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1
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Ghasemiyeh P, Mohammadi-Samani S. siRNA-based delivery systems: Technologies, carriers, applications, and approved products. Eur J Pharmacol 2025; 996:177441. [PMID: 40023357 DOI: 10.1016/j.ejphar.2025.177441] [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: 12/25/2024] [Revised: 02/22/2025] [Accepted: 02/26/2025] [Indexed: 03/04/2025]
Abstract
Ribonucleic acid (RNA) therapeutics are a novel category of therapeutic agents that use different types of RNAs to regulate genes and modulate protein synthesis to treat a wide range of diseases. The main advantages of RNA therapeutics over conventional small molecule drugs would be the potential to target undruggable sites, ease of production and faster development process, and longer duration of action. Various types of RNA therapeutics including antisense oligonucleotides (ASO), RNA interference (RNAi), small interfering RNA (siRNA), microRNA (miRNA), and messenger RNA (mRNA), have been developed and used for various clinical applications, especially for gene and vaccine delivery purposes. This review is focused on various therapeutic applications of RNA-based delivery systems and then siRNA technologies are discussed in more detail. Next, the FDA-approved siRNA therapeutics and those are in clinical trials are listed and summarized. Then, various viral and non-viral vectors used for RNA delivery purposes are discussed. Finally, clinical applications of siRNA therapeutics are reviewed in detail.
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Affiliation(s)
- Parisa Ghasemiyeh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soliman Mohammadi-Samani
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutics, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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2
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Alperovich NY, Vasilyeva OB, Schaffter SW. Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity. RNA (NEW YORK, N.Y.) 2025; 31:633-645. [PMID: 40050070 PMCID: PMC12001966 DOI: 10.1261/rna.080243.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 02/19/2025] [Indexed: 03/28/2025]
Abstract
Self-cleaving ribozymes are important tools in synthetic biology, biomanufacturing, and nucleic acid therapeutics. These broad applications deploy ribozymes in many genetic and environmental contexts, which can influence activity. Thus, accurate measurements of ribozyme activity across diverse contexts are crucial for validating new ribozyme sequences and ribozyme-based biotechnologies. Ribozyme activity measurements that rely on RNA extraction, such as RNA sequencing or reverse transcription-quantitative polymerase chain reaction (RT-qPCR), are generalizable to most applications and have high sensitivity. However, the activity measurement is indirect, taking place after RNA is isolated from the environment of interest and copied to DNA. Thus, these measurements may not accurately reflect the activity in the original context. Here, we develop and validate an RT-qPCR method for measuring context-dependent ribozyme activity using a set of self-cleaving RNAs for which context-dependent ribozyme cleavage is known in vitro. We find that RNA extraction and reverse transcription conditions can induce substantial ribozyme cleavage, resulting in incorrect activity measurements with RT-qPCR. To restore the accuracy of the RT-qPCR measurements, we introduce an oligonucleotide into the sample preparation workflow that inhibits ribozyme activity. We then apply our method to measure ribozyme cleavage of RNAs produced in Escherichia coli These results have broad implications for many ribozyme measurements and technologies.
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Affiliation(s)
- Nina Y Alperovich
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Olga B Vasilyeva
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Samuel W Schaffter
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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3
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Sias F, Zoroddu S, Migheli R, Bagella L. Untangling the Role of MYC in Sarcomas and Its Potential as a Promising Therapeutic Target. Int J Mol Sci 2025; 26:1973. [PMID: 40076599 PMCID: PMC11900228 DOI: 10.3390/ijms26051973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 02/14/2025] [Accepted: 02/17/2025] [Indexed: 03/14/2025] Open
Abstract
MYC plays a pivotal role in the biology of various sarcoma subtypes, acting as a key regulator of tumor growth, proliferation, and metabolic reprogramming. This oncogene is frequently dysregulated across different sarcomas, where its expression is closely intertwined with the molecular features unique to each subtype. MYC interacts with critical pathways such as cell cycle regulation, apoptosis, and angiogenesis, amplifying tumor aggressiveness and resistance to standard therapies. Furthermore, MYC influences the tumor microenvironment by modulating cell-extracellular matrix interactions and immune evasion mechanisms, further complicating therapeutic management. Despite its well-established centrality in sarcoma pathogenesis, targeting MYC directly remains challenging due to its "undruggable" protein structure. However, emerging therapeutic strategies, including indirect MYC inhibition via epigenetic modulators, transcriptional machinery disruptors, and metabolic pathway inhibitors, offer new hope for sarcoma treatment. This review underscores the importance of understanding the intricate roles of MYC across sarcoma subtypes to guide the development of effective targeted therapies. Given MYC's central role in tumorigenesis and progression, innovative approaches aiming at MYC inhibition could transform the therapeutic landscape for sarcoma patients, providing a much-needed avenue to overcome therapeutic resistance and improve clinical outcomes.
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Affiliation(s)
- Fabio Sias
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (F.S.); (S.Z.)
| | - Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (F.S.); (S.Z.)
| | - Rossana Migheli
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100 Sassari, Italy; (F.S.); (S.Z.)
- Sbarro Institute for Cancer Research and Molecular Medicine, Centre for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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4
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Bettinsoli V, Melzi G, Marchese I, Pantaleoni S, Passoni FC, Corsini E. New approach methodologies to assess wanted and unwanted drugs-induced immunostimulation. Curr Res Toxicol 2025; 8:100222. [PMID: 40027547 PMCID: PMC11872130 DOI: 10.1016/j.crtox.2025.100222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 01/16/2025] [Accepted: 01/28/2025] [Indexed: 03/05/2025] Open
Abstract
This review examines various classes of drugs, focusing on their therapeutic and adverse effects, particularly in relation to immunostimulation. We emphasize the potential of new approach methodologies (NAMs) to study both expected and unexpected immunostimulatory effects. By evaluating the modes of action of different immunostimulatory drugs, we aim to provide insights into effectively assessing unwanted immunostimulatory responses. The review begins by exploring drugs that stimulate the immune system-including immunostimulants, monoclonal antibodies, chemotherapeutics, and nucleic acid-based drugs-to outline NAMs that could be employed to evaluate immunostimulation.
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Affiliation(s)
- Valeria Bettinsoli
- Department of Pharmacological and Biomolecular Sciences ‘Rodolfo Paoletti’, Università degli Studi di Milano, Via Balzaretti 9 20133 Milan, Italy
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Gloria Melzi
- Department of Pharmacological and Biomolecular Sciences ‘Rodolfo Paoletti’, Università degli Studi di Milano, Via Balzaretti 9 20133 Milan, Italy
| | - Irene Marchese
- Department of Pharmacological and Biomolecular Sciences ‘Rodolfo Paoletti’, Università degli Studi di Milano, Via Balzaretti 9 20133 Milan, Italy
| | - Sofia Pantaleoni
- Department of Pharmacological and Biomolecular Sciences ‘Rodolfo Paoletti’, Università degli Studi di Milano, Via Balzaretti 9 20133 Milan, Italy
| | - Francesca Carlotta Passoni
- Department of Pharmacological and Biomolecular Sciences ‘Rodolfo Paoletti’, Università degli Studi di Milano, Via Balzaretti 9 20133 Milan, Italy
| | - Emanuela Corsini
- Department of Pharmacological and Biomolecular Sciences ‘Rodolfo Paoletti’, Università degli Studi di Milano, Via Balzaretti 9 20133 Milan, Italy
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5
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Choudry MW, Riaz R, Raza MH, Nawaz P, Ahmad B, Jahan N, Rafique S, Afzal S, Amin I, Shahid M. Development of non-viral targeted RNA delivery vehicles - a key factor in success of therapeutic RNA. J Drug Target 2025; 33:171-184. [PMID: 39392510 DOI: 10.1080/1061186x.2024.2416241] [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: 06/14/2024] [Revised: 08/23/2024] [Accepted: 10/08/2024] [Indexed: 10/12/2024]
Abstract
Decade-long efforts in medicinal biotechnology have enabled large-scale in-vitro production of optimised therapeutic RNA constructs for stable in-vivo delivery and modify the expression of disease-related genes. The success of lipid nanoparticle-formulated mRNA vaccines against Severe acute respiratory syndrome Coronavirus-2 (SARS-Cov2) has opened a new era of RNA therapeutics and non-viral drug delivery systems. The major limiting factor in the clinical translation of RNA-based drugs is the availability of suitable delivery vehicles that can protect RNA payloads from degradation, offer controlled release, and pose minimal inherent toxicity. Unwanted immune response, payload size constraints, genome integration, and non-specific tissue targeting limit the application of conventional viral drug-delivery vehicles. This review summarises current research on nano-sized drug carriers, including lipid nanoparticles, polymer-based formulations, cationic nanoemulsion, and cell-penetrating peptides, for targeted therapeutic RNA delivery. Further, this paper highlights the biomimetic approaches (i.e. mimicking naturally occurring bio-compositions, molecular designs, and systems), including virus-like particles (VLPs), exosomes, and selective endogenous eNcapsidation (SEND) technology being explored as safer and more efficient alternatives.
