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Panda K, Alagarasu K, Tagore R, Paingankar M, Kumar S, Jeengar MK, Cherian S, Parashar D. RNAi-Induced Gene Silencing against Chikungunya and COVID-19: What Have We Learned So Far, and What Is the Way Forward? Viruses 2024; 16:1489. [PMID: 39339965 PMCID: PMC11437507 DOI: 10.3390/v16091489] [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: 07/19/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
RNA interference (RNAi) is a process in which small RNA molecules (such as small interfering RNAs or siRNAs) bind to specific messenger RNAs (mRNAs), leading to its degradation and inhibition of protein synthesis. Our studies have shown that RNAi can effectively silence genes involved in the replication of the Chikungunya virus (CHIKV) in cells. However, these investigations were performed only in laboratory settings and have yet to be tested in human clinical trials. Researchers need to conduct more research to determine the safety and efficacy of RNAi-based therapies as a therapeutic agent to treat viral infections. In this review, the history of evolution of siRNA as an inhibitor of protein synthesis, along with its current developments, is discussed based on our experience. Moreover, this review examines the hurdles and future implications associated with siRNA based therapeutic approaches.
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Affiliation(s)
- Kingshuk Panda
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
| | - Kalichamy Alagarasu
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Rajarshee Tagore
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
| | - Mandar Paingankar
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
| | - Satyendra Kumar
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
| | - Manish Kumar Jeengar
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
| | - Sarah Cherian
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- Bioinformatics Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Deepti Parashar
- Dengue & Chikungunya Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India; (K.P.); (K.A.); (R.T.); (M.P.); (S.K.); (M.K.J.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
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Bishani A, Meschaninova MI, Zenkova MA, Chernolovskaya EL. The Impact of Chemical Modifications on the Interferon-Inducing and Antiproliferative Activity of Short Double-Stranded Immunostimulating RNA. Molecules 2024; 29:3225. [PMID: 38999177 PMCID: PMC11243415 DOI: 10.3390/molecules29133225] [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: 05/30/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
A short 19 bp dsRNA with 3'-trinucleotide overhangs acting as immunostimulating RNA (isRNA) demonstrated strong antiproliferative action against cancer cells, immunostimulatory activity through activation of cytokines and Type-I IFN secretion, as well as anti-tumor and anti-metastatic effects in vivo. The aim of this study was to determine the tolerance of chemical modifications (2'-F, 2'-OMe, PS, cholesterol, and amino acids) located at different positions within this isRNA to its ability to activate the innate immune system. The obtained duplexes were tested in vivo for their ability to activate the synthesis of interferon-α in mice, and in tumor cell cultures for their ability to inhibit their proliferation. The obtained data show that chemical modifications in the composition of isRNA have different effects on its individual functions, including interferon-inducing and antiproliferative effects. The effect of modifications depends not only on the type of modification but also on its location and the surrounding context of the modifications. This study made it possible to identify leader patterns of modifications that enhance the properties of isRNA: F2/F2 and F2_S/F2 for interferon-inducing activity, as well as F2_S5/F2_S5, F2-NH2/F2-NH2, and Ch-F2/Ch-F2 for antiproliferative action. These modifications can improve the pharmacokinetic and pharmacodynamic properties, as well as increase the specificity of isRNA action to obtain the desired effect.
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Affiliation(s)
| | | | | | - Elena L. Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.B.); (M.I.M.); (M.A.Z.)
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Sánchez-Meza LV, Bello-Rios C, Eloy JO, Gómez-Gómez Y, Leyva-Vázquez MA, Petrilli R, Bernad-Bernad MJ, Lagunas-Martínez A, Medina LA, Serrano-Bello J, Organista-Nava J, Illades-Aguiar B. Cationic Liposomes Carrying HPV16 E6-siRNA Inhibit the Proliferation, Migration, and Invasion of Cervical Cancer Cells. Pharmaceutics 2024; 16:880. [PMID: 39065577 PMCID: PMC11279637 DOI: 10.3390/pharmaceutics16070880] [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: 06/03/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
The E6 and E7 oncoproteins of high-risk types of human papillomavirus (HR-HPV) are crucial for the development of cervical cancer (CC). Small interfering RNAs (siRNAs) are explored as novel therapies that silence these oncogenes, but their clinical use is hampered by inefficient delivery systems. Modification (pegylation) with polyethylene glycol (PEG) of liposomal siRNA complexes (siRNA lipoplexes) may improve systemic stability. We studied the effect of siRNA targeting HPV16 E6, delivered via cationic liposomes (lipoplexes), on cellular processes in a cervical carcinoma cell line (CaSki) and its potential therapeutic use. Lipoplexes-PEG-HPV16 E6, composed of DOTAP, Chol, DOPE, and DSPE-PEG2000 were prepared. The results showed that pegylation (5% DSPE-PEG2000) provided stable siRNA protection, with a particle size of 86.42 ± 3.19 nm and a complexation efficiency of over 80%; the siRNA remained stable for 30 days. These lipoplexes significantly reduced HPV16 E6 protein levels and restored p53 protein expression, inhibiting carcinogenic processes such as proliferation by 25.74%, migration (95.7%), and cell invasion (97.8%) at concentrations of 20 nM, 200 nM, and 80 nM, respectively. In conclusion, cationic lipoplexes-PEG-HPV16 E6 show promise as siRNA carriers for silencing HPV16 E6 in CC.
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Affiliation(s)
- Luz Victoria Sánchez-Meza
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Chilpancingo 39090, Guerrero, Mexico; (L.V.S.-M.); (C.B.-R.); (Y.G.-G.); (M.A.L.-V.)
| | - Ciresthel Bello-Rios
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Chilpancingo 39090, Guerrero, Mexico; (L.V.S.-M.); (C.B.-R.); (Y.G.-G.); (M.A.L.-V.)
| | - Josimar O. Eloy
- Department of Pharmacy, Dentistry and Nursing, Faculty of Pharmacy, Federal University of Ceará, 1210 Pastor Samuel Munguba Street, Fortaleza 60430-160, CE, Brazil;
| | - Yazmín Gómez-Gómez
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Chilpancingo 39090, Guerrero, Mexico; (L.V.S.-M.); (C.B.-R.); (Y.G.-G.); (M.A.L.-V.)
| | - Marco Antonio Leyva-Vázquez
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Chilpancingo 39090, Guerrero, Mexico; (L.V.S.-M.); (C.B.-R.); (Y.G.-G.); (M.A.L.-V.)
| | - Raquel Petrilli
- Institute of Health Sciences, University of International Integration of the Afro-Brazilian Lusophony, Redenção 62790-000, CE, Brazil;
| | | | - Alfredo Lagunas-Martínez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca 62100, Morelos, Mexico;
| | - Luis Alberto Medina
- Instituto de Física, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico;
- Unidad de Investigación Biomédica en Cáncer INCan/UNAM, Instituto Nacional de Cancerología, Actualmente Hospital Ángeles Puebla, Ciudad de Mexico 14080, Mexico
| | - Janeth Serrano-Bello
- Facultad de Odontología, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04360, Mexico;
| | - Jorge Organista-Nava
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Chilpancingo 39090, Guerrero, Mexico; (L.V.S.-M.); (C.B.-R.); (Y.G.-G.); (M.A.L.-V.)
| | - Berenice Illades-Aguiar
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Chilpancingo 39090, Guerrero, Mexico; (L.V.S.-M.); (C.B.-R.); (Y.G.-G.); (M.A.L.-V.)
