1
|
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.
Collapse
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
| |
Collapse
|
2
|
Diwan R, Bhatt HN, Beaven E, Nurunnabi M. Emerging delivery approaches for targeted pulmonary fibrosis treatment. Adv Drug Deliv Rev 2024; 204:115147. [PMID: 38065244 PMCID: PMC10787600 DOI: 10.1016/j.addr.2023.115147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/02/2023] [Accepted: 11/29/2023] [Indexed: 01/01/2024]
Abstract
Pulmonary fibrosis (PF) is a progressive, and life-threatening interstitial lung disease which causes scarring in the lung parenchyma and thereby affects architecture and functioning of lung. It is an irreversible damage to lung functioning which is related to epithelial cell injury, immense accumulation of immune cells and inflammatory cytokines, and irregular recruitment of extracellular matrix. The inflammatory cytokines trigger the differentiation of fibroblasts into activated fibroblasts, also known as myofibroblasts, which further increase the production and deposition of collagen at the injury sites in the lung. Despite the significant morbidity and mortality associated with PF, there is no available treatment that efficiently and effectively treats the disease by reversing their underlying pathologies. In recent years, many therapeutic regimens, for instance, rho kinase inhibitors, Smad signaling pathway inhibitors, p38, BCL-xL/ BCL-2 and JNK pathway inhibitors, have been found to be potent and effective in treating PF, in preclinical stages. However, due to non-selectivity and non-specificity, the therapeutic molecules also result in toxicity mediated severe side effects. Hence, this review demonstrates recent advances on PF pathology, mechanism and targets related to PF, development of various drug delivery systems based on small molecules, RNAs, oligonucleotides, peptides, antibodies, exosomes, and stem cells for the treatment of PF and the progress of various therapeutic treatments in clinical trials to advance PF treatment.
Collapse
Affiliation(s)
- Rimpy Diwan
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, United States; Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX 79968, United States
| | - Himanshu N Bhatt
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, United States; Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX 79968, United States
| | - Elfa Beaven
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, United States; Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX 79968, United States
| | - Md Nurunnabi
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas El Paso, El Paso, TX 79902, United States; Department of Biomedical Engineering, College of Engineering, The University of Texas El Paso, El Paso, TX 79968, United States; The Border Biomedical Research Center, The University of Texas El Paso, El Paso, TX 79968, United States.
| |
Collapse
|
3
|
Beheshtizadeh N, Salimi A, Golmohammadi M, Ansari JM, Azami M. In-silico engineering of RNA nanoplatforms to promote the diabetic wound healing. BMC Chem 2023; 17:52. [PMID: 37291669 DOI: 10.1186/s13065-023-00969-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
One of the most notable required features of wound healing is the enhancement of angiogenesis, which aids in the acceleration of regeneration. Poor angiogenesis during diabetic wound healing is linked to a shortage of pro-angiogenic or an increase in anti-angiogenic factors. As a result, a potential treatment method is to increase angiogenesis promoters and decrease suppressors. Incorporating microRNAs (miRNAs) and small interfering RNAs (siRNAs), two forms of quite small RNA molecules, is one way to make use of RNA interference. Several different types of antagomirs and siRNAs are now in the works to counteract the negative effects of miRNAs. The purpose of this research is to locate novel antagonists for miRNAs and siRNAs that target multiple genes to promote angiogenesis and wound healing in diabetic ulcers.In this context, we used gene ontology analysis by exploring across several datasets. Following data analysis, it was processed using a systems biology approach. The feasibility of incorporating the proposed siRNAs and miRNA antagomirs into polymeric bioresponsive nanocarriers for wound delivery was further investigated by means of a molecular dynamics (MD) simulation study. Among the three nanocarriers tested (Poly (lactic-co-glycolic acid) (PLGA), Polyethylenimine (PEI), and Chitosan (CTS), MD simulations show that the integration of PLGA/hsa-mir-422a is the most stable (total energy = -1202.62 KJ/mol, Gyration radius = 2.154 nm, and solvent-accessible surface area = 408.416 nm2). With values of -25.437 KJ/mol, 0.047 nm for the Gyration radius, and 204.563 nm2 for the SASA, the integration of the second siRNA/ Chitosan took the last place. The results of the systems biology and MD simulations show that the suggested RNA may be delivered through bioresponsive nanocarriers to speed up wound healing by boosting angiogenesis.
Collapse
Affiliation(s)
- Nima Beheshtizadeh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
- Students? Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Alireza Salimi
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Advanced Technologies, School of Medicine, North Khorasan University of Medical Science, Bojnurd, Iran
| | - Mahsa Golmohammadi
- Department of Polymer Engineering and Color Technology, Amirkabir University of Technology, Tehran, Iran
| | - Javad Mohajer Ansari
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Anatomy, School of Medicine, Hormozgan University of Medical Sciences, Jomhuri Eslami Blvd, Bandar Abbas, 7919915519, Iran
| | - Mahmoud Azami
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| |
Collapse
|
4
|
Wang C, Chen L, Huang Y, Li K, Jinye A, Fan T, Zhao R, Xia X, Shen B, Du J, Liu Y. Exosome-delivered TRPP2 siRNA inhibits the epithelial-mesenchymal transition of FaDu cells. Oncol Lett 2018; 17:1953-1961. [PMID: 30675260 DOI: 10.3892/ol.2018.9752] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 10/23/2018] [Indexed: 12/14/2022] Open
Abstract
The prognosis for patients with head and neck cancer (HNC) remains poor, owing to uncontrolled tumor invasion and metastasis. Epithelial-mesenchymal transition (EMT) serves an important role in this invasion and metastasis, and transient receptor potential polycystic 2 (TRPP2) enhances metastasis and invasion by regulating EMT in human laryngeal squamous cell carcinoma. The present study examined whether exosomes/TRPP2 small interfering RNA (siRNA) complexes were able to reduce EMT by suppressing TRPP2 expression in FaDu cells, a cell line of human pharyngeal squamous cell carcinoma. Using agarose gel electrophoresis, it was determined that exosome/TRPP2 siRNA complexes were stable in the presence of nucleases and serum. A fluorescence assay and western blotting analysis was performed, and it was reported that the FaDu cells took up exosomes, the exosomes effectively delivered TRPP2 siRNA into FaDu cells and that exosome/TRPP2 siRNA complexes significantly suppressed TRPP2 protein expression levels in FaDu cells. Furthermore, expression levels of E-cadherin were significantly increased, whereas expression levels of N-cadherin and vimentin were significantly decreased in FaDu cells transfected with TRPP2 siRNA. Thus, exosome/TRPP2 siRNA complexes markedly suppressed TRPP2 expression and EMT in FaDu cells. These results suggested that further development of exosome/TRPP2 siRNA complexes for use as an RNA-based gene therapy in the treatment of HNC is warranted.