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Affiliation(s)
- Muhammad Waqas Choudry
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Rabia Riaz
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Hassan Raza
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Pashma Nawaz
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Bilal Ahmad
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Neelam Jahan
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Iram Amin
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Shahid
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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6
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Haque MA, Shrestha A, Mikelis CM, Mattheolabakis G. Comprehensive analysis of lipid nanoparticle formulation and preparation for RNA delivery. Int J Pharm X 2024; 8:100283. [PMID: 39309631 PMCID: PMC11415597 DOI: 10.1016/j.ijpx.2024.100283] [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: 05/02/2024] [Revised: 08/21/2024] [Accepted: 09/07/2024] [Indexed: 09/25/2024] Open
Abstract
Nucleic acid-based therapeutics are a common approach that is increasingly popular for a wide spectrum of diseases. Lipid nanoparticles (LNPs) are promising delivery carriers that provide RNA stability, with strong transfection efficiency, favorable and tailorable pharmacokinetics, limited toxicity, and established translatability. In this review article, we describe the lipid-based delivery systems, focusing on lipid nanoparticles, the need of their use, provide a comprehensive analysis of each component, and highlight the advantages and disadvantages of the existing manufacturing processes. We further summarize the ongoing and completed clinical trials utilizing LNPs, indicating important aspects/questions worth of investigation, and analyze the future perspectives of this significant and promising therapeutic approach.
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Affiliation(s)
- Md. Anamul Haque
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA
| | - Archana Shrestha
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA
| | - Constantinos M. Mikelis
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Patras 26504, Greece
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - George Mattheolabakis
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA
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Haghighi E, Abolmaali SS, Dehshahri A, Mousavi Shaegh SA, Azarpira N, Tamaddon AM. Navigating the intricate in-vivo journey of lipid nanoparticles tailored for the targeted delivery of RNA therapeutics: a quality-by-design approach. J Nanobiotechnology 2024; 22:710. [PMID: 39543630 PMCID: PMC11566655 DOI: 10.1186/s12951-024-02972-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 11/03/2024] [Indexed: 11/17/2024] Open
Abstract
RNA therapeutics, such as mRNA, siRNA, and CRISPR-Cas9, present exciting avenues for treating diverse diseases. However, their potential is commonly hindered by vulnerability to degradation and poor cellular uptake, requiring effective delivery systems. Lipid nanoparticles (LNPs) have emerged as a leading choice for in vivo RNA delivery, offering protection against degradation, enhanced cellular uptake, and facilitation of endosomal escape. However, LNPs encounter numerous challenges for targeted RNA delivery in vivo, demanding advanced particle engineering, surface functionalization with targeting ligands, and a profound comprehension of the biological milieu in which they function. This review explores the structural and physicochemical characteristics of LNPs, in-vivo fate, and customization for RNA therapeutics. We highlight the quality-by-design (QbD) approach for targeted delivery beyond the liver, focusing on biodistribution, immunogenicity, and toxicity. In addition, we explored the current challenges and strategies associated with LNPs for in-vivo RNA delivery, such as ensuring repeated-dose efficacy, safety, and tissue-specific gene delivery. Furthermore, we provide insights into the current clinical applications in various classes of diseases and finally prospects of LNPs in RNA therapeutics.
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Affiliation(s)
- Elahe Haghighi
- Department of Pharmaceutical Nanotechnology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Samira Sadat Abolmaali
- Department of Pharmaceutical Nanotechnology, Shiraz University of Medical Sciences, Shiraz, Iran.
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Dehshahri
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Ali Mousavi Shaegh
- Laboratory of Microfluidics and Medical Microsystems, Research Institute for Medical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Orthopedic Research Center, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
- Clinical Research Development Unit, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Negar Azarpira
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Tamaddon
- Department of Pharmaceutical Nanotechnology, Shiraz University of Medical Sciences, Shiraz, Iran.
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutics, Shiraz University of Medical Sciences, Shiraz, Iran.
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8
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Grillone K, Caridà G, Luciano F, Cordua A, Di Martino MT, Tagliaferri P, Tassone P. A systematic review of non-coding RNA therapeutics in early clinical trials: a new perspective against cancer. J Transl Med 2024; 22:731. [PMID: 39103911 PMCID: PMC11301835 DOI: 10.1186/s12967-024-05554-4] [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: 05/22/2024] [Accepted: 07/28/2024] [Indexed: 08/07/2024] Open
Abstract
Targeting non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), has recently emerged as a promising strategy for treating malignancies and other diseases. In recent years, the development of ncRNA-based therapeutics for targeting protein-coding and non-coding genes has also gained momentum. This review systematically examines ongoing and completed clinical trials to provide a comprehensive overview of the emerging landscape of ncRNA-based therapeutics. Significant efforts have been made to advance ncRNA therapeutics to early clinical studies. The most advanced trials have been conducted with small interfering RNAs (siRNAs), miRNA replacement using nanovector-entrapped miRNA mimics, or miRNA silencing by antisense oligonucleotides. While siRNA-based therapeutics have already received FDA approval, miRNA mimics, inhibitors, and lncRNA-based therapeutics are still under evaluation in preclinical and early clinical studies. We critically discuss the rationale and methodologies of ncRNA targeting strategies to illustrate this rapidly evolving field.
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Affiliation(s)
- Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - Giulio Caridà
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - Francesco Luciano
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - Alessia Cordua
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy.
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy.
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Mamdouh S, Mohamed Khorshed FELZ, Hammad G, Magdy M, Abdelraouf A, Hemida E, Shemis M. RNA Interference based Midkine Gene Therapy for Hepatocellular Carcinoma. Asian Pac J Cancer Prev 2024; 25:2371-2379. [PMID: 39068570 PMCID: PMC11480621 DOI: 10.31557/apjcp.2024.25.7.2371] [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: 02/13/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) arises from hepatocytes and accounts for 90% of primary liver cancer. Reasons for HCC prognosis remaining dismal are that HCC is asymptomatic in its early stages, leading to late diagnosis, and it is markedly resistant to conventional chemo- and radiotherapy. In this study, we investigated RNA interference (RNAi)-based treatment for HCC by targeting MDK. AIM The present study aimed to evaluate MDK serum levels as a diagnostic biomarker for HCC detection and the effect of MDK silencing by RNAi on HCC. SUBJECTS AND METHODS A total of 140 participants, including 120 patients diagnosed with HCC and 20 healthy volunteers were enrolled in this study, all patients who underwent liver resection were sampled for tumor and adjacent non-tumor liver tissues, in addition to 5 ml of blood sample. Midkine expression levels were evaluated by ELISA and by qRT-PCR. The in vitro transfection and gene knockdown efficiency of midkine by MDK-siRNA was detected by qRT-PCR and ELISA. Gene knockdown effect at the molecule level on the proliferation of HepG2 in vitro was determined by cell counting. RESULTS The results showed that the expression of MDK was significantly increased in the serum of HCC patients compared to control serum samples with P<0.001 and significant elevated expression levels of MDK in tumor tissues compared to non-tumor ones with P<0.001. It also showed that down-regulation of MDK using RNAi can significantly inhibit HepG2 cells. CONCLUSION Molecular targeting of MDK using RNAi interference decreases proliferation and could be a therapeutic target.
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Affiliation(s)
- Samah Mamdouh
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt.
| | | | - Gehan Hammad
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt.
| | - Mona Magdy
- Department of Pathology, Theodor Bilharz Research Institute, Cairo, Egypt.
| | - Amr Abdelraouf
- Department of Hepatobiliopancreatic Surgery, National Hepatology and Tropical Medicine Research Institute, (NHTMRI), Cairo, Egypt.
| | - Eman Hemida
- Fellow of Biochemistry, Obstetrics and Gynecology Hospital, Ain Shams University, Cairo, Egypt.
| | - Mohamed Shemis
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt.