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Singh D, Singh L, Kaur S, Arora A. Nucleic acids based integrated macromolecular complexes for SiRNA delivery: Recent advancements. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-24. [PMID: 38693628 DOI: 10.1080/15257770.2024.2347499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/18/2024] [Indexed: 05/03/2024]
Abstract
The therapeutic potential of small interfering RNA (siRNA) is monumental, offering a pathway to silence disease-causing genes with precision. However, the delivery of siRNA to target cells in-vivo remains a formidable challenge, owing to degradation by nucleases, poor cellular uptake and immunogenicity. This overview examines recent advancements in the design and application of nucleic acid-based integrated macromolecular complexes for the efficient delivery of siRNA. We dissect the innovative delivery vectors developed in recent years, including lipid-based nanoparticles, polymeric carriers, dendrimer complexes and hybrid systems that incorporate stimuli-responsive elements for targeted and controlled release. Advancements in bioconjugation techniques, active targeting strategies and nanotechnology-enabled delivery platforms are evaluated for their contribution to enhancing siRNA delivery. It also addresses the complex interplay between delivery system design and biological barriers, highlighting the dynamic progress and remaining hurdles in translating siRNA therapies from bench to bedside. By offering a comprehensive overview of current strategies and emerging technologies, we underscore the future directions and potential impact of siRNA delivery systems in personalized medicine.
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Affiliation(s)
- Dilpreet Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
- University Centre for Research and Development, Chandigarh University, Mohali, India
| | - Lovedeep Singh
- University Institute of Pharma Sciences, Chandigarh University, Mohali, India
| | - Simranjeet Kaur
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Akshita Arora
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
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Klementieva NV, Lunev EA, Shmidt AA, Loseva EM, Savchenko IM, Svetlova EA, Galkin II, Polikarpova AV, Usachev EV, Vassilieva SG, Marina VI, Dzhenkova MA, Romanova AD, Agutin AV, Timakova AA, Reshetov DA, Egorova TV, Bardina MV. RNA Interference Effectors Selectively Silence the Pathogenic Variant GNAO1 c.607 G > A In Vitro. Nucleic Acid Ther 2024; 34:90-99. [PMID: 38215303 DOI: 10.1089/nat.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
RNA interference (RNAi)-based therapeutics hold the potential for dominant genetic disorders, enabling sequence-specific inhibition of pathogenic gene products. We aimed to direct RNAi for the selective suppression of the heterozygous GNAO1 c.607 G > A variant causing GNAO1 encephalopathy. By screening short interfering RNA (siRNA), we showed that GNAO1 c.607G>A is a druggable target for RNAi. The si1488 candidate achieved at least twofold allelic discrimination and downregulated mutant protein to 35%. We created vectorized RNAi by incorporating the si1488 sequence into the short hairpin RNA (shRNA) in the adeno-associated virus (AAV) vector. The shRNA stem and loop were modified to improve the transcription, processing, and guide strand selection. All tested shRNA constructs demonstrated selectivity toward mutant GNAO1, while tweaking hairpin structure only marginally affected the silencing efficiency. The selectivity of shRNA-mediated silencing was confirmed in the context of AAV vector transduction. To conclude, RNAi effectors ranging from siRNA to AAV-RNAi achieve suppression of the pathogenic GNAO1 c.607G>A and discriminate alleles by the single-nucleotide substitution. For gene therapy development, it is crucial to demonstrate the benefit of these RNAi effectors in patient-specific neurons and animal models of the GNAO1 encephalopathy.
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Affiliation(s)
- Natalia V Klementieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgenii A Lunev
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Shmidt
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Irina M Savchenko
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Svetlova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Ivan I Galkin
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Polikarpova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgeny V Usachev
- Laboratory of Translational Biomedicine, Gamaleya National Research Center for Epidemiology, Moscow, Russia
| | - Svetlana G Vassilieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | | | - Marina A Dzhenkova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Anna D Romanova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Anton V Agutin
- State Budgetary Healthcare Institution of Moscow Region "Balashikha Hospital," Balashikha, Russia
| | - Anna A Timakova
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | - Tatiana V Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Maryana V Bardina
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Nguyen TT, Nguyen Thi YV, Chu DT. RNA therapeutics: Molecular mechanisms, and potential clinical translations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:65-82. [PMID: 38360006 DOI: 10.1016/bs.pmbts.2023.12.012] [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
RNA therapies involve the utilization of natural and artificial RNA molecules to control the expression and function of cellular genes and proteins. Initializing from 1990s, RNA therapies now show the rapid growth in the development and application of RNA therapeutics for treating various conditions, especially for undruggable diseases. The outstanding success of recent mRNA vaccines against COVID-19 infection again highlighted the important role of RNA therapies in future medicine. In this review, we will first briefly provide the crucial investigations on RNA therapy, from the first pieces of discovery on RNA molecules to clinical applications of RNA therapeutics. We will then classify the mechanisms of RNA therapeutics from various classes in the treatment of diseases. To emphasize the huge potential of RNA therapies, we also provide the key RNA products that have been on clinical trials or already FDA-approved. With comprehensive knowledge on RNA biology, and the advances in analysis, technology and computer-aid science, RNA therapies can bring a promise to be more expanding to the market in the future.
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Affiliation(s)
- Tiep Tien Nguyen
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Epibiotech Co. Ltd., Incheon, Republic of Korea
| | - Yen Vi Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Nguyen DH, Uddin MJ, Al-Tawfiq JA, Memish ZA, Chu DT. RNA therapeutics for diarrhea. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:295-309. [PMID: 38458741 DOI: 10.1016/bs.pmbts.2023.12.004] [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: 03/10/2024]
Abstract
Diarrhea is caused by a variety of bacterial and viral agents, inflammatory conditions, medications, and hereditary conditions. Secretory diarrhea involves several ion and solute transporters, activation of the cyclic nucleotide and Ca2+ signaling pathways, as well as intestinal epithelial secretion. In many cases of secretory diarrhea, activation of Cl- channels, such as the cystic transmembrane conduction regulator and the Ca2+stimulated Cl- channel fibrosis, promote secretion while concurrently inhibiting Na+ transport expressing fluid absorption. Current diarrhea therapies include rehydration and electrolyte replacement via oral rehydration solutions, as well as medications that target peristalsis or fluid secretion. The rising understanding of RNA function and its importance in illness has encouraged the use of various RNAs to operate selectively on "untreatable" proteins, transcripts, and genes. Some RNA-based medications have received clinical approval, while others are currently in research or preclinical studies. Despite major obstacles in the development of RNA-based therapies, many approaches have been investigated to improve intracellular RNA trafficking and metabolic stability.
