-Mediated shRNAs. Front Vet Sci 2021; 8:708591. [PMID: 34447803 PMCID: PMC8382959 DOI: 10.3389/fvets.2021.708591] [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] [Received: 05/12/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Border disease is believed to be one of the most important diseases in the animal husbandry industry, which has not yet been eradicated in Iran. The development of approaches based on the application of interfering RNA (RNAi) for antiviral therapy has attracted a great deal of attention over the recent years. The present research was conducted to design, construct, and apply shRNA against the NS3 gene of BDV to evaluate the prevention of BDV proliferation in the cell culture system. For this purpose, the suitable oligonucleotide sequence of NS3 gene coding was selected utilizing BDV- X818 strain. Afterwards, using shRNA design software, shRNA molecules were designed and synthesized. These shRNAs were cloned into the desired vectors and were finally transfected in HEK293T cells employing the third generation of lentiviral packaging system. Subsequently, these shRNA expressing lentiviruses were transduced to the MDBK cell line to challenge to border virus. In order to evaluate the efficacy of shRNAs, the viral infectious titer and RNA copy number were calculated with TCID50 and Real-time RT-PCR tests, respectively. Results: The results revealed that shRNAs 1, 2, and 3 decreased viral RNA by more than 90% compared to the control groups. BDV titer noticeably decreased after the challenge with shRNAs 1, 2, and 3 from ~88% up to 99% in comparison with the control groups. Conclusions: Overall, it could be concluded that RNAi may be considered as a strong treatment proposal against viruses, such as BDV.
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Affiliation(s)
| | - Azam Mokhtari
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
- Zoonotic Disease Research Institute, Shahrekord University, Shahrekord, Iran
| | - Behnaz Saffar
- Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Biotechnology Research Institute, Shahrekord University, Shahrekord, Iran
| | - Leila Asadi Samani
- Department of Genetics, Faculty of Science, Shahrekord University, Shahrekord, Iran
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17
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Fonseca PLC, Mucherino M JJ, Porto JAM, Armache JN, de Almeida JPP, da Silva FF, Olmo RP, Faria IJDS, de Carvalho DS, Góes-Neto A, Corrêa RX, Pirovani CP, Pacheco LGC, Costa MA, Aguiar ERGR. Genome-wide identification of miRNAs and target regulatory network in the invasive ectoparasitic mite Varroa destructor. Genomics 2021; 113:2290-2303. [PMID: 34044154 DOI: 10.1016/j.ygeno.2021.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 12/29/2022]
Abstract
Varroa destructor is an ectoparasite mite that attacks bees leading to colony disorders worldwide. microRNAs (miRNAs) are key molecules used by eukaryotes to post-transcriptional control of gene expression. Nevertheless, still lack information aboutV. destructor miRNAs and its regulatory networks. Here, we used an integrative strategy to characterize the miRNAs in the V. destructor mite. We identified 310 precursors that give rise to 500 mature miRNAs, which 257 are likely mite-specific elements. miRNAs showed canonical length ranging between 18 and 25 nucleotides and 5' uracil preference. Top 10 elements concentrated over 80% of total miRNA expression, with bantam alone representing ~50%. We also detected non-templated bases in precursor-derived small RNAs, indicative of miRNA post-transcriptional regulatory mechanisms. Finally, we note that conserved miRNAs control similar processes in different organisms, suggesting a conservative role. Altogether, our findings contribute to the better understanding of the mite biology that can assist future studies on varroosis control.
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Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Jonathan J Mucherino M
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil; Department of Forest Management, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Mérida 5101, Venezuela
| | - Joel A M Porto
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Juliana N Armache
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - João Paulo P de Almeida
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Felipe F da Silva
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Roenick P Olmo
- Université de Strasbourg, CNRS UPR9022, Inserm, Strasbourg, France
| | - Isaque J da S Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Daniel S de Carvalho
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil; Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Ronan X Corrêa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Carlos P Pirovani
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Marco Antônio Costa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil.
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Kim H, Yuk SA, Dieterly AM, Kwon S, Park J, Meng F, Gadalla HH, Cadena MJ, Lyle LT, Yeo Y. Nanosac, a Noncationic and Soft Polyphenol Nanocapsule, Enables Systemic Delivery of siRNA to Solid Tumors. ACS NANO 2021; 15:4576-4593. [PMID: 33645963 PMCID: PMC8023695 DOI: 10.1021/acsnano.0c08694] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
For systemic delivery of small interfering RNA (siRNA) to solid tumors, the carrier must circulate avoiding premature degradation, extravasate and penetrate tumors, enter target cells, traffic to the intracellular destination, and release siRNA for gene silencing. However, existing siRNA carriers, which typically exhibit positive charges, fall short of these requirements by a large margin; thus, systemic delivery of siRNA to tumors remains a significant challenge. To overcome the limitations of existing approaches, we have developed a carrier of siRNA, called "Nanosac", a noncationic soft polyphenol nanocapsule. A siRNA-loaded Nanosac is produced by sequential coating of mesoporous silica nanoparticles (MSNs) with siRNA and polydopamine, followed by removal of the sacrificial MSN core. The Nanosac recruits serum albumin, co-opts caveolae-mediated endocytosis to enter tumor cells, and efficiently silences target genes. The softness of Nanosac improves extravasation and penetration into tumors compared to its hard counterpart. As a carrier of siRNA targeting PD-L1, Nanosac induces a significant attenuation of CT26 tumor growth by immune checkpoint blockade. These results support the utility of Nanosac in the systemic delivery of siRNA for solid tumor therapy.
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Affiliation(s)
- Hyungjun Kim
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Simseok A. Yuk
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Alexandra M. Dieterly
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, IN, 47907, USA
| | - Soonbum Kwon
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Jinho Park
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Fanfei Meng
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Hytham H. Gadalla
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Maria Jose Cadena
- School of Mechanical Engineering, College of Engineering, Purdue University, 585 Purdue Mall, West Lafayette, IN 47907, USA
| | - L. Tiffany Lyle
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, IN, 47907, USA
| | - Yoon Yeo
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr., West Lafayette, IN 47907, USA
- Corresponding author: Yoon Yeo, Ph.D., Phone: 1.765.496.9608, Fax: 1.765.494.6545,
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Hassanzadeh P. The significance of bioengineered nanoplatforms against SARS-CoV-2: From detection to genome editing. Life Sci 2021; 274:119289. [PMID: 33676931 PMCID: PMC7930743 DOI: 10.1016/j.lfs.2021.119289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/19/2022]
Abstract
COVID-19 outbreak can impose serious negative impacts on the infrastructures of societies including the healthcare systems. Despite the increasing research efforts, false positive or negative results that may be associated with serologic or even RT-PCR tests, inappropriate or variable immune response, and high rates of mutations in coronavirus may negatively affect virus detection process and effectiveness of the vaccines or drugs in development. Nanotechnology-based research attempts via developing state-of-the-art techniques such as nanomechatronics ones and advanced materials including the sensors for detecting the pathogen loads at very low concentrations or site-specific delivery of therapeutics, and real-time protections against the pandemic outbreaks by nanorobots can provide outstanding biomedical breakthroughs. Considering the unique characteristics of pathogens particularly the newly-emerged ones and avoiding the exaggerated optimism or simplistic views on the prophylactic and therapeutic approaches including the one-size-fits-all ones or presenting multiple medications that may be associated with synergistic toxicities rather than enhanced efficiencies might pave the way towards the development of more appropriate treatment strategies with reduced safety concerns. This paper highlights the significance of nanoplatforms against the viral disorders and their capabilities of genome editing that may facilitate taking more appropriate measures against SARS-CoV-2.