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10
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Traber GM, Yu AM. The Growing Class of Novel RNAi Therapeutics. Mol Pharmacol 2024; 106:13-20. [PMID: 38719476 PMCID: PMC11187687 DOI: 10.1124/molpharm.124.000895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/15/2024] [Indexed: 06/20/2024] Open
Abstract
The clinical use of RNA interference (RNAi) molecular mechanisms has introduced a novel, growing class of RNA therapeutics capable of treating diseases by controlling target gene expression at the posttranscriptional level. With the newly approved nedosiran (Rivfloza), there are now six RNAi-based therapeutics approved by the United States Food and Drug Administration (FDA). Interestingly, five of the six FDA-approved small interfering RNA (siRNA) therapeutics [patisiran (Onpattro), lumasiran (Oxlumo), inclisiran (Leqvio), vutrisiran (Amvuttra), and nedosiran] were revealed to act on the 3'-untranslated regions of target mRNAs, instead of coding sequences, thereby following the common mechanistic action of genome-derived microRNAs (miRNA). Furthermore, three of the FDA-approved siRNA therapeutics [patisiran, givosiran (Givlaari), and nedosiran] induce target mRNA degradation or cleavage via near-complete rather than complete base-pair complementarity. These features along with previous findings confound the currently held characteristics to distinguish siRNAs and miRNAs or biosimilars, of which all converge in the RNAi regulatory pathway action. Herein, we discuss the RNAi mechanism of action and current criteria for distinguishing between miRNAs and siRNAs while summarizing the common and unique chemistry and molecular pharmacology of the six FDA-approved siRNA therapeutics. The term "RNAi" therapeutics, as used previously, provides a coherently unified nomenclature for broader RNAi forms as well as the growing number of therapeutic siRNAs and miRNAs or biosimilars that best aligns with current pharmacological nomenclature by mechanism of action. SIGNIFICANCE STATEMENT: The common and unique chemistry and molecular pharmacology of six FDA-approved siRNA therapeutics are summarized, in which nedosiran is newly approved. We point out rather a surprisingly mechanistic action as miRNAs for five siRNA therapeutics and discuss the differences and similarities between siRNAs and miRNAs that supports using a general and unified term "RNAi" therapeutics to align with current drug nomenclature criteria in pharmacology based on mechanism of action and embraces broader forms and growing number of novel RNAi therapeutics.
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Affiliation(s)
- Gavin M Traber
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California - Davis, Sacramento, California
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California - Davis, Sacramento, California
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11
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Yuan W, Shi X, Lee LTO. RNA therapeutics in targeting G protein-coupled receptors: Recent advances and challenges. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102195. [PMID: 38741614 PMCID: PMC11089380 DOI: 10.1016/j.omtn.2024.102195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
G protein-coupled receptors (GPCRs) are the major targets of existing drugs for a plethora of human diseases and dominate the pharmaceutical market. However, over 50% of the GPCRs remain undruggable. To pursue a breakthrough and overcome this situation, there is significant clinical research for developing RNA-based drugs specifically targeting GPCRs, but none has been approved so far. RNA therapeutics represent a unique and promising approach to selectively targeting previously undruggable targets, including undruggable GPCRs. However, the development of RNA therapeutics faces significant challenges in areas of RNA stability and efficient in vivo delivery. This review presents an overview of the advances in RNA therapeutics and the diverse types of nanoparticle RNA delivery systems. It also describes the potential applications of GPCR-targeted RNA drugs for various human diseases.
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Affiliation(s)
- Wanjun Yuan
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, People’s Republic of China
| | - Leo Tsz On Lee
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China
- Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Taipa 999078, Macau, China
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12
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024; 56:1235-1249. [PMID: 38871819 PMCID: PMC11263585 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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13
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Coll De Peña A, Vaduva M, Li NS, Shah S, Ben Frej M, Tripathi A. Enzymatic isolation and microfluidic electrophoresis analysis of residual dsRNA impurities in mRNA vaccines and therapeutics. Analyst 2024; 149:1509-1517. [PMID: 38265070 DOI: 10.1039/d3an02157b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The versatility, rapid development, and ease of production scalability of mRNA therapeutics have placed them at the forefront of biopharmaceutical research. However, despite their vast potential to treat diseases, their novelty comes with unsolved analytical challenges. A key challenge in ensuring sample purity has been monitoring residual, immunostimulatory dsRNA impurities generated during the in vitro transcription of mRNA. Here, we present a method that combines an enzyme, S1 nuclease, to identify and isolate dsRNA from an mRNA sample with a microfluidic electrophoresis analytical platform to characterize the impurity. After the method was developed and optimized, it was tested with clinically relevant, pseudouridine-modified 700 and 1800 bp dsRNA and 818-4451 nt mRNA samples. While the treatment impacted the magnitude of the fluorescent signal used to analyze the samples due to the interference of the buffer with the labeling of the sample, this signal loss was mitigated by 8.8× via treatment optimization. In addition, despite the mRNA concentration being up to 400× greater than that of the dsRNA, under every condition, there was a complete disappearance of the main mRNA peak. While the mRNA peak was digested, the dsRNA fragments remained physically unaffected by the treatment, with no change to their migration time. Using these samples, we detected 0.25% dsRNA impurities in mRNA samples using 15 μL with an analytical runtime of 1 min per sample after digestion and were able to predict their size within 8% of the expected length. The short runtime, sample consumption, and high throughput compatibility make it suitable to support the purity assessment of mRNA during purification and downstream.
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Affiliation(s)
- Adriana Coll De Peña
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| | - Matei Vaduva
- Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Nina S Li
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
| | | | | | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
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14
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Thi HV, Hoang TN, Le NQK, Chu DT. Application of data science and bioinformatics in RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:83-97. [PMID: 38360007 DOI: 10.1016/bs.pmbts.2023.12.019] [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
Nowadays, information technology (IT) has been holding a significant role in daily life worldwide. The trajectory of data science and bioinformatics promises pioneering personalized therapies, reshaping medical landscapes and patient care. For RNA therapy to reach more patients, a comprehensive understanding of the application of data science and bioinformatics to this therapy is essential. Thus, this chapter has summarized the application of data science and bioinformatics in RNA therapeutics. Data science applications in RNA therapy, such as data integration and analytics, machine learning, and drug development, have been discussed. In addition, aspects of bioinformatics such as RNA design and evaluation, drug delivery system simulation, and databases for personalized medicine have also been covered in this chapter. These insights have shed light on existing evidence and opened potential future directions. From there, scientists can elevate RNA-based therapeutics into an era of tailored treatments and revolutionary healthcare.
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Affiliation(s)
- Hue Vu 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
| | - Thanh-Nhat Hoang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, Taiwan
| | - 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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15
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Bui NL, Chu DT. An introduction to RNA therapeutics and their potentials. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:1-12. [PMID: 38359993 DOI: 10.1016/bs.pmbts.2023.12.020] [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 therapeutics is a biological term regarding the usage of RNA-based molecules for medical purposes. Thanks to the success of mRNA-vaccine production against COVID-19, RNA therapeutics has gained more and more attention and investigation from worldwide scientists. It is considered as one of the promising alternatives for conventional drugs. In this first chapter, we presented an overview of the history and perspectives of RNA therapeutics' development. This chapter also explained the underlying mechanisms of different RNA-based molecules, including antisense oligonucleotide, interfering RNA (iRNA), aptamer, and mRNA, from degrading mRNA to inactivating targeted protein. Although there are many advantages of RNA therapeutics, its challenges in designing RNA chemical structure and the delivery vehicle need to be discussed. We described advanced technologies in the development of drug delivery systems that are positively correlated to the efficacy of the drug. Our aim is to provide a general background of RNA therapeutics to the audience before introducing plenty of more detailed parts, including clinical applications in certain diseases in the following chapters of the "RNA therapeutics" book.
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Affiliation(s)
- Nhat-Le Bui
- 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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16
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Abbas H, Derkaoui DK, Jeammet L, Adicéam E, Tiollier J, Sicard H, Braun T, Poyet JL. Apoptosis Inhibitor 5: A Multifaceted Regulator of Cell Fate. Biomolecules 2024; 14:136. [PMID: 38275765 PMCID: PMC10813780 DOI: 10.3390/biom14010136] [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: 12/19/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Apoptosis, or programmed cell death, is a fundamental process that maintains tissue homeostasis, eliminates damaged or infected cells, and plays a crucial role in various biological phenomena. The deregulation of apoptosis is involved in many human diseases, including cancer. One of the emerging players in the intricate regulatory network of apoptosis is apoptosis inhibitor 5 (API5), also called AAC-11 (anti-apoptosis clone 11) or FIF (fibroblast growth factor-2 interacting factor). While it may not have yet the same level of notoriety as some other cancer-associated proteins, API5 has garnered increasing attention in the cancer field in recent years, as elevated API5 levels are often associated with aggressive tumor behavior, resistance to therapy, and poor patient prognosis. This review aims to shed light on the multifaceted functions and regulatory mechanisms of API5 in cell fate decisions as well as its interest as therapeutic target in cancer.