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Affiliation(s)
| | - Md Jamal Uddin
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh; Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea
| | - Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States; Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ziad A Memish
- Director Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Zhang Z, Huang Y, Li J, Su F, Kuo JC, Hu Y, Zhao X, Lee RJ. Antitumor Activity of Anti-miR-21 Delivered through Lipid Nanoparticles. Adv Healthc Mater 2023; 12:e2202412. [PMID: 36412002 PMCID: PMC11468686 DOI: 10.1002/adhm.202202412] [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: 09/20/2022] [Revised: 11/17/2022] [Indexed: 11/23/2022]
Abstract
The ability of lipid nanoparticles (LNPs) to deliver nucleic acids have shown a great therapeutic potential to treat a variety of diseases. Here, an optimized formulation of QTsome lipid nanoparticles (QTPlus) is utilized to deliver an anti-miR-21 (AM21) against cancer. The miR-21 downstream gene regulation and antitumor activity is evaluated using mouse and human cancer cells and macrophages. The antitumor activity of QTPlus encapsulating AM21 (QTPlus-AM21) is further evaluated in combination with erlotinib and atezolizumab (ATZ). QTPlus-AM21 demonstrates a superior miR-21-dependent gene regulation and eventually inhibits A549 non-small cell lung cancer growth in vitro. QTPlus-AM21 further induces chemo-sensitization of A549 cells to erlotinib with a combination index of 0.6 in inhibiting A549 cell growth. When systemically administers to MC38 tumor-bearing mouse model, QTPlus-AM21 exhibits an antitumor immune response with over 80% tumor growth inhibition (TGI%) and over twofold and fourfold PD-1 and PD-L1 upregulation in tumors and spleens. The combination therapy of QTPlus-AM21 and ATZ further shows a higher antitumor response (TGI% over 90%) and successfully increases M1 macrophages and CD8 T cells into TME. This study provides new insights into the antitumor mechanism of AM21 and shows great promise of QTPlus-AM21 in combination with chemotherapies and immunotherapies.
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Affiliation(s)
- Zhongkun Zhang
- Division of Pharmaceutics and PharmacologyCollege of PharmacyThe Ohio State University500 W 12th AvenueColumbusOH43210USA
| | - Yirui Huang
- Division of Pharmaceutics and PharmacologyCollege of PharmacyThe Ohio State University500 W 12th AvenueColumbusOH43210USA
| | - Jing Li
- Zhejiang Haichang Biotechnology Co., Ltd.HangzhouZhejiang310000P. R. China
| | - Fei Su
- Zhejiang Haichang Biotechnology Co., Ltd.HangzhouZhejiang310000P. R. China
| | - Jimmy Chun‐Tien Kuo
- Division of Pharmaceutics and PharmacologyCollege of PharmacyThe Ohio State University500 W 12th AvenueColumbusOH43210USA
| | - Yingwen Hu
- The Whiteoak Group, Inc.RockvilleMD20855USA
| | | | - Robert J. Lee
- Division of Pharmaceutics and PharmacologyCollege of PharmacyThe Ohio State University500 W 12th AvenueColumbusOH43210USA
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Paul A, Muralidharan A, Biswas A, Venkatesh Kamath B, Joseph A, Alex AT. siRNA Therapeutics and its Challenges: Recent Advances in Effective Delivery for Cancer Therapy. OPENNANO 2022. [DOI: 10.1016/j.onano.2022.100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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10
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Białkowska K, Komorowski P, Gomez-Ramirez R, de la Mata FJ, Bryszewska M, Miłowska K. Interaction of Cationic Carbosilane Dendrimers and Their siRNA Complexes with MCF-7 Cells Cultured in 3D Spheroids. Cells 2022; 11:cells11101697. [PMID: 35626734 PMCID: PMC9140188 DOI: 10.3390/cells11101697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/01/2023] Open
Abstract
Cationic dendrimers are effective carriers for the delivery of siRNA into cells; they can penetrate cell membranes and protect nucleic acids against RNase degradation. Two types of dendrimers (CBD-1 and CBD-2) and their complexes with pro-apoptotic siRNA (Mcl-1 and Bcl-2) were tested on MCF-7 cells cultured as spheroids. Cytotoxicity of dendrimers and dendriplexes was measured using the live–dead test and Annexin V-FITC Apoptosis Detection Kit (flow cytometry). Uptake of dendriplexes was examined using flow cytometry and confocal microscopy. The live–dead test showed that for cells in 3D, CBD-2 is more toxic than CBD-1, contrasting with the data for 2D cultures. Attaching siRNA to a dendrimer molecule did not lead to increased cytotoxic effect in cells, either after 24 or 48 h. Measurements of apoptosis did not show a high increase in the level of the apoptosis marker after 24 h exposure of spheroids to CBD-2 and its dendriplexes. Measurements of the internalization of dendriplexes and microscopy images confirmed that the dendriplexes were transported into cells of the spheroids. Flow cytometry analysis of internalization indicated that CBD-2 transported siRNAs more effectively than CBD-1. Cytotoxic effects were visible after incubation with 3 doses of complexes for CBD-1 and both siRNAs.
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Affiliation(s)
- Kamila Białkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (M.B.); (K.M.)
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland;
- Correspondence:
| | - Piotr Komorowski
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland;
- Department of Biophysics, Institute of Materials Science, Lodz University of Technology, 1/15 Stefanowskiego St., 90-924 Lodz, Poland
| | - Rafael Gomez-Ramirez
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - Francisco Javier de la Mata
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - Maria Bryszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (M.B.); (K.M.)
| | - Katarzyna Miłowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (M.B.); (K.M.)