Collapse
Affiliation(s)
- Chunhui Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Lei Chen
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yuanyuan Huang
- Department of Gastroenterology and Hepatology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Kun Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Anqi Jinye
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Taotao Fan
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ren Zhao
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xianming Xia
- Department of Gastroenterology and Hepatology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Bing Shen
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Juan Du
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yehai Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| |
Collapse
|
5
|
Wang S, Wei X, Sun X, Chen C, Zhou J, Zhang G, Wu H, Guo B, Wei L. A novel therapeutic strategy for cartilage diseases based on lipid nanoparticle-RNAi delivery system. Int J Nanomedicine 2018; 13:617-631. [PMID: 29440889 PMCID: PMC5798567 DOI: 10.2147/ijn.s142797] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Cartilage degeneration affects millions of people but preventing its degeneration is a big challenge. Although RNA interference (RNAi) has been used in human trials via silencing specific genes, the cartilage RNAi has not been possible to date because the cartilage is an avascular and very dense tissue with very low permeability. Purpose The objective of this study was to develop and validate a novel lipid nanoparticle (LNP)-siRNA delivery system that can prevent cartilage degeneration by knocking down specific genes. Methods LNP transfection efficiency was evaluated in vitro and ex vivo. Indian Hedgehog (Ihh) has been correlated with cartilage degeneration. The in vivo effects of LNP-Ihh siRNA complexes on cartilage degeneration were evaluated in a rat model of surgery-induced osteoarthritis (OA). Results In vitro, 100% of chondrocytes were transfected with siRNA in the LNP-siRNA group. In accordance with the cell culture results, red positive signals could be detected even in the deep layer of cartilage tissue cultures treated by LNP-beacon. In vivo data showed that LNP is specific for cartilage, since positive signals were detected by fluorescence molecular tomography and confocal microscopy in joint cartilage injected with LNP-beacon, but not on the surface of the synovium. In the rat model of OA, intraarticular injection of LNP-Ihh siRNA attenuated OA progression, and PCR results showed LNP-Ihh siRNA exerted a positive impact on anabolic metabolism and negative impact on catabolic metabolism. Conclusion This study demonstrates that our LNP-RNAi delivery system has a significantly chondroprotective effect that attenuates cartilage degeneration and holds great promise as a powerful tool for treatment of cartilage diseases by knocking down specific genes.
Collapse
Affiliation(s)
- Shaowei Wang
- Department of Orthopaedics, The 2nd Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaochun Wei
- Department of Orthopaedics, The 2nd Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaojuan Sun
- Department of Orthopaedics, The 2nd Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Chongwei Chen
- Department of Orthopaedics, The 2nd Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jingming Zhou
- Department of Orthopaedics, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Ge Zhang
- Integrated Traditional Chinese and Western Medicine, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Heng Wu
- Integrated Traditional Chinese and Western Medicine, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Baosheng Guo
- Integrated Traditional Chinese and Western Medicine, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong
| | - Lei Wei
- Department of Orthopaedics, The 2nd Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Orthopaedics, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| |
Collapse
|
6
|
Lusthaus JA, Goldberg I. Investigational and experimental drugs for intraocular pressure reduction in ocular hypertension and glaucoma. Expert Opin Investig Drugs 2016; 25:1201-8. [DOI: 10.1080/13543784.2016.1223042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
7
|
Man DK, Chow MY, Casettari L, Gonzalez-Juarrero M, Lam JK. Potential and development of inhaled RNAi therapeutics for the treatment of pulmonary tuberculosis. Adv Drug Deliv Rev 2016; 102:21-32. [PMID: 27108702 DOI: 10.1016/j.addr.2016.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB), caused by the infection of Mycobacterium tuberculosis (Mtb), continues to pose a serious threat to public health, and the situation is worsening with the rapid emergence of multidrug resistant (MDR) TB. Current TB regimens require long duration of treatment, and their toxic side effects often lead to poor adherence and low success rates. There is an urgent need for shorter and more effective treatment for TB. In recent years, RNA interference (RNAi) has become a powerful tool for studying gene function by silencing the target genes. The survival of Mtb in host macrophages involves the attenuation of the antimicrobial responses mounted by the host cells. RNAi technology has helped to improve our understanding of how these bacilli interferes with the bactericidal effect and host immunity during TB infection. It has been suggested that the host-directed intervention by modulation of host pathways can be employed as a novel and effective therapy against TB. This therapeutic approach could be achieved by RNAi, which holds enormous potential beyond a laboratory to the clinic. RNAi therapy targeting TB is being investigated for enhancing host antibacterial capacity or improving drug efficacy on drug resistance strains while minimizing the associated adverse effects. One of the key challenges of RNAi therapeutics arises from the delivery of the RNAi molecules into the target cells, and inhalation could serve as a direct administration route for the treatment of pulmonary TB in a non-invasive manner. However, there are still major obstacles that need to be overcome. This review focuses on the RNAi candidates that are currently explored for the treatment of TB and discusses the major barriers of pulmonary RNAi delivery. From this, we hope to stimulate further studies of local RNAi therapeutics for pulmonary TB treatment.