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Affiliation(s)
- Hafsia Abbas
- Université Oran 1, Ahmed Ben Bella, Oran 31000, Algeria; (H.A.); (D.K.D.)
| | | | - Louise Jeammet
- Jalon Therapeutics, 75010 Paris, France; (L.J.); (J.T.); (H.S.)
| | - Emilie Adicéam
- Jalon Therapeutics, 75010 Paris, France; (L.J.); (J.T.); (H.S.)
| | - Jérôme Tiollier
- Jalon Therapeutics, 75010 Paris, France; (L.J.); (J.T.); (H.S.)
| | - Hélène Sicard
- Jalon Therapeutics, 75010 Paris, France; (L.J.); (J.T.); (H.S.)
| | - Thorsten Braun
- Laboratoire de Transfert des Leucémies, EA3518, Institut de Recherche Saint Louis, Hôpital Saint Louis, Université de Paris, 75010 Paris, France;
- AP-HP, Service d’Hématologie Clinique, Hôpital Avicenne, Université Paris XIII, 93000 Bobigny, France
- OPALE Carnot Institute, The Organization for Partnerships in Leukemia, Hôpital Saint-Louis, 75010 Paris, France
| | - Jean-Luc Poyet
- INSERM UMRS976, Institut de Recherche Saint Louis, Hôpital Saint Louis, 75010 Paris, France
- Université Paris Cité, 75015 Paris, France
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17
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Vuong HL, Lan CT, Le HTT. The development and technologies of RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:13-39. [PMID: 38359995 DOI: 10.1016/bs.pmbts.2023.12.017] [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
Since it was discovered for over 20 years ago, the potentiality of siRNAs in gene silencing in vitro and in vivo models has been recognized. Several studies in the new generation, molecular mechanisms, target attachment, and purification of RNA have supported the development of RNA therapeutics for a variety of applications. RNA therapeutics are growing rapidly with various platforms contributing to the standard of personalized medicine and rare disease treatment. Therefore, understanding the development and technologies of RNA therapeutics becomes a crucial point for new drug generation. Here, the primary purpose of this review is to provide a general view of six therapeutic categories that make up RNA-based therapeutic approaches, including RNA-target therapeutics, protein-targeted therapeutics, cellular reprogramming and tissues engineering, RNA-based protein replacement therapeutics, RNA-based genome editing, and RNA-based immunotherapies based on non-coding RNAs and coding RNA. Furthermore, we present an overview of the RNA strategies regarding viral approaches and nonviral approaches in designing a new generation of RNA technologies. The advantages and challenges of using RNA therapeutics are also discussed along with various approaches for RNA delivery. Therefore, this review is designed to provide updated reference evidence of RNA therapeutics in the battle against rare or difficult-to-treat diseases for researchers in this field.
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Affiliation(s)
- Huong Lan Vuong
- Pharmacy Department, National Hospital for Tropical Diseases, Hanoi, Vietnam
| | - Chu Thanh Lan
- Department of Regenerative Medicine, Institute of Tissue Regeneration, College of Medicine, Soonchunghyang University, South Korea
| | - Hien Thi Thu Le
- Intestinal Signaling and Epigenetics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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18
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Alkan AH, Ensoy M, Cansaran-Duman D. Strategic and Innovative Roles of lncRNAs Regulated by Naturally-derived Small Molecules in Cancer Therapy. Curr Med Chem 2024; 31:6672-6691. [PMID: 37921177 DOI: 10.2174/0109298673264372230919102758] [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: 05/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 11/04/2023]
Abstract
In the field of precision and personalized medicine, the next generation sequencing method has begun to take an active place as genome-wide screening applications in the diagnosis and treatment of diseases. Studies based on the determination of the therapeutic efficacy of personalized drug use in cancer treatment in the size of the transcriptome and its extension, lncRNA, have been increasing rapidly in recent years. Targeting and/or regulating noncoding RNAs (ncRNAs) consisting of long noncoding RNAs (lncRNAs) are promising strategies for cancer treatment. Within the scope of rapidly increasing studies in recent years, it has been shown that many natural agents obtained from biological organisms can potentially alter the expression of many lncRNAs associated with oncogenic functions. Natural agents include effective small molecules that provide anti-cancer effects and have been used as chemotherapy drugs or in combination with standard anti-cancer drugs used in routine treatment. In this review, it was aimed to provide detailed information about the potential of natural agents to regulate and/or target non-coding RNAs and their mechanisms of action to provide an approach for cancer therapy. The discovery of novel anti-cancer targets and subsequent development of effective drugs or combination strategies that are still needed for most cancers will be promising for cancer treatment.
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Affiliation(s)
- Ayşe Hale Alkan
- Biotechnology Institute, Ankara University, Keçiören, Ankara, Turkey
- Department of Molecular Biology and Genetics, Faculty of Science, Bartın University, Bartın, Turkey
| | - Mine Ensoy
- Biotechnology Institute, Ankara University, Keçiören, Ankara, Turkey
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19
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Zhang B, Li J, Jiang J, Lin X, Sun X, Wang Q. Overcoming delivery barriers for RNA therapeutics in the treatment of rheumatoid arthritis. Eur J Pharm Biopharm 2023; 192:147-160. [PMID: 37844708 DOI: 10.1016/j.ejpb.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
RNA therapeutics can manipulate gene expression or protein production, making them suitable for treating a wide range of diseases. Theoretically, any disease that has a definite biological target would probably find feasible therapeutic approach from RNA-based therapeutics. Numerous clinical trials using RNA therapeutics fighting against cancer, infectious diseases or inherited diseases have been reported and achieved desirable therapeutic efficacy. So far, encouraging findings from various animal experimental studies have also confirmed the great potential of RNA-based therapies in the treatment of rheumatic arthritis (RA). However, the in vivo multiple physiological barriers still seriously compromise the therapeutic efficacy of RNA drugs. Thus, safe and effective delivery strategies for RNA therapeutics are quite essential for their further and wide application in RA therapy. In this review, we will discuss the recent progress achieved using RNA-based therapeutics and focus on delivery strategies that can overcome the in vivo delivery barriers in RA treatment. Furthermore, discussion about the existing problems in current RNA delivery systems for RA therapy has been also included here.
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Affiliation(s)
- Bin Zhang
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Jiao Li
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Jiayu Jiang
- Patent Examination Cooperation Sichuan Center of the Patent office, Chengdu 610213, China
| | - Xin Lin
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education and School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xun Sun
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Chengdu 610041, China
| | - Qin Wang
- Institute of Biomedical Engineering, College of Medicine, Southwest Jiaotong University, Chengdu 610031, China.
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20
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Niu D, Wu Y, Lian J. Circular RNA vaccine in disease prevention and treatment. Signal Transduct Target Ther 2023; 8:341. [PMID: 37691066 PMCID: PMC10493228 DOI: 10.1038/s41392-023-01561-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/02/2023] [Accepted: 07/09/2023] [Indexed: 09/12/2023] Open
Abstract
CircRNAs are a class of single-stranded RNAs with covalently linked head-to-tail topology. In the decades since its initial discovery, their biogenesis, regulation, and function have rapidly disclosed, permitting a better understanding and adoption of them as new tools for medical applications. With the development of biotechnology and molecular medicine, artificial circRNAs have been engineered as a novel class of vaccines for disease treatment and prevention. Unlike the linear mRNA vaccine which applications were limited by its instability, inefficiency, and innate immunogenicity, circRNA vaccine which incorporate internal ribosome entry sites (IRESs) and open reading frame (ORF) provides an improved approach to RNA-based vaccination with safety, stability, simplicity of manufacture, and scalability. However, circRNA vaccines are at an early stage, and their optimization, delivery and applications require further development and evaluation. In this review, we comprehensively describe circRNA vaccine, including their history and superiority. We also summarize and discuss the current methodological research for circRNA vaccine preparation, including their design, synthesis, and purification. Finally, we highlight the delivery options of circRNA vaccine and its potential applications in diseases treatment and prevention. Considering their unique high stability, low immunogenicity, protein/peptide-coding capacity and special closed-loop construction, circRNA vaccine, and circRNA-based therapeutic platforms may have superior application prospects in a broad range of diseases.
