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Li X, Jin K, Cheng TC, Liao YC, Lee WJ, Bhullar AS, Chen LC, Rychahou P, Phelps MA, Ho YS, Guo P. RNA four-way junction (4WJ) for spontaneous cancer-targeting, effective tumor-regression, metastasis suppression, fast renal excretion and undetectable toxicity. Biomaterials 2024; 305:122432. [PMID: 38176263 PMCID: PMC10994150 DOI: 10.1016/j.biomaterials.2023.122432] [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: 08/12/2023] [Revised: 11/14/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024]
Abstract
The field of RNA therapeutics has been emerging as the third milestone in pharmaceutical drug development. RNA nanoparticles have displayed motile and deformable properties to allow for high tumor accumulation with undetectable healthy organ accumulation. Therefore, RNA nanoparticles have the potential to serve as potent drug delivery vehicles with strong anti-cancer responses. Herein, we report the physicochemical basis for the rational design of a branched RNA four-way junction (4WJ) nanoparticle that results in advantageous high-thermostability and -drug payload for cancer therapy, including metastatic tumors in the lung. The 4WJ nanostructure displayed versatility through functionalization with an anti-cancer chemical drug, SN38, for the treatment of two different cancer models including colorectal cancer xenograft and orthotopic lung metastases of colon cancer. The resulting 4WJ RNA drug complex spontaneously targeted cancers effectively for cancer inhibition with and without ligands. The 4WJ displayed fast renal excretion, rapid body clearance, and little organ accumulation with undetectable toxicity and immunogenicity. The safety parameters were documented by organ histology, blood biochemistry, and pathological analysis. The highly efficient cancer inhibition, undetectable drug toxicity, and favorable Chemical, Manufacturing, and Control (CMC) production of RNA nanoparticles document a candidate with high potential for translation in cancer therapy.
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Affiliation(s)
- Xin Li
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Kai Jin
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Tzu-Chun Cheng
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, 406040, Taiwan
| | - You-Cheng Liao
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 110031, Taiwan
| | - Wen-Jui Lee
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Abhjeet S Bhullar
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Li-Ching Chen
- Department of Biological Science & Technology, China Medical University, Taichung, 406040, Taiwan
| | - Piotr Rychahou
- Markey Cancer Center, Department of Surgery, University of Kentucky, Lexington, KY, 40536, USA
| | - Mitch A Phelps
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Yuan Soon Ho
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, 406040, Taiwan.
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Nanotechnology and Nanomedicine, The Ohio State University, Columbus, OH, 43210, USA; James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
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2
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Dobrovolskaia MA. Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies. Molecules 2019; 24:molecules24244620. [PMID: 31861154 PMCID: PMC6943637 DOI: 10.3390/molecules24244620] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Vaccines and immunotherapies involve a variety of technologies and act through different mechanisms to achieve a common goal, which is to optimize the immune response against an antigen. The antigen could be a molecule expressed on a pathogen (e.g., a disease-causing bacterium, a virus or another microorganism), abnormal or damaged host cells (e.g., cancer cells), environmental agent (e.g., nicotine from a tobacco smoke), or an allergen (e.g., pollen or food protein). Immunogenic vaccines and therapies optimize the immune response to improve the eradication of the pathogen or damaged cells. In contrast, tolerogenic vaccines and therapies retrain or blunt the immune response to antigens, which are recognized by the immune system as harmful to the host. To optimize the immune response to either improve the immunogenicity or induce tolerance, researchers employ different routes of administration, antigen-delivery systems, and adjuvants. Nanocarriers and adjuvants are of particular interest to the fields of vaccines and immunotherapy as they allow for targeted delivery of the antigens and direct the immune response against these antigens in desirable direction (i.e., to either enhance immunogenicity or induce tolerance). Recently, nanoparticles gained particular attention as antigen carriers and adjuvants. This review focuses on a particular subclass of nanoparticles, which are made of nucleic acids, so-called nucleic acid nanoparticles or NANPs. Immunological properties of these novel materials and considerations for their clinical translation are discussed.
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Affiliation(s)
- Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
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3
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Cai R, Price IR, Ding F, Wu F, Chen T, Zhang Y, Liu G, Jardine PJ, Lu C, Ke A. ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor. Nucleic Acids Res 2019; 47:9818-9828. [PMID: 31396619 PMCID: PMC6765105 DOI: 10.1093/nar/gkz692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 11/19/2022] Open
Abstract
Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA–gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a ‘Z’-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.