Collapse
|
8
|
Aptamer-functionalized lipid nanoparticles targeting osteoblasts as a novel RNA interference-based bone anabolic strategy. Nat Med 2015; 21:288-94. [PMID: 25665179 DOI: 10.1038/nm.3791] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 12/02/2014] [Indexed: 12/24/2022]
Abstract
Currently, major concerns about the safety and efficacy of RNA interference (RNAi)-based bone anabolic strategies still exist because of the lack of direct osteoblast-specific delivery systems for osteogenic siRNAs. Here we screened the aptamer CH6 by cell-SELEX, specifically targeting both rat and human osteoblasts, and then we developed CH6 aptamer-functionalized lipid nanoparticles (LNPs) encapsulating osteogenic pleckstrin homology domain-containing family O member 1 (Plekho1) siRNA (CH6-LNPs-siRNA). Our results showed that CH6 facilitated in vitro osteoblast-selective uptake of Plekho1 siRNA, mainly via macropinocytosis, and boosted in vivo osteoblast-specific Plekho1 gene silencing, which promoted bone formation, improved bone microarchitecture, increased bone mass and enhanced mechanical properties in both osteopenic and healthy rodents. These results indicate that osteoblast-specific aptamer-functionalized LNPs could act as a new RNAi-based bone anabolic strategy, advancing the targeted delivery selectivity of osteogenic siRNAs from the tissue level to the cellular level.
Collapse
|
9
|
Ma Z, Yang C, Song W, Wang Q, Kjems J, Gao S. Chitosan hydrogel as siRNA vector for prolonged gene silencing. J Nanobiotechnology 2014; 12:23. [PMID: 24946934 PMCID: PMC4104730 DOI: 10.1186/1477-3155-12-23] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 06/04/2014] [Indexed: 01/13/2023] Open
Abstract
Background The periodontitis is one of the most prevalent diseases with alveolar resorption in adult people and is the main cause of the tooth loss. To investigate the possibility for protecting the loss of alveolar bone in periodontal diseases, a RNAi-based therapeutic strategy is applied for silencing RANK signaling using thermosensitive chitosan hydrogel as siRNA reservoir and vector. Results The thermosensitive chitosan hydrogel was formed from solution (PH = 7.2, at 4°C) at 37°C within 8 minutes. The degradation rates of hydrogel were ~50% and 5% (W remaining/W beginning) in the presence and absence of lysozyme, respectively, over a period of 20 days. The concurrent cumulative in vitro release of Cy3-labeled siRNA from the hydrogel was 50% and 17% over 14 days, with or without lysozyme digestion, respectively. High cell viability (>88%) was maintained for cells treated with hydrogel loaded with RANK specific siRNA and RANK knockdown was prolonged for up to 9 days when cells were incubated with siRNA/hydrogel complex. In vivo release of siRNA was investigated in a subcutaneous delivery setup in mice. The fluorescent signal from siRNA within hydrogel was remained for up to 14 days compared to less than one day for siRNA alone. Conclusions Chitosan hydrogel can potentially serve as a suitable reservoir and vector for local sustained delivery of siRNA in potential therapy.
Collapse
Affiliation(s)
| | | | | | - Qintao Wang
- State Key Laboratory of Military Stomatology, Department of Periodontology and Oral Medicine, The School of Stomatology, Fourth Military Medical University, Xi-an, China.
| | | | | |
Collapse
|
10
|
In vitro and in vivo efficacy of SYL040012, a novel siRNA compound for treatment of glaucoma. Mol Ther 2013; 22:81-91. [PMID: 24025749 DOI: 10.1038/mt.2013.216] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/03/2013] [Indexed: 12/30/2022] Open
Abstract
Glaucoma is a progressive ocular syndrome characterized by degeneration of the optic nerve and irreversible visual field loss. Elevated intraocular pressure (IOP) is the main risk factor for glaucoma. Increased IOP is the result of an imbalance between synthesis and outflow of aqueous humor (AH). Blocking β2 adrenergic receptor (ADRB2) has shown to reduce IOP by decreasing production of AH at the ciliary body (CB). SYL040012 is a siRNA designed to specifically silence ADRB2 currently under development for glaucoma treatment. Here, we show that SYL040012 specifically reduces ADRB2 expression in cell cultures and eye tissues. The compound enters the eye shortly after administration in eye drops and is rapidly distributed among structures of the anterior segment of the eye. In addition, SYL040012 is actively taken up by cells of the CB but not by cells of systemic organs such as the lungs, where inhibition of ADRB2 could cause undesirable side effects. Moreover, SYL040012 reduces IOP in normotensive and hypertensive animal models and the effect appears to be long lasting and extremely well tolerated both locally and systemically.