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Affiliation(s)
- Dun Niu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Yaran Wu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Jiqin Lian
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
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21
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Wei HH, Zheng L, Wang Z. mRNA therapeutics: New vaccination and beyond. FUNDAMENTAL RESEARCH 2023; 3:749-759. [PMID: 38933291 PMCID: PMC10017382 DOI: 10.1016/j.fmre.2023.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The idea of mRNA therapy had been conceived for decades before it came into reality during the Covid-19 pandemic. The mRNA vaccine emerges as a powerful and general tool against new viral infections, largely due to its versatility and rapid development. In addition to prophylactic vaccines, mRNA technology also offers great promise for new applications as a versatile drug modality. However, realizing the conceptual potential faces considerable challenges, such as minimal immune stimulation, high and long-term expression, and efficient delivery to target cells and tissues. Here we review the applications of mRNA-based therapeutics, with emphasis on the innovative design and future challenges/solutions. In addition, we also discuss the next generation of mRNA therapy, including circular mRNA and self-amplifying RNAs. We aim to provide a conceptual overview and outlook on mRNA therapeutics beyond prophylactic vaccines.
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Affiliation(s)
- Huan-Huan Wei
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Shanghai Institute of Nutrition and Health, Shanghai 200032, China
| | | | - Zefeng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Shanghai Institute of Nutrition and Health, Shanghai 200032, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing 100049, China
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22
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Ribeiro J, Lopes I, Gomes AC. A New Perspective for the Treatment of Alzheimer's Disease: Exosome-like Liposomes to Deliver Natural Compounds and RNA Therapies. Molecules 2023; 28:6015. [PMID: 37630268 PMCID: PMC10458935 DOI: 10.3390/molecules28166015] [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: 06/15/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increment of the aging population in recent years, neurodegenerative diseases exert a major global disease burden, essentially as a result of the lack of treatments that stop the disease progression. Alzheimer's Disease (AD) is an example of a neurodegenerative disease that affects millions of people globally, with no effective treatment. Natural compounds have emerged as a viable therapy to fill a huge gap in AD management, and in recent years, mostly fueled by the COVID-19 pandemic, RNA-based therapeutics have become a hot topic in the treatment of several diseases. Treatments of AD face significant limitations due to the complex and interconnected pathways that lead to their hallmarks and also due to the necessity to cross the blood-brain barrier. Nanotechnology has contributed to surpassing this bottleneck in the treatment of AD by promoting safe and enhanced drug delivery to the brain. In particular, exosome-like nanoparticles, a hybrid delivery system combining exosomes and liposomes' advantageous features, are demonstrating great potential in the treatment of central nervous system diseases.
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Affiliation(s)
- Joana Ribeiro
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (J.R.); (I.L.)
- Institute of Science and Innovation for Sustainability (IB-S), Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ivo Lopes
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (J.R.); (I.L.)
| | - Andreia Castro Gomes
- Centre of Molecular and Environmental Biology (CBMA)/Aquatic Research Network (ARNET) Associate Laboratory, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (J.R.); (I.L.)
- Institute of Science and Innovation for Sustainability (IB-S), Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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23
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Zheng L, Bandara SR, Tan Z, Leal C. Lipid nanoparticle topology regulates endosomal escape and delivery of RNA to the cytoplasm. Proc Natl Acad Sci U S A 2023; 120:e2301067120. [PMID: 37364130 PMCID: PMC10318962 DOI: 10.1073/pnas.2301067120] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 06/28/2023] Open
Abstract
RNA therapeutics have the potential to resolve a myriad of genetic diseases. Lipid nanoparticles (LNPs) are among the most successful RNA delivery systems. Expanding their use for the treatment of more genetic diseases hinges on our ability to continuously evolve the design of LNPs with high potency, cellular-specific targeting, and low side effects. Overcoming the difficulty of releasing cargo from endocytosed LNPs remains a significant hurdle. Here, we investigate the fundamental properties of nonviral RNA nanoparticles pertaining to the activation of topological transformations of endosomal membranes and RNA translocation into the cytosol. We show that, beyond composition, LNP fusogenicity can be prescribed by designing LNP nanostructures that lower the energetic cost of fusion and fusion-pore formation with a target membrane. The inclusion of structurally active lipids leads to enhanced LNP endosomal fusion, fast evasion of endosomal entrapment, and efficacious RNA delivery. For example, conserving the lipid make-up, RNA-LNPs having cuboplex nanostructures are significantly more efficacious at endosomal escape than traditional lipoplex constructs.
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Affiliation(s)
- Lining Zheng
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Sarith R. Bandara
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Zhengzhong Tan
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Cecilia Leal
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
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24
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Jaiswal A, Kaushik N, Choi EH, Kaushik NK. Functional impact of non-coding RNAs in high-grade breast carcinoma: Moving from resistance to clinical applications: A comprehensive review. Biochim Biophys Acta Rev Cancer 2023; 1878:188915. [PMID: 37196783 DOI: 10.1016/j.bbcan.2023.188915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/08/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Despite the recent advances in cancer therapy, triple-negative breast cancers (TNBCs) are the most relapsing cancer sub-type. It is partly due to their propensity to develop resistance against the available therapies. An intricate network of regulatory molecules in cellular mechanisms leads to the development of resistance in tumors. Non-coding RNAs (ncRNAs) have gained widespread attention as critical regulators of cancer hallmarks. Existing research suggests that aberrant expression of ncRNAs modulates the oncogenic or tumor suppressive signaling. This can mitigate the responsiveness of efficacious anti-tumor interventions. This review presents a systematic overview of biogenesis and down streaming molecular mechanism of the subgroups of ncRNAs. Furthermore, it explains ncRNA-based strategies and challenges to target the chemo-, radio-, and immunoresistance in TNBCs from a clinical standpoint.
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Affiliation(s)
- Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Suwon 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
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25
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Vatish M, Powys VR, Cerdeira AS. Novel therapeutic and diagnostic approaches for preeclampsia. Curr Opin Nephrol Hypertens 2023; 32:124-133. [PMID: 36683536 DOI: 10.1097/mnh.0000000000000870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
PURPOSE OF REVIEW This review will summarize recent findings relating to the diagnostic approach to preeclampsia and current avenues of research aimed at modifying the underlying disease process. RECENT FINDINGS Growing international consensus supports a broad preeclampsia definition that incorporates maternal end-organ and uteroplacental dysfunction. Recent evidence demonstrates that this definition better identifies women and babies at risk of adverse outcomes compared to the traditional definition of hypertension and proteinuria. Multiple studies have demonstrated the usefulness and cost-effectiveness of angiogenic biomarkers such as soluble fms-like tyrosine kinase-1 and placental growth factor as a clinical adjunct to diagnose and predict severity of preeclampsia associated outcomes. Current novel therapeutic approaches to preeclampsia target pathogenic pathways (e.g. antiangiogenesis) or downstream effects such as oxidative stress and nitric oxide. Recent findings relating to these promising candidates are discussed. Multicenter clinical trials are needed to evaluate their effectiveness and ability to improve fetal and maternal outcomes. SUMMARY We provide an updated framework of the current approaches to define and diagnose preeclampsia. Disease modifying therapies (in particular, targeting the angiogenic pathway) are being developed for the first time and promise to revolutionize the way we manage preeclampsia.
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Affiliation(s)
- Manu Vatish
- Nuffield Department of Women's Health and Reproductive Research, University of Oxford, Oxford
| | | | - Ana Sofia Cerdeira
- Nuffield Department of Women's Health and Reproductive Research, University of Oxford, Oxford
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26
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Castro-Muñoz LJ, Vázquez Ulloa E, Sahlgren C, Lizano M, De La Cruz-Hernández E, Contreras-Paredes A. Modulating epigenetic modifications for cancer therapy (Review). Oncol Rep 2023; 49:59. [PMID: 36799181 PMCID: PMC9942256 DOI: 10.3892/or.2023.8496] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/08/2022] [Indexed: 02/12/2023] Open
Abstract
Cancer is a global public health concern. Alterations in epigenetic processes are among the earliest genomic aberrations occurring during cancer development and are closely related to progression. Unlike genetic mutations, aberrations in epigenetic processes are reversible, which opens the possibility for novel pharmacological treatments. Non‑coding RNAs (ncRNAs) represent an essential epigenetic mechanism, and emerging evidence links ncRNAs to carcinogenesis. Epigenetic drugs (epidrugs) are a group of promising target therapies for cancer treatment acting as coadjuvants to reverse drug resistance in cancer. The present review describes central epigenetic aberrations during malignant transformation and explains how epidrugs target DNA methylation, histone modifications and ncRNAs. Furthermore, clinical trials focused on evaluating the effect of these epidrugs alone or in combination with other anticancer therapies and other ncRNA‑based therapies are discussed. The use of epidrugs promises to be an effective tool for reversing drug resistance in some patients with cancer.