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11
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Shiohama Y, Fujita R, Sonokawa M, Hisano M, Kotake Y, Krstic-Demonacos M, Demonacos C, Kashiwazaki G, Kitayama T, Fujii M. Elimination of Off-Target Effect by Chemical Modification of 5′-End of Small Interfering RNA. Nucleic Acid Ther 2022; 32:438-447. [DOI: 10.1089/nat.2021.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yasuo Shiohama
- Environmental and Biological Information Group, Tropical Biosphere Research Centre, University of the Ryukyus, Nishihara, Japan
| | - Ryosuke Fujita
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Maika Sonokawa
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Masaaki Hisano
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Yojiro Kotake
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
| | - Marija Krstic-Demonacos
- School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - Constantinos Demonacos
- Division of Pharmacy and Optometry, Faculty of Biology Medicine and Health, School of Health Science, University of Manchester, Manchester, United Kingdom
| | - Gengo Kashiwazaki
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Takashi Kitayama
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Masayuki Fujii
- Department of Biological & Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Iizuka, Japan
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12
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Romero-López C, Ramos-Lorente SE, Berzal-Herranz A. In Vitro Methods to Decipher the Structure of Viral RNA Genomes. Pharmaceuticals (Basel) 2021; 14:ph14111192. [PMID: 34832974 PMCID: PMC8620418 DOI: 10.3390/ph14111192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/05/2023] Open
Abstract
RNA viruses encode essential information in their genomes as conserved structural elements that are involved in efficient viral protein synthesis, replication, and encapsidation. These elements can also establish complex networks of RNA-RNA interactions, the so-called RNA interactome, to shape the viral genome and control different events during intracellular infection. In recent years, targeting these conserved structural elements has become a promising strategy for the development of new antiviral tools due to their sequence and structural conservation. In this context, RNA-based specific therapeutic strategies, such as the use of siRNAs have been extensively pursued to target the genome of different viruses. Importantly, siRNA-mediated targeting is not a straightforward approach and its efficiency is highly dependent on the structure of the target region. Therefore, the knowledge of the viral structure is critical for the identification of potentially good target sites. Here, we describe detailed protocols used in our laboratory for the in vitro study of the structure of viral RNA genomes. These protocols include DMS (dimethylsulfate) probing, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) analysis, and HMX (2'-hydroxyl molecular interference). These methodologies involve the use of high-throughput analysis techniques that provide extensive information about the 3D folding of the RNA under study and the structural tuning derived from the interactome activity. They are therefore a good tool for the development of new RNA-based antiviral compounds.
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13
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Białkowska K, Miłowska K, Michlewska S, Sokołowska P, Komorowski P, Lozano-Cruz T, Gomez-Ramirez R, de la Mata FJ, Bryszewska M. Interaction of Cationic Carbosilane Dendrimers and Their siRNA Complexes with MCF-7 Cells. Int J Mol Sci 2021; 22:ijms22137097. [PMID: 34281151 PMCID: PMC8269323 DOI: 10.3390/ijms22137097] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
The application of siRNA in gene therapy is mainly limited because of the problems with its transport into cells. Utilization of cationic dendrimers as siRNA carriers seems to be a promising solution in overcoming these issues, due to their positive charge and ability to penetrate cell membranes. The following two types of carbosilane dendrimers were examined: CBD-1 and CBD-2. Dendrimers were complexed with pro-apoptotic siRNA (Mcl-1 and Bcl-2) and the complexes were characterized by measuring their zeta potential, circular dichroism and fluorescence of ethidium bromide associated with dendrimers. CBD-2/siRNA complexes were also examined by agarose gel electrophoresis. Both dendrimers form complexes with siRNA. Moreover, the cellular uptake and influence on the cell viability of the dendrimers and dendriplexes were evaluated using microscopic methods and XTT assay on MCF-7 cells. Microscopy showed that both dendrimers can transport siRNA into cells; however, a cytotoxicity assay showed differences in the toxicity of these dendrimers.
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Affiliation(s)
- Kamila Białkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (K.M.); (M.B.)
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland; (P.S.); (P.K.)
- Correspondence:
| | - Katarzyna Miłowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (K.M.); (M.B.)
| | - Sylwia Michlewska
- Laboratory of Microscopic Imaging and Specialized Biological Techniques, Faculty of Biology and Environmental Protection, University of Lodz, Banacha12/16, 90-237 Lodz, Poland;
| | - Paulina Sokołowska
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland; (P.S.); (P.K.)
- Department of Pharmacology and Toxicology, Medical University of Lodz, Żeligowskiego St. 7/9, 90-752 Lodz, Poland
| | - Piotr Komorowski
- Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., 114/116 Dubois St., 93-465 Lodz, Poland; (P.S.); (P.K.)
- Department of Biophysics, Institute of Materials Science, Lodz University of Technology, 1/15 Stefanowskiego St., 90-924 Lodz, Poland
| | - Tania Lozano-Cruz
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (T.L.-C.); (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Rafael Gomez-Ramirez
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (T.L.-C.); (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Francisco Javier de la Mata
- Department of Organic and Inorganic Chemistry, IQAR, University of Alcalá, 28805 Madrid, Spain; (T.L.-C.); (R.G.-R.); (F.J.d.l.M.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Maria Bryszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; (K.M.); (M.B.)
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14
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Splichal RC, Gredell JA, Vogel EB, Malefyt A, Comiskey G, Smith MR, Chan C, Walton SP. Modulating Polymer-siRNA Binding Does Not Promote Polyplex-Mediated Silencing. Nucleic Acid Ther 2021; 31:229-236. [PMID: 32749923 PMCID: PMC8215420 DOI: 10.1089/nat.2020.0857] [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: 02/10/2020] [Accepted: 07/02/2020] [Indexed: 11/12/2022] Open
Abstract
The development of delivery vehicles for small interfering RNAs (siRNAs) remains a bottleneck to widespread clinical use. Cationic polymers represent an important class of potential delivery vehicles. In this study, we used alkyne-azide click chemistry to synthesize a variety of cationic poly(propargyl glycolide) backbone polymers to bind and deliver siRNAs. We demonstrated control over the binding interactions of these polymers and siRNAs by varying binding strength by more than three orders of magnitude. Binding strength was found to meet or exceed that of commercially available transfection agents. Our polymers effectively delivered siRNAs with no detectable cytotoxicity. Despite accumulation of siRNAs at levels comparable with commercial reagents, we did not observe silencing of the targeted protein. The implications of our results for future siRNA delivery vehicle design are discussed.