Collapse
|
11
|
Martínez T, Wright N, López-Fraga M, Jiménez AI, Pañeda C. Silencing human genetic diseases with oligonucleotide-based therapies. Hum Genet 2013; 132:481-93. [PMID: 23494242 DOI: 10.1007/s00439-013-1288-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 03/05/2013] [Indexed: 12/11/2022]
Abstract
RNA interference is an endogenous mechanism present in most eukaryotic cells that enables degradation of specific mRNAs. Pharmacological exploitation of this mechanism for therapeutic purposes attracted a whole amount of attention in its initial years, but was later hampered due to difficulties in delivery of the pharmacological agents to the appropriate organ or tissue. Advances in recent years have to a certain level started to address this specific issue. Genetic diseases are caused by aberrations in gene sequences or structure; these particular abnormalities are in theory easily addressable by RNAi therapeutics. Sequencing of the human genome has largely contributed to the identification of alterations responsible for genetic conditions, thus facilitating the design of compounds that can address these diseases. This review addresses the currently on-going programs with the aim of developing RNAi and other antisense compounds for the treatment of genetic conditions and the pros and cons that these products may encounter along the way. The authors have focused on those programs that have reached clinical trials or are very close to do so.
Collapse
Affiliation(s)
- Tamara Martínez
- Sylentis, PCM C/Santiago Grisolía no 2, Tres Cantos, 28760, Madrid, Spain
| | | | | | | | | |
Collapse
|
12
|
Manskikh VN, Perelmuter VM. Collateral presentation of antigens as physiological prototype for lymph node metastases. BIOCHEMISTRY (MOSCOW) 2013; 78:314-23. [DOI: 10.1134/s0006297913030152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
13
|
Pauley KM, Gauna AE, Grichtchenko II, Chan EKL, Cha S. A secretagogue-small interfering RNA conjugate confers resistance to cytotoxicity in a cell model of Sjögren's syndrome. ACTA ACUST UNITED AC 2013; 63:3116-25. [PMID: 21567383 DOI: 10.1002/art.30450] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Sjögren's syndrome (SS) is characterized by xerophthalmia and xerostomia resulting from loss of secretory function due to immune cell infiltration in lacrimal and salivary glands. Current therapeutic strategies for SS use secretagogues to induce secretion via muscarinic receptor stimulation. The purpose of this study was to create a secretagogue-small interfering RNA (siRNA) conjugate to deliver siRNA into cells via receptor-mediated endocytosis, thereby altering epithelial cell responses to external cues, such as proinflammatory or death signals, while simultaneously stimulating secretion. METHODS Based on our expertise with type 3 muscarinic receptor (M3), we used carbachol, a ligand specific for muscarinic receptor, as the secretagogue. Carbachol was synthesized with an active choline group and was conjugated with an siRNA that targets caspase 3. A human salivary gland (HSG) cell line was used to test the efficacy of this secretagogue-siRNA conjugate. RESULTS Lipofectamine transfection of the conjugate into HSG cells resulted in a 78% reduction in the expression of the caspase 3 gene, while external conjugate treatment of HSG cells resulted in intracellular calcium release and induction of endocytosis at levels similar to those of carbachol stimulation, indicating that the siRNA and carbachol portions of the conjugate retained their function after conjugation. HSG cells treated with conjugate (without Lipofectamine transfection) exhibited a 50% reduction in caspase 3 gene and protein expression, indicating that our conjugate was effective in delivering functional siRNA into cells via receptor-mediated endocytosis. Furthermore, tumor necrosis factor α-induced apoptosis was significantly reduced in conjugate-treated cells. CONCLUSION Our secretagogue-siRNA conjugate prevented cytokine-induced apoptosis in salivary gland epithelial cells, which is critical to maintaining fluid secretion and potentially reversing the clinical hallmark of SS.
Collapse
Affiliation(s)
- Kaleb M Pauley
- Department of Oral Diagnostic Sciences, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | |
Collapse
|
14
|
|
15
|
Real-time quantification of antibody–short interfering RNA conjugate in serum by antigen capture reverse transcription–polymerase chain reaction. Anal Biochem 2012; 430:171-8. [DOI: 10.1016/j.ab.2012.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/18/2012] [Accepted: 08/20/2012] [Indexed: 11/15/2022]
|
16
|
Zhang L, Yang L, Li JJ, Sun L. Potential use of nucleic acid-based agents in the sensitization of nasopharyngeal carcinoma to radiotherapy. Cancer Lett 2012; 323:1-10. [DOI: 10.1016/j.canlet.2012.03.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 03/26/2012] [Accepted: 03/26/2012] [Indexed: 11/27/2022]
|
17
|
Zhu X, Li H, Long L, Hui L, Chen H, Wang X, Shen H, Xu W. miR-126 enhances the sensitivity of non-small cell lung cancer cells to anticancer agents by targeting vascular endothelial growth factor A. Acta Biochim Biophys Sin (Shanghai) 2012; 44:519-26. [PMID: 22510476 DOI: 10.1093/abbs/gms026] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Increasing evidence suggests that hsa-miR-126 (miR-126) is down-regulated in non-small cell lung cancer (NSCLC) cell lines and the restoration of miR-126 impairs tumor cell proliferation, migration, invasion, and survival by targeting specific molecules. Here, we reported for the first time that miR-126 was involved in regulating the response of NSCLC cells to cancer chemotherapy. After transfected A549 cells with miR-126 mimic or inhibitor, we found that an elevated level of miR-126 was significantly associated with a decreased half maximal inhibitory concentration of adriamycin (ADM) and vincristine, an increased accumulation of ADM, down-regulation of vascular endothelial growth factor A (VEGFA) and multidrug resistance-associated protein 1 (MRP1), and inactivation of the Akt signaling pathway. Furthermore, enhanced expression of miR-126 suppressed the growth of A549 xenograft and inhibited the expression of VEGFA and MRP1. miR-126 could efficiently down-regulate VEGFA expression through the interaction with the VEGFA 3'-untranslated region, whereas restoration of VEGFA could partially attenuate the suppression of MRP1 by miR-126. However, LY294002, an inhibitor of the PI3K/Akt signaling pathway, diminished this effect, suggesting that enhanced expression of miR-126 increased the sensitivity of NSCLC cells to anticancer agents through negative regulation of a VEGF/PI3K/Akt/MRP1 signaling pathway.