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Affiliation(s)
- Parichehr Hassanzadeh
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551, Iran.
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20
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Zhou J, Krishnan N, Jiang Y, Fang RH, Zhang L. Nanotechnology for virus treatment. NANO TODAY 2021; 36:101031. [PMID: 33519948 PMCID: PMC7836394 DOI: 10.1016/j.nantod.2020.101031] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 04/14/2023]
Abstract
The continued emergence of novel viruses poses a significant threat to global health. Uncontrolled outbreaks can result in pandemics that have the potential to overburden our healthcare and economic systems. While vaccination is a conventional modality that can be employed to promote herd immunity, antiviral vaccines can only be applied prophylactically and do little to help patients who have already contracted viral infections. During the early stages of a disease outbreak when vaccines are unavailable, therapeutic antiviral drugs can be used as a stopgap solution. However, these treatments do not always work against emerging viral strains and can be accompanied by adverse effects that sometimes outweigh the benefits. Nanotechnology has the potential to overcome many of the challenges facing current antiviral therapies. For example, nanodelivery vehicles can be employed to drastically improve the pharmacokinetic profile of antiviral drugs while reducing their systemic toxicity. Other unique nanomaterials can be leveraged for their virucidal or virus-neutralizing properties. In this review, we discuss recent developments in antiviral nanotherapeutics and provide a perspective on the application of nanotechnology to the SARS-CoV-2 outbreak and future virus pandemics.
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Affiliation(s)
- Jiarong Zhou
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nishta Krishnan
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yao Jiang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ronnie H Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
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Zantye P, Shende S, Ramanan SR, Talukdar I, Kowshik M. Design of a Biocompatible Hydroxyapatite-Based Nanovehicle for Efficient Delivery of Small Interference Ribonucleic Acid into Mouse Embryonic Stem Cells. Mol Pharm 2021; 18:796-806. [PMID: 33464088 DOI: 10.1021/acs.molpharmaceut.0c00684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The small interference RNA (siRNA)-assisted RNA interference approach in stem cells for differentiating into cell-specific lineages is gaining importance for its therapeutic potential. An effective gene delivery platform is crucial to achieve this goal. In this context, self-fluorescent, cell-penetrating peptide (CPP)-functionalized hydroxyapatite nanoparticles (R8HNPs) were synthesized by a modified sol gel technique. R8HNPs were crystalline, displayed characteristic bands, and exhibited broad emission spectra from 350 to 750 nm corresponding to green and red fluorescence. The biocompatible R8HNPs displayed robust binding with siRNA and excellent uptake in R1 ESCs. This was attributed to functionalization with CPP. Moreover, the R8HNP-complexed siRNA exhibited excellent serum and room temperature stability. The NPs protected the siRNA from sonication, pH, and temperature-induced stress and efficiently delivered siRNA to trigger 80% silencing of a pluripotency marker gene, Oct4, in R1 ESCs at 48 h. The transient downregulation was also observed at the protein level. Our findings demonstrate R8HNPs as a promising delivery agent for siRNA therapeutics with the potential for lineage-specific differentiation and future applications in regenerative medicine.
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Affiliation(s)
- Pranjita Zantye
- Department of Biological Sciences, BITS Pilani K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Soniya Shende
- Department of Biological Sciences, BITS Pilani K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Sutapa Roy Ramanan
- Department of Chemical Engineering, BITS Pilani K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Indrani Talukdar
- Department of Biological Sciences, BITS Pilani K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Meenal Kowshik
- Department of Biological Sciences, BITS Pilani K.K. Birla Goa Campus, Zuarinagar, Goa 403726, India
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22
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Ullah A, Qazi J, Rahman L, Kanaras AG, Khan WS, Hussain I, Rehman A. Nanoparticles-assisted delivery of antiviral-siRNA as inhalable treatment for human respiratory viruses: A candidate approach against SARS-COV-2. NANO SELECT 2020; 1:612-621. [PMID: 34485978 PMCID: PMC7675679 DOI: 10.1002/nano.202000125] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has challenged healthcare structures across the globe. Although a few therapies are approved by FDA, the search for better treatment options is continuously on rise. Clinical management includes infection prevention and supportive care such as supplemental oxygen and mechanical ventilatory support. Given the urgent nature of the pandemic and the number of companies and researchers developing COVID-19 related therapies, FDA has created an emergency program to move potential treatments with already approved drugs to patients as quickly as possible in parallel to the development of new drugs that must first pass the clinical trials. In this manuscript, we have reviewed the available literature on the use of sequence-specific degradation of viral genome using short-interfering RNA (siRNA) suggesting it as a possible treatment against SARS-CoV-2. Delivery of siRNA can be promoted by the use of FDA approved lipids, polymers or lipid-polymer hybrids. These nanoparticulate systems can be engineered to exhibit increased targetability and formulated as inhalable aerosols.
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Affiliation(s)
- Ata Ullah
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Javaria Qazi
- Department of BiotechnologyQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Lutfur Rahman
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Antonios G. Kanaras
- Physics and AstronomyInstitute for Life SciencesUniversity of SouthamptonSouthamptonSO171BJUK
| | - Waheed S. Khan
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
| | - Irshad Hussain
- Department of Chemistry and Chemical EngineeringSBA School of Science & Engineering (SBASSE)Lahore University of Management Sciences (LUMS)LahorePakistan
| | - Asma Rehman
- National Institute for Biotechnology and Genetic EngineeringFaisalabadPakistan
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Small Interfering RNAs and RNA Therapeutics in Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:369-381. [PMID: 32285425 DOI: 10.1007/978-981-15-1671-9_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleic acid (RNA) is being exploited and understood in its many aspects of function and structure for development of valuable tools in the therapeutics of various diseases such as cardiovascular etc. The expanded knowledge regarding function of RNA in the genomics and inside the cell has dramatically changed the therapeutic strategies in the past few years. RNA has become a spotlight of attention for developing novel therapeutic schemes and hence variety of therapeutic strategies is being coming into the picture that includes RNA interference, use of aptamers, role of microRNA (miRNA) that can alter the complex gene expression patterns. It is due to the fact that RNA offers various advantages in disease management as it can be edited and modified in its various forms such as secondary and tertiary structures. Although scientists are in process of manufacturing RNA-targeting therapies using variety of endogenous gene silencing regulators, Small interfering RNAs (Si RNAs), aptamers and microRNA for cardiovascular diseases yet the development of a novel, risk free therapeutic strategy is a major challenge and need of the hour in cardiovascular medicine. In this regard these agents are required to overcome pleothra of barriers such as stability of drug targets, immunogenicity, adequate binding, targeted delivery etc. to become effective drugs. Recent years have witnessed the progress of RNA therapeutic strategies in cardiovascular diseases that are likely to significantly expand the cardiovascular therapeutic repertoire within the next decade. The present manuscript has been compiled to summarize various approaches of siRNA based therapies in cardiovascular diseases along with the advantages, outcomes and limitations if any in this regard. In addition, the future prospects of RNA therapeutic modalities in cardiovascular diseases are summarized.