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Affiliation(s)
- R. Chauncey Splichal
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
| | - Joseph A. Gredell
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
- Novozymes Biologicals, Inc, Salem, Virginia, USA
| | - Erin B. Vogel
- Department of Chemistry, and Michigan State University, East Lansing, Michigan, USA
- Dow Chemical Co, Midland, Michigan, USA
| | - Amanda Malefyt
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
- McKetta Department of Chemical & Bioprocess Engineering, Trine University, Angola, Indiana, USA
| | - Georgina Comiskey
- Department of Chemistry, and Michigan State University, East Lansing, Michigan, USA
- ChemTrend LP, Howell, Michigan, USA
| | - Milton R. Smith
- Department of Chemistry, and Michigan State University, East Lansing, Michigan, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - S. Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, USA
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15
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Hu X, Boeckman CJ, Cong B, Steimel JP, Richtman NM, Sturtz K, Wang Y, Walker CA, Yin J, Unger A, Farris C, Lu AL. Characterization of DvSSJ1 transcripts targeting the smooth septate junction (SSJ) of western corn rootworm (Diabrotica virgifera virgifera). Sci Rep 2020; 10:11139. [PMID: 32636422 PMCID: PMC7341793 DOI: 10.1038/s41598-020-68014-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022] Open
Abstract
Transgenic maize plants expressing dsRNA targeting western corn rootworm (WCR, Diabrotica virgifera virgifera) DvSSJ1 mRNA, a Drosophila snakeskin (ssk) ortholog, show insecticidal activity and significant plant protection from WCR damage. The gene encodes a membrane protein associated with the smooth sepate junction (SSJ) which is required for intestinal barrier function. To understand the active RNA form that leads to the mortality of WCR larvae by DvSSJ1 RNA interference (RNAi), we characterized transgenic plants expressing DvSSJ1 RNA transcripts targeting WCR DvSSJ1 mRNA. The expression of the silencing cassette results in the full-length transcript of 901 nucleotides containing a 210 bp inverted fragment of the DvSSJ1 gene, the formation of a double-stranded RNA (dsRNA) transcript and siRNAs in transgenic plants. Our artificial diet-feeding study indicates that dsRNAs greater than or equal to approximately 60 base-pairs (bp) are required for DvSSJ1 insecticidal activity. Impact of specificity of dsRNA targeting DvSSJ1 mRNA on insecticidal activities was also evaluated in diet bioassay, which showed a single nucleotide mutation can have a significant impact or abolish diet activities against WCR. These results provide insights as to the functional forms of plant-delivered dsRNA for the protection of transgenic maize from WCR feeding damage and information contributing to the risk assessment of transgenic maize expressing insecticidal dsRNA.
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Affiliation(s)
- Xu Hu
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA.
| | - Chad J Boeckman
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA.
| | - Bin Cong
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA.
| | - Joe P Steimel
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Nina M Richtman
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Kristine Sturtz
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Yiwei Wang
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Carl A Walker
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Jiaming Yin
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Anita Unger
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Caitlin Farris
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
| | - Albert L Lu
- Corteva Agriscience, 7300 NW 62nd Ave., Johnston, IA, 50131, USA
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16
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Vocelle D, Chan C, Walton SP. Endocytosis Controls siRNA Efficiency: Implications for siRNA Delivery Vehicle Design and Cell-Specific Targeting. Nucleic Acid Ther 2020; 30:22-32. [PMID: 31718426 PMCID: PMC6987736 DOI: 10.1089/nat.2019.0804] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
While small interfering RNAs (siRNAs) are commonly used for laboratory studies, development of siRNA therapeutics has been slower than expected, due, in part, to a still limited understanding of the endocytosis and intracellular trafficking of siRNA-containing complexes. With the recent characterization of multiple clathrin-/caveolin-independent endocytic pathways, that is, those mediated by Graf1, Arf6, and flotillin, it has become clear that the endocytic mechanism influences subsequent intracellular processing of the internalized cargo. To explore siRNA delivery in light of these findings, we developed a novel assay that differentiates uptake by each of the endocytic pathways and can be used to determine whether endocytosis by a pathway leads to the initiation of RNA interference (RNAi). Using Lipofectamine 2000 (LF2K), we determined the endocytosis pathway leading to active silencing (whether by clathrin, caveolin, Arf6, Graf1, flotillin, or macropinocytosis) across multiple cell types (HeLa, H1299, HEK293, and HepG2). We showed that LF2K is internalized by Graf1-, Arf6-, or flotillin-mediated endocytosis for the initiation of RNAi, depending on cell type. In addition, we found that a portion of siRNA-containing complexes is internalized by pathways that do not lead to initiation of silencing. Inhibition of these pathways enhanced intracellular levels of siRNAs with concomitant enhancement of silencing.
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Affiliation(s)
- Daniel Vocelle
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - S. Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan
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17
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Bartoszewski R, Sikorski AF. Editorial focus: understanding off-target effects as the key to successful RNAi therapy. Cell Mol Biol Lett 2019; 24:69. [PMID: 31867046 PMCID: PMC6902517 DOI: 10.1186/s11658-019-0196-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/03/2019] [Indexed: 12/21/2022] Open
Abstract
With the first RNA interference (RNAi) drug (ONPATTRO (patisiran)) on the market, we witness the RNAi therapy field reaching a critical turning point, when further improvements in drug candidate design and delivery pipelines should enable fast delivery of novel life changing treatments to patients. Nevertheless, ignoring parallel development of RNAi dedicated in vitro pharmacological profiling aiming to identify undesirable off-target activity may slow down or halt progress in the RNAi field. Since academic research is currently fueling the RNAi development pipeline with new therapeutic options, the objective of this article is to briefly summarize the basics of RNAi therapy, as well as to discuss how to translate basic research into better understanding of related drug candidate safety profiles early in the process.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F. Sikorski
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
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18
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Current Transport Systems and Clinical Applications for Small Interfering RNA (siRNA) Drugs. Mol Diagn Ther 2019; 22:551-569. [PMID: 29926308 DOI: 10.1007/s40291-018-0338-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Small interfering RNAs (siRNAs) are an attractive new agent with potential as a therapeutic tool because of its ability to inhibit specific genes for many conditions, including viral infections and cancers. However, despite this potential, many challenges remain, including off-target effects, difficulties with delivery, immune responses, and toxicity. Traditional genetic vectors do not guarantee that siRNAs will silence genes in vivo. Rational design strategies, such as chemical modification, viral vectors, and non-viral vectors, including cationic liposomes, polymers, nanocarriers, and bioconjugated siRNAs, provide important opportunities to overcome these challenges. We summarize the results of research into vector delivery of siRNAs as a therapeutic agent from their design to clinical trials in ophthalmic diseases, cancers, respiratory diseases, and liver virus infections. Finally, we discuss the current state of siRNA delivery methods and the need for greater understanding of the requirements.
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19
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To accelerate the Zika beat: Candidate design for RNA interference-based therapy. Virus Res 2018; 255:133-140. [DOI: 10.1016/j.virusres.2018.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/11/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022]
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20
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He S, Cen B, Liao L, Wang Z, Qin Y, Wu Z, Liao W, Zhang Z, Ji A. A tumor-targeting cRGD-EGFR siRNA conjugate and its anti-tumor effect on glioblastoma in vitro and in vivo. Drug Deliv 2017; 24:471-481. [PMID: 28181832 PMCID: PMC8241002 DOI: 10.1080/10717544.2016.1267821] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is an important anti-tumor target. The development of novel molecular-targeted anti-tumor drugs that can target the interior of tumor cells and specifically silence EGFR expression is valuable and promising. In this work, a promising anti-tumor conjugate comprising methoxy-modified EGFR siRNA and cyclic arginine-glycine-aspartic acid (cRGD) peptides, which selectively bind to αvβ3 integrins, was synthesized and examined. To prepare cRGD-EGFR siRNA (cRGD-siEGFR), cRGD was covalently conjugated to the 5'-end of an siRNA sense strand using a thiol-maleimide linker. The cellular uptake and cytotoxicity of cRGD-siEGFR in vitro were tested using an αvβ3-positive U87MG cell line. In vivo bio-distribution, anti-tumor activity, immunogenicity and toxicity were investigated in a nude mouse tumor model through repeated i.v. administration of cRGD-siEGFR (7 times over a 48 h interval). Analyses of in vitro data showed that cRGD-siEGFR silenced EGFR expression effectively, with high tumor targeting ability. Administration of cRGD-siEGFR to tumor-bearing nude mice led to significant inhibition of tumor growth, obvious reduction of EGFR expression and down-regulation of EGFR mRNA and protein in tumor tissue. Furthermore, serum biochemistry and pathological section evaluation did not indicate any serious toxicity of cRGD-siEGFR in vivo. cRGD-siEGFR is likely a promising candidate with high targeting ability, substantial anti-tumor effects and low toxicity in vitro and in vivo.