Collapse
Affiliation(s)
- Xiaolan Zhu
- The Affiliated People's Hospital, Jiangsu University, Zhenjiang 212001, China
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Simmons O, Maples PB, Senzer N, Nemunaitis J. Ewing's Sarcoma: Development of RNA Interference-Based Therapy for Advanced Disease. ISRN ONCOLOGY 2012; 2012:247657. [PMID: 22523703 PMCID: PMC3317005 DOI: 10.5402/2012/247657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/04/2011] [Indexed: 12/12/2022]
Abstract
Ewing's sarcoma tumors are associated with chromosomal translocation between the EWS gene and the ETS transcription factor gene. These unique target sequences provide opportunity for RNA interference(i)-based therapy. A summary of RNAi mechanism and therapeutically designed products including siRNA, shRNA and bi-shRNA are described. Comparison is made between each of these approaches. Systemic RNAi-based therapy, however, requires protected delivery to the Ewing's sarcoma tumor site for activity. Delivery systems which have been most effective in preclinical and clinical testing are reviewed, followed by preclinical assessment of various silencing strategies with demonstration of effectiveness to EWS/FLI-1 target sequences. It is concluded that RNAi-based therapeutics may have testable and achievable activity in management of Ewing's sarcoma.
Collapse
Affiliation(s)
| | | | - Neil Senzer
- Gradalis, Inc., Dallas, TX 75201, USA
- Mary Crowley Cancer Research Centers, Dallas, TX 75201, USA
- Texas Oncology, PA, Dallas, TX 75251, USA
- Medical City Dallas Hospital, Dallas, TX 75230, USA
| | - John Nemunaitis
- Gradalis, Inc., Dallas, TX 75201, USA
- Mary Crowley Cancer Research Centers, Dallas, TX 75201, USA
- Texas Oncology, PA, Dallas, TX 75251, USA
- Medical City Dallas Hospital, Dallas, TX 75230, USA
| |
Collapse
|
19
|
Zhang G, Guo B, Wu H, Tang T, Zhang BT, Zheng L, He Y, Yang Z, Pan X, Chow H, To K, Li Y, Li D, Wang X, Wang Y, Lee K, Hou Z, Dong N, Li G, Leung K, Hung L, He F, Zhang L, Qin L. A delivery system targeting bone formation surfaces to facilitate RNAi-based anabolic therapy. Nat Med 2012; 18:307-14. [PMID: 22286306 DOI: 10.1038/nm.2617] [Citation(s) in RCA: 297] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/13/2011] [Indexed: 02/06/2023]
Abstract
Metabolic skeletal disorders associated with impaired bone formation are a major clinical challenge. One approach to treat these defects is to silence bone-formation-inhibitory genes by small interference RNAs (siRNAs) in osteogenic-lineage cells that occupy the niche surrounding the bone-formation surfaces. We developed a targeting system involving dioleoyl trimethylammonium propane (DOTAP)-based cationic liposomes attached to six repetitive sequences of aspartate, serine, serine ((AspSerSer)(6)) for delivering siRNAs specifically to bone-formation surfaces. Using this system, we encapsulated an osteogenic siRNA that targets casein kinase-2 interacting protein-1 (encoded by Plekho1, also known as Plekho1). In vivo systemic delivery of Plekho1 siRNA in rats using our system resulted in the selective enrichment of the siRNAs in osteogenic cells and the subsequent depletion of Plekho1. A bioimaging analysis further showed that this approach markedly promoted bone formation, enhanced the bone micro-architecture and increased the bone mass in both healthy and osteoporotic rats. These results indicate (AspSerSer)(6)-liposome as a promising targeted delivery system for RNA interference-based bone anabolic therapy.
Collapse
Affiliation(s)
- Ge Zhang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Thakur N, Qureshi A, Kumar M. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res 2012; 40:D230-6. [PMID: 22139916 PMCID: PMC3245049 DOI: 10.1093/nar/gkr1147] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/04/2011] [Accepted: 11/09/2011] [Indexed: 12/22/2022] Open
Abstract
RNAi technology has been emerging as a potential modality to inhibit viruses during past decade. In literature a few siRNA databases have been reported that focus on targeting human and mammalian genes but experimentally validated viral siRNA databases are lacking. We have developed VIRsiRNAdb, a manually curated database having comprehensive details of 1358 siRNA/shRNA targeting viral genome regions. Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. Important fields included in the database are siRNA sequence, virus subtype, target genome region, cell type, target object, experimental assay, efficacy, off-target and siRNA matching with reference viral sequences. Database also provides the users with facilities of advance search, browsing, data submission, linking to external databases and useful siRNA analysis tools especially siTarAlign which align the siRNA with reference viral genomes or user defined sequences. VIRsiRNAdb contains extensive details of siRNA/shRNA targeting 42 important human viruses including influenza virus, hepatitis B virus, HPV and SARS Corona virus. VIRsiRNAdb would prove useful for researchers in picking up the best viral siRNA for antiviral therapeutics development and also for developing better viral siRNA design tools. The database is freely available at http://crdd.osdd.net/servers/virsirnadb.