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Coinfections and their molecular consequences in the porcine respiratory tract. Vet Res 2020; 51:80. [PMID: 32546263 PMCID: PMC7296899 DOI: 10.1186/s13567-020-00807-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/02/2020] [Indexed: 01/15/2023] Open
Abstract
Understudied, coinfections are more frequent in pig farms than single infections. In pigs, the term “Porcine Respiratory Disease Complex” (PRDC) is often used to describe coinfections involving viruses such as swine Influenza A Virus (swIAV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), and Porcine CircoVirus type 2 (PCV2) as well as bacteria like Actinobacillus pleuropneumoniae, Mycoplasma hyopneumoniae and Bordetella bronchiseptica. The clinical outcome of the various coinfection or superinfection situations is usually assessed in the studies while in most of cases there is no clear elucidation of the fine mechanisms shaping the complex interactions occurring between microorganisms. In this comprehensive review, we aimed at identifying the studies dealing with coinfections or superinfections in the pig respiratory tract and at presenting the interactions between pathogens and, when possible, the mechanisms controlling them. Coinfections and superinfections involving viruses and bacteria were considered while research articles including protozoan and fungi were excluded. We discuss the main limitations complicating the interpretation of coinfection/superinfection studies, and the high potential perspectives in this fascinating research field, which is expecting to gain more and more interest in the next years for the obvious benefit of animal health.
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Asadi Samani L, Saffar B, Mokhtari A, Arefian E. Lentivirus expressing shRNAs inhibit the replication of contagious ecthyma virus by targeting DNA polymerase gene. BMC Biotechnol 2020; 20:18. [PMID: 32293394 PMCID: PMC7092477 DOI: 10.1186/s12896-020-00611-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/06/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Contagious ecthyma or Orf is known as a zoonotic disease remains prevalently worldwide despite the application of some control strategies against it. RNAi particularly shRNA provides us with the chance to tackle this obstacle by an encouraging new approach. The current study indicates the design and experiment of third-generation lentivirus packaging systems delivering shRNAs to inhibit Orf virus (ORFV) replication and infection. Given the importance of DNA-pol gene in virus replication, in this study, three shRNAs against this gene were designed and cloned into lentiviral vectors to stabilize the expression of shRNAs. After producing lentivectors expressing ORFV-DNA- pol in HEK293T cells, the synthesized shRNAs were applied to downregulate viral replication and gene expression. The reduction in viral titer and RNA was evaluated by TCID50 test as well as real-time RT-PCR. The results were then analyzed in comparison with the control group. RESULTS Designed shRNAs significantly reduced virus yield approximately 90 to 97% and 96.8 to 99.4%, respectively compared to the control groups (cells infected with ORFV and infected with ORFV and scrambled vector) by TCID50 test. Real-time RT-PCR revealed a dramatic reduction in the expression of viral RNA approximately 99% compared to cells infected with ORFV and from 92.6 to 99%, respectively compared to cells infected with ORFV and scrambled vector. CONCLUSIONS Therefore, it can be stated that RNAi is capable of being used as a potent therapeutically option against viruses like ORFV.
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Affiliation(s)
- Leila Asadi Samani
- Department of Genetics, Faculty of Science, Shahrekord University, Rahbar Boulevard, Postal Box: 115, Shahrekord, Iran
| | - Behnaz Saffar
- Department of Genetics, Faculty of Science, Shahrekord University, Rahbar Boulevard, Postal Box: 115, Shahrekord, Iran.
- Biotechnology Research Institute, Shahrekord University, Shahrekord, Iran.
| | - Azam Mokhtari
- Department of Pathobiology, Faculty of veterinary medicine, Shahrekord University, Shahrekord, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Raja MAG, Katas H, Amjad MW. Design, mechanism, delivery and therapeutics of canonical and Dicer-substrate siRNA. Asian J Pharm Sci 2019; 14:497-510. [PMID: 32104477 PMCID: PMC7032099 DOI: 10.1016/j.ajps.2018.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/07/2018] [Accepted: 12/24/2018] [Indexed: 12/12/2022] Open
Abstract
Upon the discovery of RNA interference (RNAi), canonical small interfering RNA (siRNA) has been recognized to trigger sequence-specific gene silencing. Despite the benefits of siRNAs as potential new drugs, there are obstacles still to be overcome, including off-target effects and immune stimulation. More recently, Dicer substrate siRNA (DsiRNA) has been introduced as an alternative to siRNA. Similarly, it also is proving to be potent and target-specific, while rendering less immune stimulation. DsiRNA is 25–30 nucleotides in length, and is further cleaved and processed by the Dicer enzyme. As with siRNA, it is crucial to design and develop a stable, safe, and efficient system for the delivery of DsiRNA into the cytoplasm of targeted cells. Several polymeric nanoparticle systems have been well established to load DsiRNA for in vitro and in vivo delivery, thereby overcoming a major hurdle in the therapeutic uses of DsiRNA. The present review focuses on a comparison of siRNA and DsiRNA on the basis of their design, mechanism, in vitro and in vivo delivery, and therapeutics.