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Affiliation(s)
- Shuai He
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and.,b Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou , China
| | - Bohong Cen
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Lumin Liao
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Zhen Wang
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Yixin Qin
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Zhuomin Wu
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Wenjie Liao
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Zhongyi Zhang
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and
| | - Aimin Ji
- a Department of Pharmacy, Zhujiang Hospital of Southern Medical University , Guangzhou , China and.,b Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou , China
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21
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Kunz-Schughart LA, Dubrovska A, Peitzsch C, Ewe A, Aigner A, Schellenburg S, Muders MH, Hampel S, Cirillo G, Iemma F, Tietze R, Alexiou C, Stephan H, Zarschler K, Vittorio O, Kavallaris M, Parak WJ, Mädler L, Pokhrel S. Nanoparticles for radiooncology: Mission, vision, challenges. Biomaterials 2016; 120:155-184. [PMID: 28063356 DOI: 10.1016/j.biomaterials.2016.12.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 12/29/2022]
Abstract
Cancer is one of the leading non-communicable diseases with highest mortality rates worldwide. About half of all cancer patients receive radiation treatment in the course of their disease. However, treatment outcome and curative potential of radiotherapy is often impeded by genetically and/or environmentally driven mechanisms of tumor radioresistance and normal tissue radiotoxicity. While nanomedicine-based tools for imaging, dosimetry and treatment are potential keys to the improvement of therapeutic efficacy and reducing side effects, radiotherapy is an established technique to eradicate the tumor cells. In order to progress the introduction of nanoparticles in radiooncology, due to the highly interdisciplinary nature, expertise in chemistry, radiobiology and translational research is needed. In this report recent insights and promising policies to design nanotechnology-based therapeutics for tumor radiosensitization will be discussed. An attempt is made to cover the entire field from preclinical development to clinical studies. Hence, this report illustrates (1) the radio- and tumor-biological rationales for combining nanostructures with radiotherapy, (2) tumor-site targeting strategies and mechanisms of cellular uptake, (3) biological response hypotheses for new nanomaterials of interest, and (4) challenges to translate the research findings into clinical trials.
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Affiliation(s)
- Leoni A Kunz-Schughart
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Anna Dubrovska
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Claudia Peitzsch
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Alexander Ewe
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Germany
| | - Achim Aigner
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Germany
| | - Samuel Schellenburg
- Institute of Pathology, University Hospital, Carl Gustav Carus, TU Dresden, Germany
| | - Michael H Muders
- Institute of Pathology, University Hospital, Carl Gustav Carus, TU Dresden, Germany
| | - Silke Hampel
- Leibniz Institute of Solid State and Material Research Dresden, 01171 Dresden, Germany
| | - Giuseppe Cirillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, CS, Italy
| | - Francesca Iemma
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, CS, Italy
| | - Rainer Tietze
- ENT-Department, Section for Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius Professorship, University Hospital Erlangen, Erlangen, Germany
| | - Christoph Alexiou
- ENT-Department, Section for Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius Professorship, University Hospital Erlangen, Erlangen, Germany
| | - Holger Stephan
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, 01314 Dresden, Germany
| | - Kristof Zarschler
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, 01314 Dresden, Germany
| | - Orazio Vittorio
- Children's Cancer Institute Australia, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, Sydney, UNSW, Australia
| | - Maria Kavallaris
- Children's Cancer Institute Australia, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, Sydney, UNSW, Australia
| | - Wolfgang J Parak
- Fachbereich Physik, Philipps Universität Marburg, 35037 Marburg, Germany; CIC Biomagune, 20009 San Sebastian, Spain
| | - Lutz Mädler
- Foundation Institute of Materials Science (IWT), Department of Production Engineering, University of Bremen, 28359 Bremen, Germany
| | - Suman Pokhrel
- Foundation Institute of Materials Science (IWT), Department of Production Engineering, University of Bremen, 28359 Bremen, Germany.
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22
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Angart PA, Carlson RJ, Adu-Berchie K, Walton SP. Terminal Duplex Stability and Nucleotide Identity Differentially Control siRNA Loading and Activity in RNA Interference. Nucleic Acid Ther 2016; 26:309-317. [PMID: 27399870 PMCID: PMC5067871 DOI: 10.1089/nat.2016.0612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/06/2016] [Indexed: 01/17/2023] Open
Abstract
Efficient short interfering RNA (siRNA)-mediated gene silencing requires selection of a sequence that is complementary to the intended target and possesses sequence and structural features that encourage favorable functional interactions with the RNA interference (RNAi) pathway proteins. In this study, we investigated how terminal sequence and structural characteristics of siRNAs contribute to siRNA strand loading and silencing activity and how these characteristics ultimately result in a functionally asymmetric duplex in cultured HeLa cells. Our results reiterate that the most important characteristic in determining siRNA activity is the 5' terminal nucleotide identity. Our findings further suggest that siRNA loading is controlled principally by the hybridization stability of the 5' terminus (Nucleotides: 1-2) of each siRNA strand, independent of the opposing terminus. Postloading, RNA-induced silencing complex (RISC)-specific activity was found to be improved by lower hybridization stability in the 5' terminus (Nucleotides: 3-4) of the loaded siRNA strand and greater hybridization stability toward the 3' terminus (Nucleotides: 17-18). Concomitantly, specific recognition of the 5' terminal nucleotide sequence by human Argonaute 2 (Ago2) improves RISC half-life. These findings indicate that careful selection of siRNA sequences can maximize both the loading and the specific activity of the intended guide strand.