Collapse
Affiliation(s)
| | | | - Manoj Kumar
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh-160036, India
| |
Collapse
|
21
|
Nemunaitis J, Rao DD, Liu SH, Brunicardi FC. Personalized cancer approach: using RNA interference technology. World J Surg 2011; 35:1700-14. [PMID: 21557010 DOI: 10.1007/s00268-011-1100-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Normal cellular survival is dependent on the cooperative expression of genes' signaling through a broad array of DNA patterns. Cancer, however, has an Achilles' heel. Its altered cellular survival is dependent on a limited subset of signals through mutated DNA, possibly as few as three. Identification and control of these signals through the use of RNA interference (RNAi) technology may provide a unique clinical opportunity for the management of cancer that employs genomic-proteomic profiling to provide a molecular characterization of the cancer, leading to targeted therapy customized to an individual cancer signal. Such an approach has been described as "personalized therapy." The present review identifies unique developing technology that employs RNAi as a method to target, and therefore block, signaling from mutated DNA and describes a clinical pathway toward its development in cancer therapy.
Collapse
Affiliation(s)
- John Nemunaitis
- Mary Crowley Cancer Research Centers, 1700 Pacific Avenue, Suite 1100, Dallas, TX, USA.
| | | | | | | |
Collapse
|
22
|
Abstract
MicroRNAs (miRNAs) are small physiological non-coding RNAs that regulate gene expression through an RNA interference (RNAi) mechanism. The expression of miRNAs is tightly controlled both spatially and temporally. Aberrant miRNA expression has been correlated with various cancers. Recent findings suggest that some miRNAs can function as tumor suppressors or oncogenes. In model experiments, the cancer phenotype of some cells can be reverted to normal when the cells are treated with miRNA mimics or inhibitors. Here, we discuss in brief the potential utility of miRNA-based cancer therapy as well as the current limitations thwarting their useful clinical application.
Collapse
Affiliation(s)
- Man Lung Yeung
- Department of Microbiology, the University of Hong Kong, SAR, China
| | - Kuan-Teh Jeang
- Molecular Virology Section, Laboratory of Molecular Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA
| |
Collapse
|
23
|
Yeung ML, Jeang KT. Roles of miRNAs in virus-mediated cellular transformation: lessons from human T-cell leukemia virus type 1. Future Virol 2011. [DOI: 10.2217/fvl.11.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
miRNAs are small noncoding RNAs of ˜18–25 nucleotides that contribute to the regulation of a diverse variety of biological pathways. Perturbed miRNA expression is seen in many diseases, including cancers. Here, we first discuss the oncogenic and tumor suppressor roles of miRNA, including the roles played by miRNAs in the replication of some oncogenic viruses. Next, using human T-cell leukemia virus type 1 as an example, we discuss the contributions of virus-induced miRNAs in human T-cell leukemia virus type 1-transformation of human cells. Finally, we briefly survey the therapeutic potential of miRNA mimics or anti-miRNAs, antagomirs, to reverse cancer phenotypes.
Collapse
Affiliation(s)
- Man Lung Yeung
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
- Research Centre of Infection & Immunology, The University of Hong Kong, Hong Kong
- Department of Microbiology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Kuan-Teh Jeang
- Molecular Virology Section, Laboratory of Molecular Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 4, Room 306, 9000 Rockville Pike, Bethesda, MD 20892–0460, USA
| |
Collapse
|
24
|
Rousseau J, Escriou V, Lamoureux F, Brion R, Chesneau J, Battaglia S, Amiaud J, Scherman D, Heymann D, Rédini F, Trichet V. Formulated siRNAs targeting Rankl prevent osteolysis and enhance chemotherapeutic response in osteosarcoma models. J Bone Miner Res 2011; 26:2452-62. [PMID: 21713988 DOI: 10.1002/jbmr.455] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The development of osteosarcoma, the most common malignant primary bone tumor is characterized by a vicious cycle established between tumor proliferation and paratumor osteolysis. This osteolysis is mainly regulated by the receptor activator of nuclear factor κB ligand (RANKL). Preclinical studies have demonstrated that Rankl blockade by soluble receptors is an effective strategy to prevent osteolytic lesions leading to osteosarcoma inhibition. A new therapeutic option could be to directly inhibit Rankl expression by small interfering RNAs (Rkl-siRNAs) and combine these molecules with chemotherapy to counteract the osteosarcoma development more efficiently. An efficient siRNA sequence directed against both mouse and rat mRNAs coding Rankl was first validated in vitro and tested in two models of osteosarcoma: a syngenic osteolytic POS-1 model induced in immunocompetent mice and a xenograft osteocondensant model of rat OSRGA in athymic mice. Intratumor injections of Rankl-directed siRNAs in combination with the cationic liposome RPR209120/DOPE reduced the local and systemic Rankl production and protected bone from paratumor osteolysis. Although Rkl-siRNAs alone had no effect on tumor development in both osteosarcoma models, it significantly blocked tumor progression when combined with ifosfamide compared with chemotherapy alone. Our results indicate that siRNAs could be delivered using cationic liposomes and thereby could inhibit Rankl production in a specific manner in osteosarcoma models. Moreover, the Rankl inhibition mediated by RNA interference strategy improves the therapeutic response of primary osteosarcoma to chemotherapy.