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Affiliation(s)
- Maria Abdul Ghafoor Raja
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Rafha 73211, Saudi Arabia
| | - Haliza Katas
- Centre for Drug Delivery Research, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Muhammad Wahab Amjad
- Department of Pharmaceutics, Faculty of Pharmacy, Northern Border University, Rafha 73211, Saudi Arabia
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Efficient Inhibition of Avian and Seasonal Influenza A Viruses by a Virus-Specific Dicer-Substrate Small Interfering RNA Swarm in Human Monocyte-Derived Macrophages and Dendritic Cells. J Virol 2019; 93:JVI.01916-18. [PMID: 30463970 DOI: 10.1128/jvi.01916-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 11/09/2018] [Indexed: 11/20/2022] Open
Abstract
Influenza A viruses (IAVs) are viral pathogens that cause epidemics and occasional pandemics of significant mortality. The generation of efficacious vaccines and antiviral drugs remains a challenge due to the rapid appearance of new influenza virus types and antigenic variants. Consequently, novel strategies for the prevention and treatment of IAV infections are needed, given the limitations of the presently available antivirals. Here, we used enzymatically produced IAV-specific double-stranded RNA (dsRNA) molecules and Giardia intestinalis Dicer for the generation of a swarm of small interfering RNA (siRNA) molecules. The siRNAs target multiple conserved genomic regions of the IAVs. In mammalian cells, the produced 25- to 27-nucleotide-long siRNA molecules are processed by endogenous Dicer into 21-nucleotide siRNAs and are thus designated Dicer-substrate siRNAs (DsiRNAs). We evaluated the efficacy of the above DsiRNA swarm at preventing IAV infections in human primary monocyte-derived macrophages and dendritic cells. The replication of different IAV strains, including avian influenza H5N1 and H7N9 viruses, was significantly inhibited by pretransfection of the cells with the IAV-specific DsiRNA swarm. Up to 7 orders of magnitude inhibition of viral RNA expression was observed, which led to a dramatic inhibition of IAV protein synthesis and virus production. The IAV-specific DsiRNA swarm inhibited virus replication directly through the RNA interference pathway although a weak induction of innate interferon responses was detected. Our results provide direct evidence for the feasibility of the siRNA strategy and the potency of DsiRNA swarms in the prevention and treatment of influenza, including the highly pathogenic avian influenza viruses.IMPORTANCE In spite of the enormous amount of research, influenza virus is still one of the major challenges for medical virology due to its capacity to generate new variants, which potentially lead to severe epidemics and pandemics. We demonstrated here that a swarm of small interfering RNA (siRNA) molecules, including more than 100 different antiviral RNA molecules targeting the most conserved regions of the influenza A virus genome, could efficiently inhibit the replication of all tested avian and seasonal influenza A variants in human primary monocyte-derived macrophages and dendritic cells. The wide antiviral spectrum makes the virus-specific siRNA swarm a potentially efficient treatment modality against both avian and seasonal influenza viruses.
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Misawa T, Ohoka N, Oba M, Yamashita H, Tanaka M, Naito M, Demizu Y. Development of 2-aminoisobutyric acid (Aib)-rich cell-penetrating foldamers for efficient siRNA delivery. Chem Commun (Camb) 2019; 55:7792-7795. [DOI: 10.1039/c9cc02203a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have designed and synthesized a set of cell-penetrating foldamers (CPFs), Blocks 1–8, composed of the common amino acids Leu, Arg, and Gly, as well as the helicogenic amino acid 2-aminoisobutyric acid.
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Affiliation(s)
- Takashi Misawa
- Division of Organic Chemistry
- National Institute of Health Sciences
- Kawasaki-shi
- Japan
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products
- National Institute of Health Sciences
- Kawasaki-shi
- Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences
- Nagasaki University
- Nagasaki 852-8521
- Japan
| | - Hiroko Yamashita
- Division of Organic Chemistry
- National Institute of Health Sciences
- Kawasaki-shi
- Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences
- Nagasaki University
- Nagasaki 852-8521
- Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products
- National Institute of Health Sciences
- Kawasaki-shi
- Japan
| | - Yosuke Demizu
- Division of Organic Chemistry
- National Institute of Health Sciences
- Kawasaki-shi
- Japan
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Gosal SS, Wani SH. RNAi for Resistance Against Biotic Stresses in Crop Plants. BIOTECHNOLOGIES OF CROP IMPROVEMENT, VOLUME 2 2018. [PMCID: PMC7123769 DOI: 10.1007/978-3-319-90650-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA interference (RNAi)-based gene silencing has become one of the most successful strategies in not only identifying gene function but also in improving agronomical traits of crops by silencing genes of different pathogens/pests and also plant genes for improvement of desired trait. The conserved nature of RNAi pathway across different organisms increases its applicability in various basic and applied fields. Here we attempt to summarize the knowledge generated on the fundamental mechanisms of RNAi over the years, with emphasis on insects and plant-parasitic nematodes (PPNs). This chapter also reviews the rich history of RNAi research, gene regulation by small RNAs across different organisms, and application potential of RNAi for generating transgenic plants resistant to major pests. But, there are some limitations too which restrict wider applications of this technology to its full potential. Further refinement of this technology in terms of resolving these shortcomings constitutes one of the thrust areas in present RNAi research. Nevertheless, its application especially in breeding agricultural crops resistant against biotic stresses will certainly offer the possible solutions for some of the breeding objectives which are otherwise unattainable.
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Affiliation(s)
- Satbir Singh Gosal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir India
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González C, Tabernero D, Cortese MF, Gregori J, Casillas R, Riveiro-Barciela M, Godoy C, Sopena S, Rando A, Yll M, Lopez-Martinez R, Quer J, Esteban R, Buti M, Rodríguez-Frías F. Detection of hyper-conserved regions in hepatitis B virus X gene potentially useful for gene therapy. World J Gastroenterol 2018; 24:2095-2107. [PMID: 29785078 PMCID: PMC5960815 DOI: 10.3748/wjg.v24.i19.2095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/26/2018] [Accepted: 05/06/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To detect hyper-conserved regions in the hepatitis B virus (HBV) X gene (HBX) 5’ region that could be candidates for gene therapy.
METHODS The study included 27 chronic hepatitis B treatment-naive patients in various clinical stages (from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeAg-negative and HBeAg-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/mL, the HBX 5’ end region [nucleotide (nt) 1255-1611] was PCR-amplified and submitted to next-generation sequencing (NGS). We assessed genotype variants by phylogenetic analysis, and evaluated conservation of this region by calculating the information content of each nucleotide position in a multiple alignment of all unique sequences (haplotypes) obtained by NGS. Conservation at the HBx protein amino acid (aa) level was also analyzed.
RESULTS NGS yielded 1333069 sequences from the 27 samples, with a median of 4578 sequences/sample (2487-9279, IQR 2817). In 14/27 patients (51.8%), phylogenetic analysis of viral nucleotide haplotypes showed a complex mixture of genotypic variants. Analysis of the information content in the haplotype multiple alignments detected 2 hyper-conserved nucleotide regions, one in the HBX upstream non-coding region (nt 1255-1286) and the other in the 5’ end coding region (nt 1519-1603). This last region coded for a conserved amino acid region (aa 63-76) that partially overlaps a Kunitz-like domain.
CONCLUSION Two hyper-conserved regions detected in the HBX 5’ end may be of value for targeted gene therapy, regardless of the patients’ clinical stage or HBV genotype.