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Affiliation(s)
- Rujie Cai
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Ian R Price
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Fang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Feifei Wu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Ting Chen
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Yunlong Zhang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Changrui Lu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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4
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Pi F, Zhang H, Li H, Thiviyanathan V, Gorenstein DG, Sood AK, Guo P. RNA nanoparticles harboring annexin A2 aptamer can target ovarian cancer for tumor-specific doxorubicin delivery. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2017; 13:1183-1193. [PMID: 27890659 PMCID: PMC5426907 DOI: 10.1016/j.nano.2016.11.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022]
Abstract
A novel modified nucleic acid nanoparticle harboring an annexin A2 aptamer for ovarian cancer cell targeting and a GC rich sequence for doxorubicin loading is designed and constructed. The system utilizes a highly stable three-way junction (3WJ) motif from phi29 packaging RNA as a core structure. A phosphorothioate-modified DNA aptamer targeting annexin A2, Endo28, was conjugated to one arm of the 3WJ. The pRNA-3WJ motif retains correct folding of attached aptamer, keeping its functions intact. It is of significant utility for aptamer-mediated targeted delivery. The DNA/RNA hybrid nanoparticles remained intact after systemic injection in mice and strongly bound to tumors with little accumulation in healthy organs 6 h post-injection. The Endo28-3WJ-Sph1/Dox intercalates selectively enhanced toxicity to annexin A2 positive ovarian cancer cells in vitro. The constructed RNA/DNA hybrid nanoparticles can potentially enhance the therapeutic efficiency of doxorubicin at low doses for ovarian cancer treatment through annexin A2 targeted drug delivery.
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Affiliation(s)
- Fengmei Pi
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Hui Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Varatharasa Thiviyanathan
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center, Houston, TX, USA; AM Biotechnologies, Houston, TX, USA
| | - David G Gorenstein
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center, Houston, TX, USA; AM Biotechnologies, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Center for RNA Interference and Non-Coding RNA, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
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5
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Doyle F, Lapsia S, Spadaro S, Wurz ZE, Bhaduri-McIntosh S, Tenenbaum SA. Engineering Structurally Interacting RNA (sxRNA). Sci Rep 2017; 7:45393. [PMID: 28350000 PMCID: PMC5368982 DOI: 10.1038/srep45393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/22/2017] [Indexed: 01/01/2023] Open
Abstract
RNA-based three-way junctions (3WJs) are naturally occurring structures found in many functional RNA molecules including rRNA, tRNA, snRNA and ribozymes. 3WJs are typically characterized as resulting from an RNA molecule folding back on itself in cis but could also form in trans when one RNA, for instance a microRNA binds to a second structured RNA, such as a mRNA. Trans-3WJs can influence the final shape of one or both of the RNA molecules and can thus provide a means for modulating the availability of regulatory motifs including potential protein or microRNA binding sites. Regulatory 3WJs generated in trans represent a newly identified regulatory category that we call structurally interacting RNA or sxRNA for convenience. Here we show that they can be rationally designed using familiar cis-3WJ examples as a guide. We demonstrate that an sxRNA "bait" sequence can be designed to interact with a specific microRNA "trigger" sequence, creating a regulatable RNA-binding protein motif that retains its functional activity. Further, we show that when placed downstream of a coding sequence, sxRNA can be used to switch "ON" translation of that sequence in the presence of the trigger microRNA and the amount of translation corresponded with the amount of microRNA present.