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Affiliation(s)
- Phillip A Angart
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - Rebecca J Carlson
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University , East Lansing, Michigan
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Vocelle D, Chesniak OM, Malefyt AP, Comiskey G, Adu-Berchie K, Smith MR, Chan C, Walton SP. Dextran functionalization enhances nanoparticle-mediated siRNA delivery and silencing. TECHNOLOGY 2016; 4:42. [PMID: 27774502 PMCID: PMC5072529 DOI: 10.1142/s2339547816400100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Understanding the endocytosis and intracellular trafficking of short interfering RNA (siRNA) delivery vehicle complexes remains a critical bottleneck in designing siRNA delivery vehicles for highly active RNA interference (RNAi)-based therapeutics. In this study, we show that dextran functionalization of silica nanoparticles enhanced uptake and intracellular delivery of siRNAs in cultured cells. Using pharmacological inhibitors for endocytotic pathways, we determined that our complexes are endocytosed via a previously unreported mechanism for siRNA delivery in which dextran initiates scavenger receptor-mediated endocytosis through a clathrin/caveolin-independent process. Our findings suggest that siRNA delivery efficiency could be enhanced by incorporating dextran into existing delivery platforms to activate scavenger receptor activity across a variety of target cell types.
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Affiliation(s)
- Daniel Vocelle
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Olivia M Chesniak
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Amanda P Malefyt
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Georgina Comiskey
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Kwasi Adu-Berchie
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Milton R Smith
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1226, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1226, USA
| | - S Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824-1226, USA
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siRNA Versus miRNA as Therapeutics for Gene Silencing. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e252. [PMID: 26372022 PMCID: PMC4877448 DOI: 10.1038/mtna.2015.23] [Citation(s) in RCA: 661] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/18/2015] [Indexed: 02/06/2023]
Abstract
Discovered a little over two decades ago, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are noncoding RNAs with important roles in gene regulation. They have recently been investigated as novel classes of therapeutic agents for the treatment of a wide range of disorders including cancers and infections. Clinical trials of siRNA- and miRNA-based drugs have already been initiated. siRNAs and miRNAs share many similarities, both are short duplex RNA molecules that exert gene silencing effects at the post-transcriptional level by targeting messenger RNA (mRNA), yet their mechanisms of action and clinical applications are distinct. The major difference between siRNAs and miRNAs is that the former are highly specific with only one mRNA target, whereas the latter have multiple targets. The therapeutic approaches of siRNAs and miRNAs are therefore very different. Hence, this review provides a comparison between therapeutic siRNAs and miRNAs in terms of their mechanisms of action, physicochemical properties, delivery, and clinical applications. Moreover, the challenges in developing both classes of RNA as therapeutics are also discussed.
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Effective Small Interfering RNA Therapy to Treat CLCN7-dependent Autosomal Dominant Osteopetrosis Type 2. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e248. [PMID: 26325626 PMCID: PMC4877447 DOI: 10.1038/mtna.2015.21] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/15/2015] [Indexed: 01/14/2023]
Abstract
In about 70% of patients affected by autosomal dominant osteopetrosis type 2 (ADO2), osteoclast activity is reduced by heterozygous mutations of the CLCN7 gene, encoding the ClC-7 chloride/hydrogen antiporter. CLCN7(G215R)-, CLCN7(R767W)-, and CLCN7(R286W)-specific siRNAs silenced transfected mutant mRNA/EGFP in HEK293 cells, in RAW264.7 cells and in human osteoclasts, with no change of CLCN7(WT) mRNA and no effect of scrambled siRNA on the mutant transcripts. Osteoclasts from Clcn7(G213R) ADO2 mice showed reduced bone resorption, a condition rescued by Clcn7(G213R)-specific siRNA. Treatment of ADO2 mice with Clcn7(G213R)-specific siRNA induced increase of bone resorption variables and decrease of trabecular bone mass, leading to an overall improvement of the osteopetrotic bone phenotype. Treatment did not induce overt adverse effects and was effective also with siRNAs specific for other mutants. These results demonstrate that a siRNA-based experimental treatment of ADO2 is feasible, and underscore a translational impact for future strategy to cure this therapeutically neglected form of osteopetrosis.
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Kapilov-Buchman Y, Lellouche E, Michaeli S, Lellouche JP. Unique Surface Modification of Silica Nanoparticles with Polyethylenimine (PEI) for siRNA Delivery Using Cerium Cation Coordination Chemistry. Bioconjug Chem 2015; 26:880-9. [PMID: 25830668 DOI: 10.1021/acs.bioconjchem.5b00100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The discovery of RNA interference (RNAi) as a naturally occurring mechanism for gene knockdown has attracted considerable attention toward the use of small interfering RNAs (siRNAs) for therapeutic purposes. The main obstacles of harnessing siRNAs as drugs are their inefficient delivery to cells and off-target effect making clinical applications very challenging. The positively charged, branched 25 kDa polyethylenimine (b-PEI) polymer is widely regarded as one of the most efficient nonviral commercially available transfection agents. However, it has also been shown that 25 kDa b-PEI is highly cytotoxic and can readily lead to cell death. In this specific context, this study presents the preparation and characterization of innovative 25 kDa b-PEI-decorated polycationic silica nanoparticles (SiO2 NPs) for cellular siRNA delivery and subsequent gene silencing. A new method of b-PEI attachment onto the SiO2 NP surface has been developed that makes use of cerium(III) cations (Ce(3+)), a lanthanide group element, as an effective noncovalent inorganic linker between both polyNH2-SiO2 nanoparticle (SPA NPs) surface and polycationic 25 kDa b-PEI polymer. Two resulting novel SPA-Ce-PEI NPs consist of similar amounts of b-PEI, while possessing different amounts of Ce(3+). Various analytical techniques (TEM, DLS, ζ potential, ICP-AES, and TGA) have been used to deeply characterize NPs physicochemical qualities. The observed results of Ce(3+)-dependent gene silencing and cytotoxic activities led us to conclusions about the role of Ce(3+)-N bonding during the chemical attachment of the 25 kDa b-PEI shell onto the NP surface.
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Affiliation(s)
- Yekaterina Kapilov-Buchman
- †Department of Chemistry, Faculty of Exact Sciences, ‡The Mina and Everard Goodman Faculty of Life Sciences, and §Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Emmanuel Lellouche
- †Department of Chemistry, Faculty of Exact Sciences, ‡The Mina and Everard Goodman Faculty of Life Sciences, and §Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Shulamit Michaeli
- †Department of Chemistry, Faculty of Exact Sciences, ‡The Mina and Everard Goodman Faculty of Life Sciences, and §Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002 Israel
| | - Jean-Paul Lellouche
- †Department of Chemistry, Faculty of Exact Sciences, ‡The Mina and Everard Goodman Faculty of Life Sciences, and §Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, 5290002 Israel
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Dzmitruk V, Szulc A, Shcharbin D, Janaszewska A, Shcharbina N, Lazniewska J, Novopashina D, Buyanova M, Ionov M, Klajnert-Maculewicz B, Gómez-Ramirez R, Mignani S, Majoral JP, Muñoz-Fernández MA, Bryszewska M. Anticancer siRNA cocktails as a novel tool to treat cancer cells. Part (B). Efficiency of pharmacological action. Int J Pharm 2015; 485:288-94. [PMID: 25796120 DOI: 10.1016/j.ijpharm.2015.03.034] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/10/2015] [Accepted: 03/14/2015] [Indexed: 12/14/2022]
Abstract
This paper examines a perspective to use newly engineered nanomaterials as effective and safe carriers for gene therapy of cancer. Three different groups of cationic dendrimers (PAMAM, phosphorus, and carbosilane) were complexed with anticancer siRNA and the biophysical properties of the dendriplexes created were analyzed. The potential of the dendrimers as nanocarriers for anticancer Bcl-xl, Bcl-2, Mcl-1 siRNAs and additionally a scrambled sequence siRNA has been explored. Dendrimer/siRNA complexes were characterised by various methods including fluorescence, zeta potential, dynamic light scattering, circular dichroism, gel electrophoresis and transmission electron microscopy. In this part of study, the transfection of complexes in HeLa and HL-60 cells was analyzed using both single apoptotic siRNAs and a mixture (cocktail) of them. Cocktails were more effective than single siRNAs, allowing one to decrease siRNAs concentration in treating cells. The dendrimers were compared as siRNA carriers, the most effective being the phosphorus-based ones. However, they were also the most cytotoxic on their own, so that in this regard the application of all dendrimers in anticancer therapy will be discussed.