Collapse
|
25
|
Zhou C, Shan Y, Zhao H, He P. Biological effects of lentivirus-mediated shRNA targeting collagen type I on the mesangial cells of rats. Ren Fail 2011; 33:334-40. [PMID: 21401360 DOI: 10.3109/0886022x.2011.559679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM To investigate the effects of lentivirus-mediated shRNA targeting collagen type I on the mesangial cells of rats and the feasibility of lentivirus-mediated shRNA delivery through renal parenchyma injection. METHODS Anti-collagen type I shRNA lentiviral vector was constructed, and rat mesangial cells were transfected with transfection enhancer (control group), blank lentiviral vectors (pSC-GFP group), and pSC-GFP/Col I lentiviral vectors (pSC-GFP/Col I group). Transfection efficiency and cell cycle were determined by flow cytometry. RT-PCR and Western blot were performed to detect the mRNA and protein expressions of Col I. Cell proliferation was evaluated by 3-(4,5)-dimethylthiahiazo-3, 5-di-phenytetrazolium-romide (MTT) assay and direct counting, and apoptosis was detected using AnnexinV/PE staining. The feasibility of renal parenchyma injection of lentiviral vectors was assessed. RESULTS The transfection efficiency was 75.42%. The expressions of collagen type I in pSC-GFP/Col I group was markedly decreased when compared with the other two groups. PSC-GFP/Col I group was higher than pSC-GFP group in the inhibition efficiency of mesangial cell after transfection. Results revealed that pSC-GFP/Col I transfection induced apoptosis to a certain extent. The proportion of cells in G2/M phase in pSC-GFP/Col I group and pSC-GFP group was higher than that in control group after of transfection. Moreover, cells arrested in S phase were markedly increased. Our results also revealed renal injection of lentivirus-mediated shRNA was feasible. CONCLUSION Lentivirus-mediated shRNA targeting collagen type I could stably and efficiently transfect rat mesangial cells and significantly suppressed collagen type I expressions with acceptable safety. Renal injection of Col I lentivirus-mediated shRNA was also feasible.
Collapse
Affiliation(s)
- Chunhua Zhou
- Department of Nephrology, Navy General Hospital, Haidian, Beijing, PR China.
| | | | | | | |
Collapse
|
26
|
Ali Ashfaq U, Ansar M, Sarwar MT, Javed T, Rehman S, Riazuddin S. Post-transcriptional inhibition of hepatitis C virus replication through small interference RNA. Virol J 2011; 8:112. [PMID: 21388559 PMCID: PMC3086529 DOI: 10.1186/1743-422x-8-112] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 03/10/2011] [Indexed: 12/11/2022] Open
Abstract
Background Hepatitis C Virus (HCV) infection is a major health problem throughout world that causes acute and chronic infection which resulted in liver fibrosis, hepatocellular carcinoma and death. The only therapy currently available for HCV infection is the combination of pegylated interferon alpha (PEG-IFN α) and ribavirin. This therapy can effectively clear the virus infection in only 50% of infected individuals. Hence, there is a dire need to develop antiviral agents against HCV. Results This study was design to examine the ability of exogenous small interfering RNAs (siRNAs) to block the replication of HCV in human liver cells. In the present study six 21-bp siRNAs were designed against different regions of HCV non-structural genes (NS2, NS3 serine protease/helicase, NS4Band NS5B RNA dependent RNA polymerase). siRNAs were labeled as NS2si241, NS3si-229, NS3si-858, NS4Bsi-166, NS5Bsi-241 and NS5Bsi-1064. We found that siRNAs against HCV NS2- NS5B efficiently inhibit HCV replication in Huh-7 cells. Our results demonstrated that siRNAs directed against HCV NS3 (NS3si-229 and NS3si-858) showed 58% and 88% reduction in viral titer respectively. Moreover, NS4Bsi-166 and NS5Bsi-1064 exhibited a dramatic reduction in HCV viral RNA and resulted in greater than 90% inhibition at a 20 μM concentration, while NS2si-241 showed 27% reduction in viral titer. No significant inhibition was detected in cells transfected with the negative control siRNA. Conclusion Our results suggest that siRNAs targeting against HCV non-structural genes (NS2-NS5B) efficiently inhibit HCV replication and combination of these siRNAs of different targets and interferon will be better option to treat HCV infection throughout the world.
Collapse
Affiliation(s)
- Usman Ali Ashfaq
- Division of Molecular Medicine, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | | | | | | | | | | |
Collapse
|
27
|
Méndez-Ortega MC, Restrepo S, Rodríguez-R LM, Pérez I, Mendoza JC, Martínez AP, Sierra R, Rey-Benito GJ. An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1. Virol J 2010; 7:369. [PMID: 21172023 PMCID: PMC3022682 DOI: 10.1186/1743-422x-7-369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/20/2010] [Indexed: 12/25/2022] Open
Abstract
Background HIV-1 can be inhibited by RNA interference in vitro through the expression of short hairpin RNAs (shRNAs) that target conserved genome sequences. In silico shRNA design for HIV has lacked a detailed study of virus variability constituting a possible breaking point in a clinical setting. We designed shRNAs against HIV-1 considering the variability observed in naïve and drug-resistant isolates available at public databases. Methods A Bioperl-based algorithm was developed to automatically scan multiple sequence alignments of HIV, while evaluating the possibility of identifying dominant and subdominant viral variants that could be used as efficient silencing molecules. Student t-test and Bonferroni Dunn correction test were used to assess statistical significance of our findings. Results Our in silico approach identified the most common viral variants within highly conserved genome regions, with a calculated free energy of ≥ -6.6 kcal/mol. This is crucial for strand loading to RISC complex and for a predicted silencing efficiency score, which could be used in combination for achieving over 90% silencing. Resistant and naïve isolate variability revealed that the most frequent shRNA per region targets a maximum of 85% of viral sequences. Adding more divergent sequences maintained this percentage. Specific sequence features that have been found to be related with higher silencing efficiency were hardly accomplished in conserved regions, even when lower entropy values correlated with better scores. We identified a conserved region among most HIV-1 genomes, which meets as many sequence features for efficient silencing. Conclusions HIV-1 variability is an obstacle to achieving absolute silencing using shRNAs designed against a consensus sequence, mainly because there are many functional viral variants. Our shRNA cocktail could be truly effective at silencing dominant and subdominant naïve viral variants. Additionally, resistant isolates might be targeted under specific antiretroviral selective pressure, but in both cases these should be tested exhaustively prior to clinical use.
