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Batra N, Tu MJ, Yu AM. Molecular Engineering of Functional SiRNA Agents. ACS Synth Biol 2024; 13:1906-1915. [PMID: 38733599 PMCID: PMC11197084 DOI: 10.1021/acssynbio.4c00181] [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: 03/12/2024] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Synthetic biology constitutes a scientific domain focused on intentional redesign of organisms to confer novel functionalities or create new products through strategic engineering of their genetic makeup. Leveraging the inherent capabilities of nature, one may address challenges across diverse sectors including medicine. Inspired by this concept, we have developed an innovative bioengineering platform, enabling high-yield and large-scale production of biological small interfering RNA (BioRNA/siRNA) agents via bacterial fermentation. Herein, we show that with the use of a new tRNA fused pre-miRNA carrier, we can produce various forms of BioRNA/siRNA agents within living host cells. We report a high-level overexpression of nine target BioRNA/siRNA molecules at 100% success rate, yielding 3-10 mg of BioRNA/siRNA per 0.25 L of bacterial culture with high purity (>98%) and low endotoxin (<5 EU/μg RNA). Furthermore, we demonstrate that three representative BioRNA/siRNAs against GFP, BCL2, and PD-L1 are biologically active and can specifically and efficiently silence their respective targets with the potential to effectively produce downstream antiproliferation effects by PD-L1-siRNA. With these promising results, we aim to advance the field of synthetic biology by offering a novel platform to bioengineer functional siRNA agents for research and drug development.
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Affiliation(s)
- Neelu Batra
- Department of Biochemistry
and Molecular Medicine, UC Davis School
of Medicine, Sacramento, California 95817, United States
| | - Mei-Juan Tu
- Department of Biochemistry
and Molecular Medicine, UC Davis School
of Medicine, Sacramento, California 95817, United States
| | - Ai-Ming Yu
- Department of Biochemistry
and Molecular Medicine, UC Davis School
of Medicine, Sacramento, California 95817, United States
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2
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Ahmed T. Lipid nanoparticle mediated small interfering RNA delivery as a potential therapy for Alzheimer's disease. Eur J Neurosci 2024; 59:2915-2954. [PMID: 38622050 DOI: 10.1111/ejn.16336] [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: 09/18/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative condition that exhibits a gradual decline in cognitive function and is prevalent among a significant number of individuals globally. The use of small interfering RNA (siRNA) molecules in RNA interference (RNAi) presents a promising therapeutic strategy for AD. Lipid nanoparticles (LNPs) have been developed as a delivery vehicle for siRNA, which can selectively suppress target genes, by enhancing cellular uptake and safeguarding siRNA from degradation. Numerous research studies have exhibited the effectiveness of LNP-mediated siRNA delivery in reducing amyloid beta (Aβ) levels and enhancing cognitive function in animal models of AD. The feasibility of employing LNP-mediated siRNA delivery as a therapeutic approach for AD is emphasized by the encouraging outcomes reported in clinical studies for other medical conditions. The use of LNP-mediated siRNA delivery has emerged as a promising strategy to slow down or even reverse the progression of AD by targeting the synthesis of tau phosphorylation and other genes linked to the condition. Improvement of the delivery mechanism and determination of the most suitable siRNA targets are crucial for the efficacious management of AD. This review focuses on the delivery of siRNA through LNPs as a promising therapeutic strategy for AD, based on the available literature.
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Affiliation(s)
- Tanvir Ahmed
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
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3
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Zhang B, Zhang H, Wang Z, Cao H, Zhang N, Dai Z, Liang X, Peng Y, Wen J, Zhang X, Zhang L, Luo P, Zhang J, Liu Z, Cheng Q, Peng R. The regulatory role and clinical application prospects of circRNA in the occurrence and development of CNS tumors. CNS Neurosci Ther 2024; 30:e14500. [PMID: 37953502 PMCID: PMC11017455 DOI: 10.1111/cns.14500] [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: 06/29/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Central nervous system (CNS) tumors originate from the spinal cord or brain. The study showed that even with aggressive treatment, malignant CNS tumors have high mortality rates. However, CNS tumor risk factors and molecular mechanisms have not been verified. Due to the reasons mentioned above, diagnosis and treatment of CNS tumors in clinical practice are currently fraught with difficulties. Circular RNAs (circRNAs), single-stranded ncRNAs with covalently closed continuous structures, are essential to CNS tumor development. Growing evidence has proved the numeral critical biological functions of circRNAs for disease progression: sponging to miRNAs, regulating gene transcription and splicing, interacting with proteins, encoding proteins/peptides, and expressing in exosomes. AIMS This review aims to summarize current progress regarding the molecular mechanism of circRNA in CNS tumors and to explore the possibilities of clinical application based on circRNA in CNS tumors. METHODS We have summarized studies of circRNA in CNS tumors in Pubmed. RESULTS This review summarized their connection with CNS tumors and their functions, biogenesis, and biological properties. Furthermore, we introduced current advances in clinical RNA-related technologies. Then we discussed the diagnostic and therapeutic potential (especially for immunotherapy, chemotherapy, and radiotherapy) of circRNA in CNS tumors in the context of the recent advanced research and application of RNA in clinics. CONCLUSIONS CircRNA are increasingly proven to participate in decveloping CNS tumors. An in-depth study of the causal mechanisms of circRNAs in CNS tomor progression will ultimately advance their implementation in the clinic and developing new strategies for preventing and treating CNS tumors.