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Affiliation(s)
- Carolina González
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Marçall Yll, Josep Quer, Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Josep Gregori
- Marçall Yll, Josep Quer, Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès 08174, Spain
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Marçall Yll, Josep Quer, Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Rafael Esteban and Maria Buti, Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Cristina Godoy
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Marçall Yll, Josep Quer, Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Sara Sopena
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Ariadna Rando
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Marçal Yll
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Rosa Lopez-Martinez
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
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Nikam RR, Gore KR. Journey of siRNA: Clinical Developments and Targeted Delivery. Nucleic Acid Ther 2018; 28:209-224. [PMID: 29584585 DOI: 10.1089/nat.2017.0715] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Since the evolutionary discovery of RNA interference and its utilization for gene knockdown in mammalian cell, a remarkable progress has been achieved in small interfering RNA (siRNA) therapeutics. siRNA is a promising tool, utilized as therapeutic agent against various diseases. Despite its significant potential benefits, safe, efficient, and target oriented delivery of siRNA is one of the major challenges in siRNA therapeutics. This review covers major achievements in clinical trials and targeted delivery of siRNAs using various targeting ligand-receptor pair. Local and systemically administered siRNA drug candidates at various phases in clinical trials are described in this review. This review also provides a deep insight in development of targeted delivery of siRNA. Various targeting ligand-siRNA pair with complexation and conjugation approaches are discussed in this review. This will help to achieve further optimization and development in targeted delivery of siRNAs to achieve higher gene silencing efficiency with lowest siRNA dose availability.
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Affiliation(s)
| | - Kiran R Gore
- Department of Chemistry, University of Mumbai , Mumbai, India
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32
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Sharif Shohan MU, Paul A, Hossain M. Computational design of potential siRNA molecules for silencing nucleoprotein gene of rabies virus. Future Virol 2018. [DOI: 10.2217/fvl-2017-0117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aim: Rabies virus infections are a global threat to human and animal health, yet no progressive curative therapy has been developed. In this study, the nucleoprotein gene of rabies virus which is responsible for viral infection was used as a target to design our desired siRNA. Methods: The conserved regions were analyzed by doing alignment of sequences from different strains. Subsequently, different computational tools were used for designing and validation of siRNA molecules. Results: We identified four probable siRNA molecules from twelve different strains of rabies virus which may silence the nucleoprotein gene and inhibit the multiplication of the virus. Conclusion: Our study may help to take an effective therapeutic approach against rabies virus and lead to better control of rabies in humans.
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Affiliation(s)
| | - Anik Paul
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Motaher Hossain
- Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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Beitelshees M, Hill A, Rostami P, Jones CH, Pfeifer B. Pressing diseases that represent promising targets for gene therapy. DISCOVERY MEDICINE 2017; 24:313-322. [PMID: 29373809 PMCID: PMC9890200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Over time, there has been a growing interest in the application of gene therapy within the healthcare industry as demonstrated by the nearly 3,000 clinical trials associated with gene therapy that are listed in clinicaltrials.gov. However, there are various difficulties associated with gene therapy that have limited the realization of licensed gene therapies to only a handful of treatments. Furthermore, efforts to develop gene therapeutics have been narrowly focused and most clinical trials have sought to develop treatments for cancer (64.6%), monogenic diseases (10.5%), infectious diseases (7.4%), and cardiovascular diseases (7.4%). In addition, nearly 70% of clinical trials have utilized viral-based delivery systems, despite various concerns associated with this strategy. Each of these factors highlights the lack of diversity in the development of gene therapeutics that should be addressed. In recent years, developments in gene manipulation and delivery such as CRISPR and non-viral vectors (e.g., liposomes) demonstrate promise for improving outcomes for gene therapy. The increased fidelity and capacity afforded by these technologies provide the potential to improve upon contemporary gene therapy approaches and enable the development of treatments for less-emphasized disorders. In this review, we provide a summary of gene delivery technology and discuss various developments in gene therapy technology. We conclude by proposing several genetic conditions that represent promising targets for gene therapy given recent developments in gene delivery and manipulation.
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Affiliation(s)
- M. Beitelshees
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, USA
| | - A. Hill
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, USA,Abcombi Biosciences Inc., Buffalo, New York, USA
| | - P. Rostami
- Abcombi Biosciences Inc., Buffalo, New York, USA
| | - C. H. Jones
- Abcombi Biosciences Inc., Buffalo, New York, USA,Correspondence to: ,
| | - B.A. Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, USA,Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, New York, USA,Correspondence to: ,
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Saha A, Bhagyawant SS, Parida M, Dash PK. Vector-delivered artificial miRNA effectively inhibited replication of Chikungunya virus. Antiviral Res 2016; 134:42-49. [PMID: 27565991 PMCID: PMC7113671 DOI: 10.1016/j.antiviral.2016.08.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/02/2016] [Accepted: 08/22/2016] [Indexed: 12/19/2022]
Abstract
Chikungunya virus (CHIKV) has emerged as one of the most significant arboviral threats in many parts of the world. In spite of large scale morbidity, and long lasting polyarthralgia, no licensed vaccine or antivirals are available for the clinical management of CHIKV infection. In this study, a novel RNA interference based strategy has been adopted for effective inhibition of CHIKV. Four artificial microRNAs (amiRNAs) were designed to target different regions of CHIKV genome. These amiRNAs significantly inhibited CHIKV replication in Vero cells at both RNA and protein levels as assessed by qRT-PCR, immunoblotting and immunofluorescence techniques. Further inhibition of the infectious CHIKV up to 99.8% was demonstrated by plaque reduction assay. Concatemerization of amiRNA resulted in higher inhibition of CHIKV than individual amiRNAs. In addition, we studied the effect of combination of RNAi based therapy with other classical antivirals like chloroquine, ribavirin and mycophenolic acid, that helped in understanding the rational selection of RNAi based combination therapy. These findings provide a promising avenue for the development of novel amiRNA or combination based therapeutics against emerging CHIKV. amiRNAs targeting different ORF of CHIKV was designed. Significant Inhibition of CHIKV replication through amiRNA was demonstrated. Concatenated amiRNAs results in higher viral inhibition. Combination of RNAi with classical drugs may obliterate failure of monotherapy.
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Affiliation(s)
- Amrita Saha
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | | | - Manmohan Parida
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Paban Kumar Dash
- Virology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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35
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Fakhr E, Zare F, Teimoori-Toolabi L. Precise and efficient siRNA design: a key point in competent gene silencing. Cancer Gene Ther 2016; 23:73-82. [DOI: 10.1038/cgt.2016.4] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 12/14/2022]
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36
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Meena CK, Borkotoky S, Murali A. Insight into virus encapsulation mechanism through in silico interaction study between coat protein and RNA operator loops of Sesbania mosaic virus. MOLECULAR BIOSYSTEMS 2016; 12:1996-2009. [DOI: 10.1039/c6mb00206d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Viruses are parasite by nature and they are responsible for many diseases. Inhibitor development is very difficult for viruses due to their rapid mutative nature.