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Affiliation(s)
- Volha Dzmitruk
- Institute of Biophysics and Cell Engineering of NASB, Minsk, Belarus
| | - Aleksandra Szulc
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Dzmitry Shcharbin
- Institute of Biophysics and Cell Engineering of NASB, Minsk, Belarus.
| | - Anna Janaszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Natallia Shcharbina
- Republican Research and Practical Center of Neurology and Neurosurgery, Minsk, Belarus
| | - Joanna Lazniewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Darya Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina Buyanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Maksim Ionov
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Barbara Klajnert-Maculewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland; Leibniz-Institut fur Polymerforschung Dresden e.V., HoheStrasse 6,01069 Dresden, Germany
| | - Rafael Gómez-Ramirez
- Departamento Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares, Spain; Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, CIBER-BBN, Spain
| | - Serge Mignani
- Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR, 860, Paris, France
| | | | - Maria Angeles Muñoz-Fernández
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, CIBER-BBN, Spain; Laboratorio de Inmunobiología Molecular, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Maria Bryszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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28
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Thang BN, Ho TB, Kanda T. A semi-supervised tensor regression model for siRNA efficacy prediction. BMC Bioinformatics 2015; 16:80. [PMID: 25888201 PMCID: PMC4379720 DOI: 10.1186/s12859-015-0495-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Short interfering RNAs (siRNAs) can knockdown target genes and thus have an immense impact on biology and pharmacy research. The key question of which siRNAs have high knockdown ability in siRNA research remains challenging as current known results are still far from expectation. RESULTS This work aims to develop a generic framework to enhance siRNA knockdown efficacy prediction. The key idea is first to enrich siRNA sequences by incorporating them with rules found for designing effective siRNAs and representing them as enriched matrices, then to employ the bilinear tensor regression to predict knockdown efficacy of those matrices. Experiments show that the proposed method achieves better results than existing models in most cases. CONCLUSIONS Our model not only provides a suitable siRNA representation but also can predict siRNA efficacy more accurate and stable than most of state-of-the-art models. Source codes are freely available on the web at: http://www.jaist.ac.jp/\~bao/BiLTR/ .
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Affiliation(s)
- Bui Ngoc Thang
- School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan. .,University of Engineering and Technology, Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, Vietnam.
| | - Tu Bao Ho
- School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, Japan. .,John von Neumann Institute, Vietnam National University Ho at Chi Minh City, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh, Vietnam.
| | - Tatsuo Kanda
- Graduate School of Medicine, Chiba University, 1-8-1 Inohahan, Chuo-ku, Chiba, Japan.
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Saeed M, Zeino M, Kadioglu O, Volm M, Efferth T. Overcoming of P-glycoprotein-mediated multidrug resistance of tumors in vivo by drug combinations. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.synres.2014.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Malefyt AP, Wu M, Vocelle DB, Kappes SJ, Lindeman SD, Chan C, Walton SP. Improved asymmetry prediction for short interfering RNAs. FEBS J 2014; 281:320-30. [PMID: 24393396 DOI: 10.1111/febs.12599] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/28/2013] [Accepted: 09/26/2013] [Indexed: 01/10/2023]
Abstract
In the development of RNA interference therapeutics, merely selecting short interfering RNA (siRNA) sequences that are complementary to the mRNA target does not guarantee target silencing. Current algorithms for selecting siRNAs rely on many parameters, one of which is asymmetry, often predicted through calculation of the relative thermodynamic stabilities of the two ends of the siRNA. However, we have previously shown that highly active siRNA sequences are likely to have particular nucleotides at each 5'-end, independently of their thermodynamic asymmetry. Here, we describe an algorithm for predicting highly active siRNA sequences based only on these two asymmetry parameters. The algorithm uses end-sequence nucleotide preferences and predicted thermodynamic stabilities, each weighted on the basis of training data from the literature, to rank the probability that an siRNA sequence will have high or low activity. The algorithm successfully predicts weakly and highly active sequences for enhanced green fluorescent protein and protein kinase R. Use of these two parameters in combination improves the prediction of siRNA activity over current approaches for predicting asymmetry. Going forward, we anticipate that this approach to siRNA asymmetry prediction will be incorporated into the next generation of siRNA selection algorithms.
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Affiliation(s)
- Amanda P Malefyt
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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Tabolacci E, Chiurazzi P. Epigenetics, fragile X syndrome and transcriptional therapy. Am J Med Genet A 2013; 161A:2797-808. [PMID: 24123753 DOI: 10.1002/ajmg.a.36264] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/06/2013] [Indexed: 12/13/2022]
Abstract
Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Epigenetic mechanisms therefore include all transcriptional controls that determine how genes are expressed during development and differentiation, but also in individual cells responding to environmental stimuli. The purpose of this review is to examine the basic principles of epigenetic mechanisms and their contribution to human disorders with a particular focus on fragile X syndrome (FXS), the most common monogenic form of developmental cognitive impairment. FXS represents a prototype of the so-called repeat expansion disorders due to "dynamic" mutations, namely the expansion (known as "full mutation") of a CGG repeat in the 5'UTR of the FMR1 gene. This genetic anomaly is accompanied by epigenetic modifications (mainly DNA methylation and histone deacetylation), resulting in the inactivation of the FMR1 gene. The presence of an intact FMR1 coding sequence allowed pharmacological reactivation of gene transcription, particularly through the use of the DNA demethylating agent 5'-aza-2'-deoxycytydine and/or inhibitors of histone deacetylases. These treatments suggested that DNA methylation is dominant over histone acetylation in silencing the FMR1 gene. The importance of DNA methylation in repressing FMR1 transcription is confirmed by the existence of rare unaffected males carrying unmethylated full mutations. Finally, we address the potential use of epigenetic approaches to targeted treatment of other genetic conditions.
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