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Affiliation(s)
- Francis Doyle
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA
| | - Sameer Lapsia
- Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Salvatore Spadaro
- Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Zachary E. Wurz
- HocusLocus, LLC, 253 Fuller Road, Nanofab North, Albany NY 12203, USA
| | - Sumita Bhaduri-McIntosh
- Pediatric Infectious Diseases, Departments of Pediatrics and Molecular Genetics and Microbiology, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Scott A. Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA
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6
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Jasinski DL, Khisamutdinov EF, Lyubchenko YL, Guo P. Physicochemically tunable polyfunctionalized RNA square architecture with fluorogenic and ribozymatic properties. ACS NANO 2014; 8:7620-9. [PMID: 24971772 PMCID: PMC4148160 DOI: 10.1021/nn502160s] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/27/2014] [Indexed: 05/22/2023]
Abstract
Recent advances in RNA nanotechnology allow the rational design of various nanoarchitectures. Previous methods utilized conserved angles from natural RNA motifs to form geometries with specific sizes. However, the feasibility of producing RNA architecture with variable sizes using native motifs featuring fixed sizes and angles is limited. It would be advantageous to display RNA nanoparticles of diverse shape and size derived from a given primary sequence. Here, we report an approach to construct RNA nanoparticles with tunable size and stability. Multifunctional RNA squares with a 90° angle were constructed by tuning the 60° angle of the three-way junction (3WJ) motif from the packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor. The physicochemical properties and size of the RNA square were also easily tuned by modulating the “core” strand and adjusting the length of the sides of the square via predictable design. Squares of 5, 10, and 20 nm were constructed, each showing diverse thermodynamic and chemical stabilities. Four “arms” extending from the corners of the square were used to incorporate siRNA, ribozyme, and fluorogenic RNA motifs. Unique intramolecular contact using the pre-existing intricacy of the 3WJ avoids relatively weaker intermolecular interactions via kissing loops or sticky ends. Utilizing the 3WJ motif, we have employed a modular design technique to construct variable-size RNA squares with controllable properties and functionalities for diverse and versatile applications with engineering, pharmaceutical, and medical potential. This technique for simple design to finely tune physicochemical properties adds a new angle to RNA nanotechnology.
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Affiliation(s)
- Daniel L. Jasinski
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Emil F. Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Address correspondence to
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7
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Khisamutdinov EF, Jasinski DL, Guo P. RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS NANO 2014; 8:4771-81. [PMID: 24694194 PMCID: PMC4046798 DOI: 10.1021/nn5006254] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/25/2014] [Indexed: 05/22/2023]
Abstract
RNA is a polyribonucleic acid belonging to a special class of anionic polymers, holding a unique property of self-assembly that is controllable in the construction of structures with defined size, shape, and stoichiometry. We report here the use of RNA as polymers to fabricate boiling-resistant triangular nanoscaffolds, which were used to construct hexagons and patterned hexagonal arrays. The RNA triangular scaffolds demonstrated promising potential to construct fluorogenic probes and therapeutic agents as functionalization with siRNA, ribozyme, folate, and fluorogenic RNA aptamers revealed independent functional activity of each RNA moiety. The ribozyme was able to cleave hepatitis genomic RNA fragments, the siRNA silenced the target genes, and all fluorogenic RNA aptamers retained their fluorescence emission property. The creation of boiling-temperature-resistant RNA nanoparticles opens a new dimension of RNA as a special polymer, feasible in industrial and nanotechnological applications.
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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9
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Shu Y, Shu D, Haque F, Guo P. Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat Protoc 2013; 8:1635-59. [PMID: 23928498 DOI: 10.1038/nprot.2013.097] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA nanotechnology is a term that refers to the design, fabrication and use of nanoparticles that are mainly composed of RNAs via bottom-up self-assembly. The packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor has been developed into a nanodelivery platform. This protocol describes the synthesis, assembly and functionalization of pRNA nanoparticles on the basis of three 'toolkits' derived from pRNA structural features: interlocking loops for hand-in-hand interactions, palindrome sequences for foot-to-foot interactions and an RNA three-way junction for branch extension. siRNAs, ribozymes, aptamers, chemical ligands, fluorophores and other functionalities can also be fused to the pRNA before the assembly of the nanoparticles, so as to ensure the production of homogeneous nanoparticles and the retention of appropriate folding and function of the incorporated modules. The resulting self-assembled multivalent pRNA nanoparticles are thermodynamically and chemically stable, and they remain intact at ultralow concentrations. Gene-silencing effects are progressively enhanced with increasing numbers of siRNAs in each pRNA nanoparticle. Systemic injection of the pRNA nanoparticles into xenograft-bearing mice has revealed strong binding to tumors without accumulation in vital organs or tissues. The pRNA-based nanodelivery scaffold paves a new way for nanotechnological application of pRNA-based nanoparticles for disease detection and treatment. The time required for completing one round of this protocol is 3-4 weeks when including in vitro functional assays, or 2-3 months when including in vivo studies.
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Affiliation(s)
- Yi Shu
- Nanobiotechnology Center, Markey Cancer Center, Lexington, Kentucky, USA
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