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Affiliation(s)
- Chetan Kumar Meena
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| | - Subhomoi Borkotoky
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| | - Ayaluru Murali
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
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37
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Silencing Estrogen Receptor-β with siRNA in Cultured Cells. Methods Mol Biol 2015. [PMID: 26585149 DOI: 10.1007/978-1-4939-3127-9_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Estrogen receptors α and β (ERα and ERβ) are the two genomic estrogen receptors. ERβ was the second of these receptors to be discovered; its structure is similar to that of ERα but they are different in histological distribution. However, the functions of ERα versus ERβ are still unclear. The ability of small interfering RNAs (siRNAs) to silence gene expression has proven to be invaluable for studying gene function in cultured mammalian cells. This chapter describes the use of siRNA to inhibit the expression of ERβ in renal cell carcinoma (RCC) and to further the understanding of ERβ function in RCC.
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38
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Lee HS, Lee HY, Kim YJ, Jung HD, Choi KJ, Yang JM, Kim SS, Kim K. Small interfering (Si) RNA mediated baculovirus replication reduction without affecting target gene expression. Virus Res 2015; 199:68-76. [PMID: 25630059 DOI: 10.1016/j.virusres.2015.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 12/26/2022]
Abstract
The baculovirus expression vector system (BEVS) is widely used to produce large quantities of recombinant protein with posttranslational modification. Recombinant baculoviruses (such as Autographa californica multiple nuclear polyhedrosis virus) are especially useful in producing recombinant proteins and virus-like particles (VLPs) as biodrugs or candidate vaccines for the prevention of serious infectious diseases. However, during the bioprocessing of recombinant proteins in insect cells, baculovirus replication and viral budding are coincident. In some cases, residual baculovirus contaminants remain in the recombinant protein products, even though various purification processes are applied such as ion-exchange chromatography, ultracentrifugation, or gel filtration. To reduce unexpected contamination caused by replication and budding-out of the baculovirus, we designed short interfering (si) RNAs targeting glycoprotein 64 (GP64) or single-stranded DNA-binding protein (DBP) to inhibit baculovirus replication during overexpression of recombinant foreign genes. GP64 is known to be critical both for the entry of virions into cells and for the assembly of the budded virion at the cell surface. DBP is also essential for virus assembly by regulation of the capsid protein P39 and the polyhedrin protein. This study showed that GP64 expression was suppressed by GP64 siRNAs in Western blot experiments, while the expression of recombinant proteins was unaffected. In addition, transfection of GP64 siRNAs and DBP siRNAs reduced the level of baculovirus replication, compared with the treatment with scrambled siRNAs. However, DBP siRNA also suppressed the expression of recombinant proteins. In conclusion, our GP64 siRNAs showed that an interfering RNA system, such as siRNAs and short hairpin (sh) RNAs, can be applicable to reduce baculovirus contaminants during the bioprocessing of recombinant proteins in insect cells. Further investigation should be carried out to establish transformed insect cell lines with stable expression of corresponding interfering RNAs.
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Affiliation(s)
- Han Saem Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea
| | - Ho Yeon Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea
| | - You-Jin Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea
| | - Hee-Dong Jung
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea
| | - Ki Ju Choi
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea
| | - Jai Myung Yang
- Department of Life Science, Sogang University, Seoul 121-742, South Korea
| | - Sung Soon Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea
| | - Kisoon Kim
- Division of Influenza Virus, Center for Infectious Diseases, National Institute of Health, Korea CDC, 187 Osongsaemyong2-ro, 363-951 Cheongju-si, Chungbuk, South Korea.
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Lin Y, Jia G, Xu G, Su J, Xie L, Hu X, Zhang R. Cloning and characterization of the shell matrix protein Shematrin in scallop Chlamys farreri. Acta Biochim Biophys Sin (Shanghai) 2014; 46:709-19. [PMID: 25001481 DOI: 10.1093/abbs/gmu054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Shematrin family is unique to the organic matrices of pearl oyster shells, containing repetitive, low-complexity domains designated as XGnX (where X is a hydrophobic amino acid). Current studies suggested that Shematrins are framework proteins in the prismatic layer of Pinctada fucata; however, the exact function of Shematrin during shell formation is unclear. In this study, we cloned and characterized Shematrin, a protein highly homologous to Shematrin-2, from the mantle tissue of scallop (Chlamys farreri). Semi-quantitative reverse transcript polymerase chain reaction analysis showed that Shematrin is exclusively expressed in the mantle. Knocking down the expression of Shematrin in adult scallops via double-stranded RNA injection led to an abnormal folia surface. After the shell was notched, the expression level of Shematrin remarkably increased and then gradually decreased, suggesting that Shematrin is critically involved in the shell repair progress. Injection of Shematrin double-stranded RNA reduced the speed of shell regeneration and caused abnormal surface morphology of the regenerated shell. The RNA interference and shell notching experiments indicated that Shematrin plays a key role in the folia formation of C. farreri. Structure prediction showed that Shematrin may be an intrinsically disordered protein, with high flexibility and elasticity of the molecular conformation, which facilitate binding multiple protein partners. Based on the structure features, we hypothesized that Shematrin may participate in framework organization via binding with several specific acidic proteins, functioning as a molecular hub in the protein interaction networks.
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Affiliation(s)
- Ya Lin
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ganchu Jia
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangrui Xu
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingtan Su
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Liping Xie
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China Protein Science Laboratory of the Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Rongqing Zhang
- Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China Protein Science Laboratory of the Ministry of Education, Tsinghua University, Beijing 100084, China
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Proteomic analysis of interaction between P7-1 of Southern rice black-streaked dwarf virus and the insect vector reveals diverse insect proteins involved in successful transmission. J Proteomics 2014; 102:83-97. [DOI: 10.1016/j.jprot.2014.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/20/2014] [Accepted: 03/06/2014] [Indexed: 01/06/2023]
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Administration of E2 and NS1 siRNAs inhibit chikungunya virus replication in vitro and protects mice infected with the virus. PLoS Negl Trop Dis 2013; 7:e2405. [PMID: 24040429 PMCID: PMC3764232 DOI: 10.1371/journal.pntd.0002405] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 07/23/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) has reemerged as a life threatening pathogen and caused large epidemics in several countries. So far, no licensed vaccine or effective antivirals are available and the treatment remains symptomatic. In this context, development of effective and safe prophylactics and therapeutics assumes priority. METHODS We evaluated the efficacy of the siRNAs against ns1 and E2 genes of CHIKV both in vitro and in vivo. Four siRNAs each, targeting the E2 (Chik-1 to Chik-4) and ns1 (Chik-5 to Chik-8) genes were designed and evaluated for efficiency in inhibiting CHIKV growth in vitro and in vivo. Chik-1 and Chik-5 siRNAs were effective in controlling CHIKV replication in vitro as assessed by real time PCR, IFA and plaque assay. CONCLUSIONS CHIKV replication was completely inhibited in the virus-infected mice when administered 72 hours post infection. The combination of Chik-1 and Chik-5 siRNAs exhibited additive effect leading to early and complete inhibition of virus replication. These findings suggest that RNAi capable of inhibiting CHIKV growth might constitute a new therapeutic strategy for controlling CHIKV infection and transmission.