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Affiliation(s)
| | - Elenaé Vázquez Ulloa
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Marcela Lizano
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico
- Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico 04510, Mexico
| | - Erick De La Cruz-Hernández
- Laboratory of Research in Metabolic and Infectious Diseases, Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco, Tabasco 86650, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico
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27
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Islam S, Mukherjee C. Molecular regulation of hypoxia through the lenses of noncoding RNAs and epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1750. [PMID: 35785444 DOI: 10.1002/wrna.1750] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Cells maintain homeostasis in response to environmental stress through specific cell stress responses. Hypoxic stress, well known to be associated with diverse solid tumors, is one of the main reasons for cancer-related mortality. Although cells can balance themselves well during hypoxic stress, the underlying molecular mechanisms are not well understood. The enhanced appreciation of diverse roles played by noncoding transcriptome and epigenome in recent years has brought to light the involvement of noncoding RNAs and epigenetic modifiers in hypoxic regulation. The emergence of techniques like deep sequencing has facilitated the identification of large numbers of long noncoding RNAs (lncRNAs) that are differentially regulated in various cancers. Similarly, proteomic studies have identified diverse epigenetic modifiers such as HATs, HDACs, DNMTs, polycomb groups of proteins, and their possible roles in the regulation of hypoxia. The crosstalk between lncRNAs and epigenetic modifiers play a pivotal role in hypoxia-induced cancer initiation and progression. Besides the lncRNAs, several other noncoding RNAs like circular RNAs, miRNAs, and so forth are also expressed during hypoxic conditions. Hypoxia has a profound effect on the expression of noncoding RNAs and epigenetic modifiers. Conversely, noncoding RNAs/epigenetic modifies can regulate the hypoxia signaling axis by modulating the stability of the hypoxia-inducible factors (HIFs). The focus of this review is to illustrate the molecular orchestration underlying hypoxia biology, especially in cancers, which can help in identifying promising therapeutic targets in hypoxia-induced cancers. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Safirul Islam
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
| | - Chandrama Mukherjee
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
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28
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Gándara Z, Rubio N, Castillo RR. Delivery of Therapeutic Biopolymers Employing Silica-Based Nanosystems. Pharmaceutics 2023; 15:pharmaceutics15020351. [PMID: 36839672 PMCID: PMC9963032 DOI: 10.3390/pharmaceutics15020351] [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: 12/01/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The use of nanoparticles is crucial for the development of a new generation of nanodevices for clinical applications. Silica-based nanoparticles can be tailored with a wide range of functional biopolymers with unique physicochemical properties thus providing several advantages: (1) limitation of interparticle interaction, (2) preservation of cargo and particle integrity, (3) reduction of immune response, (4) additional therapeutic effects and (5) cell targeting. Therefore, the engineering of advanced functional coatings is of utmost importance to enhance the biocompatibility of existing biomaterials. Herein we will focus on the most recent advances reported on the delivery and therapeutic use of silica-based nanoparticles containing biopolymers (proteins, nucleotides, and polysaccharides) with proven biological effects.
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Affiliation(s)
- Zoila Gándara
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Correspondence: (Z.G.); (N.R.); (R.R.C.)
| | - Noelia Rubio
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Correspondence: (Z.G.); (N.R.); (R.R.C.)
| | - Rafael R. Castillo
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Spain
- Correspondence: (Z.G.); (N.R.); (R.R.C.)
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29
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Zhao X, Xue X, Cui Z, Kwame Amevor F, Wan Y, Fu K, Wang C, Peng C, Li Y. microRNAs-based diagnostic and therapeutic applications in liver fibrosis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022:e1773. [PMID: 36585388 DOI: 10.1002/wrna.1773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 01/01/2023]
Abstract
Liver fibrosis is a process of over-extracellular matrix (ECM) aggregation and angiogenesis, which develops into cirrhosis and hepatocellular carcinoma (HCC). With the increasing pressure of liver fibrosis, new therapeutics to cure this disease requires much attention. Exosome-cargoed microRNAs (miRNAs) are emerging approaches in the precision of the liver fibrotic paradigm. In this review, we outlined the different types of hepatic cells derived miRNAs that drive intra-/extra-cellular interactive communication in liver fibrosis with different physiological and pathological processes. Specifically, we highlighted the possible mechanism of liver fibrosis pathogenesis associated with immune response and angiogenesis. In addition, potential clinical biomarkers and different stem cell transplant-derived miRNAs-based therapeutic strategies in liver fibrosis were summarized in this review. miRNAs-based approaches might help researchers devise new candidates for the cell-free treatment of liver fibrosis. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Xingtao Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinyan Xue
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhifu Cui
- College Science and Technology, Southwest University, Chongqing, China
| | - Felix Kwame Amevor
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Wan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ke Fu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cheng Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yunxia Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Ministry of Education, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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30
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Hmila I, Sudhakaran IP, Ghanem SS, Vaikath NN, Poggiolini I, Abdesselem H, El-Agnaf OMA. Inhibition of α-Synuclein Seeding-Dependent Aggregation by ssDNA Aptamers Specific to C-Terminally Truncated α-Synuclein Fibrils. ACS Chem Neurosci 2022; 13:3330-3341. [PMID: 36348612 DOI: 10.1021/acschemneuro.2c00362] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Neuropathologically, Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are characterized by the accumulation of insoluble aggregates of α-synuclein (α-syn) in the Lewy bodies (LBs). In addition to full-length α-syn fibrils, C-terminally truncated α-syn is also abundant in the LBs that acts as seeds and facilitates the aggregation of the full-length α-syn in vitro and in vivo and induces toxicity. Hence, identifying molecules that can inhibit the seeding activity of these truncated forms is of great importance. Here, we report the first in vitro selection of aptamers targeting the fibrillar forms of different C-terminally truncated α-syn using systematic evolution by an exponential enrichment method followed by quantitative high-throughput DNA sequencing. We identify a panel of aptamers that bound with high specificity to different truncated forms of α-syn fibrils with no cross-reactivity toward other amyloid fibrils. Interestingly, two of the aptamers (named Apt11 and Apt15) show higher affinity to most C-terminally truncated forms of α-syn fibrils with an evident inhibition of α-syn-seeded aggregation in vitro by Apt11. This inhibition is further confirmed by circular dichroism, Congo red binding assay, and electronic microscopy. Moreover, Apt11 is also found to reduce the insoluble phosphorylated form of α-syn at Ser-129 (pS129-α-syn) in the cell model and also can inhibit α-syn aggregation using RT-QuIC reactions seeded with brain homogenates extracted from patients affected by PD. The aptamers discovered in this study represent potential useful tools for research and diagnostics or therapy toward PD and DLB.
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Affiliation(s)
- Issam Hmila
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
| | - Indulekha P Sudhakaran
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
| | - Simona S Ghanem
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
| | - Nishant N Vaikath
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
| | - Ilaria Poggiolini
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
| | - Houari Abdesselem
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
| | - Omar M A El-Agnaf
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha 34110, Qatar
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La Rosa M, Fiannaca A, La Paglia L, Urso A. A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks. Int J Mol Sci 2022; 23:ijms232214211. [PMID: 36430688 PMCID: PMC9696923 DOI: 10.3390/ijms232214211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Many biological systems are characterised by biological entities, as well as their relationships. These interaction networks can be modelled as graphs, with nodes representing bio-entities, such as molecules, and edges representing relations among them, such as interactions. Due to the current availability of a huge amount of biological data, it is very important to consider in silico analysis methods based on, for example, machine learning, that could take advantage of the inner graph structure of the data in order to improve the quality of the results. In this scenario, graph neural networks (GNNs) are recent computational approaches that directly deal with graph-structured data. In this paper, we present a GNN network for the analysis of siRNA-mRNA interaction networks. siRNAs, in fact, are small RNA molecules that are able to bind to target genes and silence them. These events make siRNAs key molecules as RNA interference agents in many biological interaction networks related to severe diseases such as cancer. In particular, our GNN approach allows for the prediction of the siRNA efficacy, which measures the siRNA's ability to bind and silence a gene target. Tested on benchmark datasets, our proposed method overcomes other machine learning algorithms, including the state-of-the-art predictor based on the convolutional neural network, reaching a Pearson correlation coefficient of approximately 73.6%. Finally, we proposed a case study where the efficacy of a set of siRNAs is predicted for a gene of interest. To the best of our knowledge, GNNs were used for the first time in this scenario.