Collapse
Affiliation(s)
- María C Méndez-Ortega
- Grupo de Virología SRNL, Instituto Nacional de Salud, Avenida Calle 26 No, 51 - 20 ZONA 6 CAN, Bogotá, Colombia.
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Abstract
RNA interference (RNAi) is an evolutionary conserved mechanism for specific gene silencing. This mechanism has great potential for use in targeted cancer therapy. Understanding the RNAi mechanism has led to the development of several novel RNAi-based therapeutic approaches currently in the early phases of clinical trials. It remains difficult to effectively deliver the nucleic acids required in vivo to initiate RNAi, and intense effort is under way in developing effective and targeted systemic delivery systems for RNAi. Description of in vivo delivery systems is not the focus of this review. In this review, we cover the rationale for pursuing personalised cancer therapy with RNAi, briefly review the mechanism of each major RNAi therapeutic technique, summarise and sample recent results with animal models applying RNAi for cancer, and provide an update on current clinical trials with RNAi-based therapeutic agents for cancer therapy. RNAi-based cancer therapy is still in its infancy, and there are numerous obstacles and issues that need to be resolved before its application in personalised therapy focusing on patient-cancer-specific targets can become standard cancer treatment, either alone or in combination with other treatments.
Collapse
|
29
|
Falschlehner C, Steinbrink S, Erdmann G, Boutros M. High-throughput RNAi screening to dissect cellular pathways: A how-to guide. Biotechnol J 2010; 5:368-76. [DOI: 10.1002/biot.200900277] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
30
|
Grillari J, Grillari-Voglauer R. Novel modulators of senescence, aging, and longevity: Small non-coding RNAs enter the stage. Exp Gerontol 2010; 45:302-11. [PMID: 20080172 DOI: 10.1016/j.exger.2010.01.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Revised: 12/08/2009] [Accepted: 01/08/2010] [Indexed: 02/06/2023]
Abstract
During the last decade evidence has accumulated that the aging process is driven by limited allocation of energy to somatic maintenance resulting in accumulation of stochastic damage. This damage, affecting molecules, cells, and tissues, is counteracted by genetically programmed repair, the efficiency of which thus importantly determines the life and 'health span' of organisms. Therefore, understanding the regulation of gene expression during cellular and organismal aging as well as upon exposure to various damaging events is important to understand the biology of aging and to positively influence the health span. The recent identification of small non-coding RNAs (ncRNAs), has added an additional layer of complexity to the regulation of gene expression with the classes of endogenous small inhibitory RNAs (siRNAs), PIWI-interacting RNAs (piRNAs), QDE1-interacting RNAs (qiRNAs) and microRNAs (miRNAs). Some of these ncRNAs have not yet been identified in mammalian cells and are dependent on RNA-dependent RNA polymerases. The first mammalian enzyme with such activity has only now emerged and surprisingly consists of the catalytic subunit of telomerase (hTERT) together with RMPR, an alternative RNA component. The so far most studied small non-coding RNAs, miRNAs, however, are now increasingly found to operate in the complex network of cellular aging. Recent findings show that (i) miRNAs are regulated during cellular senescence in vitro, (ii) they contribute to tissue regeneration by regulation of stem cell function, and (iii) at least one miRNA modulates the life span of the model organism C. elegans. Additionally, (iv) they act as inhibitors of proteins mediating the insulin/IGF1 and target of rapamycin (TOR) signalling, both of which are conserved modulators of organism life span. Here we will give an overview on the current status of these topics. Since little is so far known on the functions of small ncRNAs in the context of aging and longevity, the entry of the RNA world into the field of biogerontology certainly holds additional surprises and promises. Even more so, as miRNAs are implicated in many age-associated pathologies, and as RNAi and miRNA based therapeutics are on their way to clinics.
Collapse
Affiliation(s)
- Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences Vienna, Austria.
| | | |
Collapse
|
31
|
Coy S, Vasiljeva L. The exosome and heterochromatin : multilevel regulation of gene silencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:105-21. [PMID: 21713681 DOI: 10.1007/978-1-4419-7841-7_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Heterochromatic silencing is important for repressing gene expression, protecting cells against viral invasion, maintaining DNA integrity and for proper chromosome segregation. Recently, it has become apparent that expression of eukaryotic genomesis far more complex than had previously been anticipated. Strikingly, it has emerged that most of the genome is transcribed including intergenic regions and heterochromatin, calling for us to re-address the question of how gene silencing is regulated and re-evaluate the concept ofheterochromatic regions of the genome being transcriptionally inactive. Although heterochromatic silencing can be regulated at the transcriptional level, RNA degrading activities supplied either by the exosome complex or RNAi also significantly contribute to this process. The exosome also regulates noncoding RNAs (ncRNAs) involved in the establishment of heterochromatin, further underscoring its role as the major cellular machinery involved in RNA processing and turn-over. This multilevel control of the transcriptome may be utilized to ensure greater accuracy of gene expression and allow distinction between functional transcripts and background noise. In this chapter, we will discuss the regulation of gene silencing across species, with special emphasis on the exosome's contribution to the process. We will also discuss the links between transcriptional and posttranscriptional mechanisms for gene silencing and their impact on the regulation of eukaryotic transcriptomes.
Collapse
Affiliation(s)
- Sarah Coy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | | |
Collapse
|
32
|
Journal Watch. Pharmaceut Med 2009; 23. [PMCID: PMC7100411 DOI: 10.1007/bf03256789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|