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Liu XY, Tang QS, Chen HC, Jiang XL, Fang H. Lentiviral miR30-based RNA interference against heparanase suppresses melanoma metastasis with lower liver and lung toxicity. Int J Biol Sci 2013; 9:564-77. [PMID: 23847439 PMCID: PMC3708037 DOI: 10.7150/ijbs.5425] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 05/18/2013] [Indexed: 12/30/2022] Open
Abstract
Aim: To construct short hairpin RNAs (shRNAs) and miR30-based shRNAs against heparanase (HPSE) to compare their safety and their effects on HPSE down-modulation in vitro and in vivo to develop a more ideal therapeutic RNA interference (RNAi) vector targeting HPSE. Methods: First, we constructed shRNAs and miR30-based shRNAs against HPSE (HPSE-shRNAs and HPSE-miRNAs) and packed them into lentiviral vectors. Next, we observed the effects of the shRNAs on knockdown for HPSE expression, adhesion, migration and invasion abilities in human malignant melanoma A375 cells in vitro. Furthermore, we compared the effects of the shRNAs on melanoma growth, metastasis and safety in xenograft models. Results: Our data showed that these artificial miRNAs targeting HPSE could be effective RNAi agents mediated by Pol II promoters in vitro and in vivo, although these miRNAs were not more potent than the HPSE-shRNAs. It was noted that obvious lung injuries, rarely revealed previously, as well as hepatotoxicity could be caused by lentivirus-mediated shRNAs (LV shRNAs) rather than lentivirus-mediated miRNAs (LV miRNAs) in vivo. Furthermore, enhanced expression of pro-inflammatory cytokines IL-6 and TGF-β1 and endogenous mmu-miR-21a-5p were detected in lung tissues of shRNAs groups, whereas the expression of mmu-let-7a-5p, mmu-let-7b-5p and mmu-let-7c-5p were down-regulated. Conclusion: These findings suggest that artificial miRNAs display an improved safety profile of lowered lung injury or hepatotoxicity relative to shRNAs in vivo. The mechanism of lung injuries caused by shRNAs may be correlated with changes of endogenous miRNAs in the lung. Our data here increase the flexibility of a miRNA-based RNAi system for functional genomic and gene therapy applications.
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Affiliation(s)
- Xiao-yan Liu
- Department of Dermatology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
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Zheng J, Tan BH, Sugrue R, Tang K. Current approaches on viral infection: proteomics and functional validations. Front Microbiol 2012; 3:393. [PMID: 23162545 PMCID: PMC3499792 DOI: 10.3389/fmicb.2012.00393] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022] Open
Abstract
Viruses could manipulate cellular machinery to ensure their continuous survival and thus become parasites of living organisms. Delineation of sophisticated host responses upon virus infection is a challenging task. It lies in identifying the repertoire of host factors actively involved in the viral infectious cycle and characterizing host responses qualitatively and quantitatively during viral pathogenesis. Mass spectrometry based proteomics could be used to efficiently study pathogen-host interactions and virus-hijacked cellular signaling pathways. Moreover, direct host and viral responses upon infection could be further investigated by activity-based functional validation studies. These approaches involve drug inhibition of secretory pathway, immunofluorescence staining, dominant negative mutant of protein target, real-time PCR, small interfering siRNA-mediated knockdown, and molecular cloning studies. In this way, functional validation could gain novel insights into the high-content proteomic dataset in an unbiased and comprehensive way.
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Affiliation(s)
- Jie Zheng
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University Singapore
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Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) that infects the silkworm, B. mori, accounts for >50% of silk cocoon crop losses globally. We speculated that simultaneous targeting of several BmNPV essential genes in transgenic silkworm would elicit a stable defense against the virus. We introduced into the silkworm germline the vectors carrying short sequences of four essential BmNPV genes in tandem, either in sense or antisense or in inverted-repeat arrangement. The transgenic silkworms carrying the inverted repeat-containing transgene showed stable protection against high doses of baculovirus infection. Further, the antiviral trait was incorporated to a commercially productive silkworm strain highly susceptible to BmNPV. This led to combining the high-yielding cocoon and silk traits of the parental commercial strain and a very high level of refractoriness (>75% survival rate as compared to <15% in nontransgenic lines) to baculovirus infection conferred by the transgene. We also observed impaired infectivity of the occlusion bodies derived from the transgenic lines as compared to the wild-type ones. Currently, large-scale exploitation of these transgenic lines is underway to bring about economic transformation of sericulture.
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Friedrich BM, Trefry JC, Biggins JE, Hensley LE, Honko AN, Smith DR, Olinger GG. Potential vaccines and post-exposure treatments for filovirus infections. Viruses 2012; 4:1619-50. [PMID: 23170176 PMCID: PMC3499823 DOI: 10.3390/v4091619] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/31/2012] [Accepted: 09/04/2012] [Indexed: 01/07/2023] Open
Abstract
Viruses of the family Filoviridae represent significant health risks as emerging infectious diseases as well as potentially engineered biothreats. While many research efforts have been published offering possibilities toward the mitigation of filoviral infection, there remain no sanctioned therapeutic or vaccine strategies. Current progress in the development of filovirus therapeutics and vaccines is outlined herein with respect to their current level of testing, evaluation, and proximity toward human implementation, specifically with regard to human clinical trials, nonhuman primate studies, small animal studies, and in vitro development. Contemporary methods of supportive care and previous treatment approaches for human patients are also discussed.