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Kandasamy G, Maity D. Current Advancements in Self-assembling Nanocarriers-Based siRNA Delivery for Cancer Therapy. Colloids Surf B Biointerfaces 2022; 221:113002. [PMID: 36370645 DOI: 10.1016/j.colsurfb.2022.113002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/01/2022] [Accepted: 10/30/2022] [Indexed: 11/07/2022]
Abstract
Different therapeutic practices for treating cancers have significantly evolved to compensate and/or overcome the failures in conventional methodologies. The demonstrated potentiality in completely inhibiting the tumors and in preventing cancer relapse has made nucleic acids therapy (NAT)/gene therapy as an attractive practice. This has been made possible because NAT-based cancer treatments are highly focused on the fundamental mechanisms - i.e., silencing the expression of oncogenic genes responsible for producing abnormal proteins (via messenger RNAs (mRNAs)). However, the future clinical translation of NAT is majorly dependent upon the effective delivery of the exogenous nucleic acids (especially RNAs - e.g., short interfering RNAs (siRNAs) - herein called biological drugs). Moreover, nano-based vehicles (i.e., nanocarriers) are involved in delivering them to prevent degradation and undesired bioaccumulation while enhancing the stability of siRNAs. Herein, we have initially discussed about three major types of self-assembling nanocarriers (liposomes, polymeric nanoparticles and exosomes). Later, we have majorly reviewed recent developments in non-targeted/targeted nanocarriers for delivery of biological drugs (individual/dual) to silence the most important genes/mRNAs accountable for inducing protein abnormality. These proteins include polo-like kinase 1 (PLK1), survivin, vascular endothelial growth factor (VEGF), B-cell lymphoma/leukaemia-2 (Bcl-2) and multi-drug resistance (MDR). Besides, the consequent therapeutic effects on cancer growth, invasion and/or metastasis have also been discussed. Finally, we have comprehensively reviewed the improvements achieved in the cutting-edge cancer therapeutics while delivering siRNAs in combination with clinically approved chemotherapeutic drugs.
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33
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Mollica L, Cupaioli FA, Rossetti G, Chiappori F. An overview of structural approaches to study therapeutic RNAs. Front Mol Biosci 2022; 9:1044126. [PMID: 36387283 PMCID: PMC9649582 DOI: 10.3389/fmolb.2022.1044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2023] Open
Abstract
RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.
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Affiliation(s)
- Luca Mollica
- Department of Medical Biotechnologies and Translational Medicine, L.I.T.A/University of Milan, Milan, Italy
| | | | | | - Federica Chiappori
- National Research Council—Institute for Biomedical Technologies, Milan, Italy
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Noncoding RNAs Emerging as Drugs or Drug Targets: Their Chemical Modification, Bio-Conjugation and Intracellular Regulation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196717. [PMID: 36235253 PMCID: PMC9573214 DOI: 10.3390/molecules27196717] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
With the increasing understanding of various disease-related noncoding RNAs, ncRNAs are emerging as novel drugs and drug targets. Nucleic acid drugs based on different types of noncoding RNAs have been designed and tested. Chemical modification has been applied to noncoding RNAs such as siRNA or miRNA to increase the resistance to degradation with minimum influence on their biological function. Chemical biological methods have also been developed to regulate relevant noncoding RNAs in the occurrence of various diseases. New strategies such as designing ribonuclease targeting chimeras to degrade endogenous noncoding RNAs are emerging as promising approaches to regulate gene expressions, serving as next-generation drugs. This review summarized the current state of noncoding RNA-based theranostics, major chemical modifications of noncoding RNAs to develop nucleic acid drugs, conjugation of RNA with different functional biomolecules as well as design and screening of potential molecules to regulate the expression or activity of endogenous noncoding RNAs for drug development. Finally, strategies of improving the delivery of noncoding RNAs are discussed.
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35
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Giordo R, Gulsha R, Kalla S, Calin GA, Lipovich L. LncRNA-Associated Genetic Etiologies Are Shared between Type 2 Diabetes and Cancers in the UAE Population. Cancers (Basel) 2022; 14:3313. [PMID: 35884374 PMCID: PMC9313416 DOI: 10.3390/cancers14143313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
Numerous epidemiological studies place patients with T2D at a higher risk for cancer. Many risk factors, such as obesity, ageing, poor diet and low physical activity, are shared between T2D and cancer; however, the biological mechanisms linking the two diseases remain largely unknown. The advent of genome wide association studies (GWAS) revealed large numbers of genetic variants associated with both T2D and cancer. Most significant disease-associated variants reside in non-coding regions of the genome. Several studies show that single nucleotide polymorphisms (SNPs) at or near long non-coding RNA (lncRNA) genes may impact the susceptibility to T2D and cancer. Therefore, the identification of genetic variants predisposing individuals to both T2D and cancer may help explain the increased risk of cancer in T2D patients. We aim to investigate whether lncRNA genetic variants with significant diabetes and cancer associations overlap in the UAE population. We first performed an annotation-based analysis of UAE T2D GWAS, confirming the high prevalence of variants at or near non-coding RNA genes. We then explored whether these T2D SNPs in lncRNAs were relevant to cancer. We highlighted six non-coding genetic variants, jointly reaching statistical significance in T2D and cancer, implicating a shared genetic architecture between the two diseases in the UAE population.
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Affiliation(s)
- Roberta Giordo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (R.G.); (R.G.); (S.K.)
| | - Rida Gulsha
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (R.G.); (R.G.); (S.K.)
| | - Sarah Kalla
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (R.G.); (R.G.); (S.K.)
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leonard Lipovich
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates; (R.G.); (R.G.); (S.K.)
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36
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Next RNA Therapeutics: The Mine of Non-Coding. Int J Mol Sci 2022; 23:ijms23137471. [PMID: 35806476 PMCID: PMC9267739 DOI: 10.3390/ijms23137471] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 12/26/2022] Open
Abstract
The growing knowledge on several classes of non-coding RNAs (ncRNAs) and their different functional roles has aroused great interest in the scientific community. Beyond the Central Dogma of Biology, it is clearly known that not all RNAs code for protein products, and they exert a broader repertoire of biological functions. As described in this review, ncRNAs participate in gene expression regulation both at transcriptional and post-transcriptional levels and represent critical elements driving and controlling pathophysiological processes in multicellular organisms. For this reason, in recent years, a great boost was given to ncRNA-based strategies with potential therapeutic abilities, and nowadays, the use of RNA molecules is experimentally validated and actually exploited in clinics to counteract several diseases. In this review, we summarize the principal classes of therapeutic ncRNA molecules that are potentially implied in disease onset and progression, which are already used in clinics or under clinical trials, highlighting the advantages and the need for a targeted therapeutic strategy design. Furthermore, we discuss the benefits and the limits of RNA therapeutics and the ongoing development of delivery strategies to limit the off-target effects and to increase the translational application.
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37
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Bignon E, Marazzi M, Miclot T, Barone G, Monari A. Specific Recognition of the 5'-Untranslated Region of West Nile Virus Genome by Human Innate Immune System. Viruses 2022; 14:v14061282. [PMID: 35746753 PMCID: PMC9227302 DOI: 10.3390/v14061282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023] Open
Abstract
In the last few years, the sudden outbreak of COVID-19 caused by SARS-CoV-2 proved the crucial importance of understanding how emerging viruses work and proliferate, in order to avoid the repetition of such a dramatic sanitary situation with unprecedented social and economic costs. West Nile Virus is a mosquito-borne pathogen that can spread to humans and induce severe neurological problems. This RNA virus caused recent remarkable outbreaks, notably in Europe, highlighting the need to investigate the molecular mechanisms of its infection process in order to design and propose efficient antivirals. Here, we resort to all-atom Molecular Dynamics simulations to characterize the structure of the 5′-untranslated region of the West Nile Virus genome and its specific recognition by the human innate immune system via oligoadenylate synthetase. Our simulations allowed us to map the interaction network between the viral RNA and the host protein, which drives its specific recognition and triggers the host immune response. These results may provide fundamental knowledge that can assist further antivirals’ design, including therapeutic RNA strategies.
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Affiliation(s)
- Emmanuelle Bignon
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France;
- Correspondence: (E.B.); (A.M.)
| | - Marco Marazzi
- Grupo de Reactividad y Estructura Molecular (RESMOL), Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28805 Madrid, Spain;
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, 28805 Madrid, Spain
| | - Tom Miclot
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France;
- Department of Biological, Chemical and Pharmaceutical Sciences, Università degli Studi di Palermo, viale delle Scienze, 90128 Palermo, Italy;
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, Università degli Studi di Palermo, viale delle Scienze, 90128 Palermo, Italy;
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France;
- ITODYS, Université Paris Cité, CNRS, F-75006 Paris, France
- Correspondence: (E.B.); (A.M.)