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Affiliation(s)
- Brian M. Friedrich
- United States Army Medical Research Institute of Infectious Diseases, Division of Virology, 1425 Porter Street, Frederick, MD 21702, USA; (B.M.F.); (J.C.T.); (J.E.B.); (A.N.H.); (D.R.S.)
| | - John C. Trefry
- United States Army Medical Research Institute of Infectious Diseases, Division of Virology, 1425 Porter Street, Frederick, MD 21702, USA; (B.M.F.); (J.C.T.); (J.E.B.); (A.N.H.); (D.R.S.)
| | - Julia E. Biggins
- United States Army Medical Research Institute of Infectious Diseases, Division of Virology, 1425 Porter Street, Frederick, MD 21702, USA; (B.M.F.); (J.C.T.); (J.E.B.); (A.N.H.); (D.R.S.)
| | - Lisa E. Hensley
- United States Food and Drug Administration (FDA), Medical Science Countermeasures Initiative (McMi), 10903 New Hampshire Avenue, Silver Spring, MD 20901, USA; (L.E.H.)
| | - Anna N. Honko
- United States Army Medical Research Institute of Infectious Diseases, Division of Virology, 1425 Porter Street, Frederick, MD 21702, USA; (B.M.F.); (J.C.T.); (J.E.B.); (A.N.H.); (D.R.S.)
| | - Darci R. Smith
- United States Army Medical Research Institute of Infectious Diseases, Division of Virology, 1425 Porter Street, Frederick, MD 21702, USA; (B.M.F.); (J.C.T.); (J.E.B.); (A.N.H.); (D.R.S.)
| | - Gene G. Olinger
- United States Army Medical Research Institute of Infectious Diseases, Division of Virology, 1425 Porter Street, Frederick, MD 21702, USA; (B.M.F.); (J.C.T.); (J.E.B.); (A.N.H.); (D.R.S.)
- Author to whom correspondence should be addressed; (G.G.O.); Tel.: +1-301-619-8581; +1-301-619-2290
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Kibenge FS, Godoy MG, Fast M, Workenhe S, Kibenge MJ. Countermeasures against viral diseases of farmed fish. Antiviral Res 2012; 95:257-81. [DOI: 10.1016/j.antiviral.2012.06.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/09/2012] [Indexed: 12/24/2022]
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Yao H, Zhang Y, He F, Wang C, Xiao Z, Zou J, Wang F, Liu Z. Short hairpin RNA targeting 2B gene of coxsackievirus B3 exhibits potential antiviral effects both in vitro and in vivo. BMC Infect Dis 2012; 12:177. [PMID: 22863145 PMCID: PMC3482581 DOI: 10.1186/1471-2334-12-177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 07/28/2012] [Indexed: 11/20/2022] Open
Abstract
Background Coxsackievirus B3 is an important infectious agent of viral myocarditis, pancreatitis and aseptic meningitis, but there are no specific antiviral therapeutic reagents in clinical use. RNA interference-based technology has been developed to prevent the viral infection. Methods To evaluate the impact of RNA interference on viral replication, cytopathogenicity and animal survival, short hairpin RNAs targeting the viral 2B region (shRNA-2B) expressed by a recombinant vector (pGCL-2B) or a recombinant lentivirus (Lenti-2B) were tansfected in HeLa cells or transduced in mice infected with CVB3. Results ShRNA-2B exhibited a significant effect on inhibition of viral production in HeLa cells. Furthermore, shRNA-2B improved mouse survival rate, reduced the viral tissues titers and attenuated tissue damage compared with those of the shRNA-NC treated control group. Lenti-2B displayed more effective role in inhibition of viral replication than pGCL-2B in vivo. Conclusions Coxsackievirus B3 2B is an effective target of gene silencing against coxsackievirus B3 infection, suggesting that shRNA-2B is a potential agent for further development into a treatment for enterviral diseases.
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Affiliation(s)
- Hailan Yao
- Molecular Immunology Laboratory, Capital Institute of Pediatrics, YaBao Road 2, Beijing, 100020, China
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An artificial miRNA against HPSE suppresses melanoma invasion properties, correlating with a down-regulation of chemokines and MAPK phosphorylation. PLoS One 2012; 7:e38659. [PMID: 22719918 PMCID: PMC3376136 DOI: 10.1371/journal.pone.0038659] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/08/2012] [Indexed: 12/16/2022] Open
Abstract
Ribonucleic acid interference (RNAi) based on microRNA (miRNA) context may provide an efficient and safe therapeutic knockdown effect and can be driven by ribonucleic acid polymerase II (RNAP II). In this study, we designed and synthesized miR155-based artificial miRNAs against heparanase (HPSE) constructed with BLOCK-iT™ Pol II miR RNAi Expression Vector Kit. The expression levels of HPSE declined significantly in both the mRNA and protein levels in HPSE-miRNA transfected melanoma cells that exhibited reduction of adhesion, migration, and invasion ability in vitro and in vivo. We also observed that HPSE miRNA could inhibit the expressions of chemokines of interleukin-8 (IL8) and chemokine (C-X-C motif) ligand 1 (CXCL1), at both the transcriptional and translational levels. Further study on its probable mechanism declared that down-regulation of IL8 and CXCL1 by HPSE-miRNA may be correlated with reduced growth-factor simulated mitogen-activated kinase (MAPK) phosphorylation including p38 MAPK, c-Jun N-terminal kinase (JNK) and extracellular-signal-regulated kinase (ERK) 1 and 2, which could be rescued by miRNA incompatible mutated HPSE cDNA. In conclusion, we demonstrated that artificial miRNAs against HPSE might serve as an alterative mean of therapy to low HPSE expression and to block the adhesion, invasion, and metastasis of melanoma cells. Furthermore, miRNA-based RNAi was also a powerful tool for gene function study.
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Denizot M, Neal JW, Gasque P. Encephalitis due to emerging viruses: CNS innate immunity and potential therapeutic targets. J Infect 2012; 65:1-16. [PMID: 22484271 DOI: 10.1016/j.jinf.2012.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 02/27/2012] [Accepted: 03/08/2012] [Indexed: 12/21/2022]
Abstract
The emerging viruses represent a group of pathogens that are intimately connected to a diverse range of animal vectors. The recent escalation of air travel climate change and urbanization has meant humans will have increased risk of contacting these pathogens resulting in serious CNS infections. Many RNA viruses enter the CNS by evading the BBB due to axonal transport from the periphery. The systemic adaptive and CNS innate immune systems express pattern recognition receptors PRR (TLRs, RiG-1 and MDA-5) that detect viral nucleic acids and initiate host antiviral response. However, several emerging viruses (West Nile Fever, Influenza A, Enterovirus 71 Ebola) are recognized and internalized by host cell receptors (TLR, MMR, DC-SIGN, CD162 and Scavenger receptor B) and escape immuno surveillance by the host systemic and innate immune systems. Many RNA viruses express viral proteins WNF (E protein), Influenza A (NS1), EV71 (protein 3C), Rabies (Glycoprotein), Ebola proteins (VP24 and VP 35) that inhibit the host cell anti-virus Interferon type I response promoting virus replication and encephalitis. The therapeutic use of RNA interference methodologies to silence gene expression of viral peptides and treat emerging virus infection of the CNS is discussed.
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Affiliation(s)
- M Denizot
- GRI, Immunopathology and Infectious Disease Research Grouping (IRG, GRI), University of La Reunion, Reunion
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Improved intratumoral delivery of PEG-coated siRNA-lipoplexes by combination with metronomic S-1 dosing in a murine solid tumor model. Drug Deliv Transl Res 2012; 2:77-86. [DOI: 10.1007/s13346-012-0059-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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