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Sartorius K, Antwi SO, Chuturgoon A, Roberts LR, Kramvis A. RNA Therapeutic Options to Manage Aberrant Signaling Pathways in Hepatocellular Carcinoma: Dream or Reality? Front Oncol 2022; 12:891812. [PMID: 35600358 PMCID: PMC9115561 DOI: 10.3389/fonc.2022.891812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the early promise of RNA therapeutics as a magic bullet to modulate aberrant signaling in cancer, this field remains a work-in-progress. Nevertheless, RNA therapeutics is now a reality for the treatment of viral diseases (COVID-19) and offers great promise for cancer. This review paper specifically investigates RNAi as a therapeutic option for HCC and discusses a range of RNAi technology including anti-sense oligonucleotides (ASOs), Aptamers, small interfering RNA (siRNA), ribozymes, riboswitches and CRISPR/Cas9 technology. The use of these RNAi based interventions is specifically outlined in three primary strategies, namely, repressing angiogenesis, the suppression of cell proliferation and the promotion of apoptosis. We also discuss some of the inherent chemical and delivery problems, as well as targeting issues and immunogenic reaction to RNAi interventions.
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Affiliation(s)
- Kurt Sartorius
- Hepatitis Virus Diversity Research Unit, School of Internal Medicine, University of the Witwatersrand, Johannesburg, South Africa
- The Africa Hepatopancreatobiliary Cancer Consortium (AHPBCC), Mayo Clinic, Jacksonville, FL, United States
- Department of Surgery, KZN Kwazulu-Natal (UKZN) Gastrointestinal Cancer Research Centre, Durban, South Africa
| | - Samuel O. Antwi
- The Africa Hepatopancreatobiliary Cancer Consortium (AHPBCC), Mayo Clinic, Jacksonville, FL, United States
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, United States
| | - Anil Chuturgoon
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban, South Africa
| | - Lewis R. Roberts
- The Africa Hepatopancreatobiliary Cancer Consortium (AHPBCC), Mayo Clinic, Jacksonville, FL, United States
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Anna Kramvis
- Hepatitis Virus Diversity Research Unit, School of Internal Medicine, University of the Witwatersrand, Johannesburg, South Africa
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Baghani L, Noroozi Heris N, Khonsari F, Dinarvand S, Dinarvand M, Atyabi F. Trimethyl-Chitosan Coated Gold Nanoparticles Enhance Delivery, Cellular Uptake and Gene Silencing Effect of EGFR-siRNA in Breast Cancer Cells. Front Mol Biosci 2022; 9:871541. [PMID: 35517864 PMCID: PMC9065351 DOI: 10.3389/fmolb.2022.871541] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: Despite the promising therapeutic effects of gene silencing with small interfering RNAs (siRNAs), the challenges associated with delivery of siRNAs to the tumor cells in vivo, has greatly limited its clinical application. To overcome these challenges, we employed gold nanoparticles modified with trimethyl chitosan (TMC) as an effective delivery carrier to improve the stability and cellular uptake of siRNAs against epidermal growth factor receptor (EGFR) that is implicated in breast cancer. Methods: AuNPs were prepared by the simple aqueous reduction of chloroauric acid (HAuCl4) with ascorbic acid and coated with synthesized TMC. EGFR-siRNA was then complexed with the AuNPs-TMC via electrostatic interaction to make AuNPs-TMC/EGFR-siRNA with a w/w ratio of 10:1. Nanoparticles were assessed for physicochemical characteristics and in vitro cellular behavior on MCF-7 breast cancer cell line. Results: Spherical and positively charged AuNPs-TMC (67 nm, +45 mV) were successfully complexed with EGFR-siRNA (82 nm, +11 mV) which were able to retard the gene migration completely. Confocal microscopy and flow cytometry analysis demonstrated complete cellular uptake of Cy5 labeled AuNPs-TMC in the MCF-7 cells after 4 h incubation. MTT test after 48 h incubation showed that the AuNPs-TMC were safe but when combined with EGFR-siRNA exert significant cytotoxicity while the cell viability was about 50%. These nanocomplexes also showed a high gene expression knockdown (86%) of EGFR and also a high apoptosis rate (Q2 + Q3 = 18.5%) after 24 h incubation. Conclusion: This study suggests that the simply synthesized AuNPs-TMC are novel, effective, and promising nanocarriers for siRNA delivery, and AuNPs-TMC/EGFR-siRNA appears to be a potential therapeutic agent for breast cancer treatment.
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Affiliation(s)
- Leila Baghani
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Niloofar Noroozi Heris
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Khonsari
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Dinarvand
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Meshkat Dinarvand
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Atyabi
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Levanova AA, Lampi M, Kalke K, Hukkanen V, Poranen MM, Eskelin K. Native RNA Purification Method for Small RNA Molecules Based on Asymmetrical Flow Field-Flow Fractionation. Pharmaceuticals (Basel) 2022; 15:261. [PMID: 35215370 PMCID: PMC8876226 DOI: 10.3390/ph15020261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
RNA molecules provide promising new possibilities for the prevention and treatment of viral infections and diseases. The rapid development of RNA biology and medicine requires advanced methods for the purification of RNA molecules, which allow fast and efficient RNA processing, preferably under non-denaturing conditions. Asymmetrical flow field-flow fractionation (AF4) enables gentle separation and purification of macromolecules based on their diffusion coefficients. The aim of the study was to develop an AF4 method for efficient purification of enzymatically produced antiviral small interfering (si)RNA molecules and to evaluate the overall potential of AF4 in the separation of short single-stranded (ss) and double-stranded (ds) RNA molecules. We show that AF4 separates monomeric ssRNA from dsRNA molecules of the same size and monomeric ssRNA from multimeric forms of the same ssRNA. The developed AF4 method enabled the separation of enzymatically produced 27-nt siRNAs from partially digested substrate dsRNA, which is potentially toxic for mammalian cells. The recovery of AF4-purified enzymatically produced siRNA molecules was about 70%, which is about 20% higher than obtained using anion-exchange chromatography. The AF4-purified siRNAs were not toxic for mammalian cells and fully retained their biological activity as confirmed by efficient inhibition of herpes simplex virus 1 replication in cell culture. Our work is the first to develop AF4 methods for the separation of short RNA molecules.
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Affiliation(s)
- Alesia A. Levanova
- Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (A.A.L.); (M.L.)
| | - Mirka Lampi
- Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (A.A.L.); (M.L.)
| | - Kiira Kalke
- Institute of Biomedicine, University of Turku, FI-20014 Turku, Finland; (K.K.); (V.H.)
| | - Veijo Hukkanen
- Institute of Biomedicine, University of Turku, FI-20014 Turku, Finland; (K.K.); (V.H.)
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (A.A.L.); (M.L.)
| | - Katri Eskelin
- Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (A.A.L.); (M.L.)
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Su CT, See DHW, Huang JW. Lipid-Based Nanocarriers in Renal RNA Therapy. Biomedicines 2022; 10:283. [PMID: 35203492 PMCID: PMC8869454 DOI: 10.3390/biomedicines10020283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Kidney disease is a multifactorial problem, with a growing prevalence and an increasing global burden. With the latest worldwide data suggesting that chronic kidney disease (CKD) is the 12th leading cause of death, it is no surprise that CKD remains a public health problem that requires urgent attention. Multiple factors contribute to kidney disease, each with its own pathophysiology and pathogenesis. Furthermore, microRNAs (miRNAs) have been linked to several types of kidney diseases. As dysregulation of miRNAs is often seen in some diseases, there is potential in the exploitation of this for therapeutic applications. In addition, uptake of interference RNA has been shown to be rapid in kidneys making them a good candidate for RNA therapy. The latest advancements in RNA therapy and lipid-based nanocarriers have enhanced the effectiveness and efficiency of RNA-related drugs, thereby making RNA therapy a viable treatment option for renal disease. This is especially useful for renal diseases, for which a suitable treatment is not yet available. Moreover, the high adaptability of RNA therapy combined with the low risk of lipid-based nanocarriers make for an attractive treatment choice. Currently, there are only a small number of RNA-based drugs related to renal parenchymal disease, most of which are in different stages of clinical trials. We propose the use of miRNAs or short interfering RNAs coupled with a lipid-based nanocarrier as a delivery vehicle for managing renal disease.
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Affiliation(s)
- Chi-Ting Su
- Department of Medicine, National Taiwan University Cancer Centre, Taipei 10672, Taiwan; (C.-T.S.); (D.H.W.S.)
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Renal Division, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Douliu 640, Taiwan
| | - Daniel H. W. See
- Department of Medicine, National Taiwan University Cancer Centre, Taipei 10672, Taiwan; (C.-T.S.); (D.H.W.S.)
| | - Jenq-Wen Huang
- Renal Division, Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Douliu 640, Taiwan
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