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Affiliation(s)
- Bo Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Hao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Department of Neurosurgery, The Second Affiliated HospitalChongqing Medical UniversityChongqingChina
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- MRC Centre for Regenerative Medicine, Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Hui Cao
- Department of Psychiatry, The School of Clinical MedicineHunan University of Chinese MedicineChangshaChina
| | - Nan Zhang
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xisong Liang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yun Peng
- Teaching and Research Section of Clinical NursingXiangya Hospital of Central South UniversityChangshaChina
- Department of Geriatrics, Xiangya HospitalCentral South UniversityChangshaChina
| | - Jie Wen
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xun Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Renjun Peng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
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4
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Teodori L, Omer M, Kjems J. RNA nanostructures for targeted drug delivery and imaging. RNA Biol 2024; 21:1-19. [PMID: 38555519 PMCID: PMC10984137 DOI: 10.1080/15476286.2024.2328440] [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] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
The RNA molecule plays a pivotal role in many biological processes by relaying genetic information, regulating gene expression, and serving as molecular machines and catalyzers. This inherent versatility of RNA has fueled significant advancements in the field of RNA nanotechnology, driving the engineering of complex nanoscale architectures toward biomedical applications, including targeted drug delivery and bioimaging. RNA polymers, serving as building blocks, offer programmability and predictability of Watson-Crick base pairing, as well as non-canonical base pairing, for the construction of nanostructures with high precision and stoichiometry. Leveraging the ease of chemical modifications to protect the RNA from degradation, researchers have developed highly functional and biocompatible RNA architectures and integrated them into preclinical studies for the delivery of payloads and imaging agents. This review offers an educational introduction to the use of RNA as a biopolymer in the design of multifunctional nanostructures applied to targeted delivery in vivo, summarizing physical and biological barriers along with strategies to overcome them. Furthermore, we highlight the most recent progress in the development of both small and larger RNA nanostructures, with a particular focus on imaging reagents and targeted cancer therapeutics in pre-clinical models and provide insights into the prospects of this rapidly evolving field.
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Affiliation(s)
- Laura Teodori
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
| | - Marjan Omer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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5
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Kim S, Kang YG, Kim J, Dua P, Lee DK. Development of Long Asymmetric siRNA Structure for Target Gene Silencing and Immune Stimulation in Mammalian Cells. Nucleic Acid Ther 2023; 33:329-337. [PMID: 37797162 DOI: 10.1089/nat.2023.0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
Post-transcriptional regulation of transcript abundances by RNA interference (RNAi) is a widely conserved regulatory mechanism to control cellular processes. We previously introduced an alternative siRNA structure called asymmetric siRNA (asiRNA), and showed that asiRNA exhibits comparable gene-silencing efficiency with reduced off-target effects compared with conventional siRNAs. However, to what extent the length of the guide strand affects the gene-silencing efficiency of asiRNAs is still elusive. In this study, we analyzed in detail the gene-silencing ability of asiRNAs along the guide strand length and immunostimulatory capacity of asiRNAs. We generated asiRNAs containing various guide strand lengths ranging from 25 to 29 nt, called long asiRNA (lasiRNA). We found that the gene-silencing activity of lasiRNAs decreased as the length of the guide strand increased. Nonetheless, the 3'-end overhangs that are complementary to the target gene have higher efficiency for gene silencing compared with mismatched overhangs. In addition, we found that the silencing efficiency of lasiRNAs correlates with their Ago2-binding affinity. Finally, replacing the mismatched overhang with a TLR7- or TLR9-associated immune response motif induced a toll-like receptor (TLR)-specific immune response and retained gene-silencing activity. Our findings demonstrate that lasiRNA structures can be tailored to function as bifunctional siRNA, which trigger a specific immune response combined with target gene silencing. Taken together, we anticipate that our findings provide a road map for the subsequent development of immune-stimulating lasiRNA, which bear the potential to be applied for therapeutic benefits.
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Affiliation(s)
- Soonkap Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Young Gyu Kang
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
- Department of Platform Technology Unit2, OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Jaejin Kim
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
| | - Pooja Dua
- Department of Platform Technology Unit2, OliX Pharmaceuticals, Inc., Suwon, Korea
| | - Dong-Ki Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, Korea
- Department of Platform Technology Unit2, OliX Pharmaceuticals, Inc., Suwon, Korea
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6
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Ren W, Duan S, Dai C, Xie C, Jiang L, Shi Y. Nanotechnology Lighting the Way for Gene Therapy in Ophthalmopathy: From Opportunities toward Applications. Molecules 2023; 28:molecules28083500. [PMID: 37110734 PMCID: PMC10141718 DOI: 10.3390/molecules28083500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Hereditary ophthalmopathy is a well-described threat to human visual health affecting millions of people. Gene therapy for ophthalmopathy has received widespread attention with the increasing understanding of pathogenic genes. Effective and safe delivery of accurate nucleic acid drugs (NADs) is the core of gene therapy. Efficient nanodelivery and nanomodification technologies, appropriate targeted genes, and the choice of drug injection methods are the guiding lights of gene therapy. Compared with traditional drugs, NADs can specifically change the expression of specific genes or restore the normal function of mutant genes. Nanodelivery carriers can improve targeting and nanomodification can improve the stability of NADs. Therefore, NADs, which can fundamentally solve pathogeny, hold great promise in the treatment of ophthalmopathy. This paper reviews the limitations of ocular disease treatment, discusses the classification of NADs in ophthalmology, reveals the delivery strategies of NADs to improve bioavailability, targeting, and stability, and summarizes the mechanisms of NADs in ophthalmopathy.
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Affiliation(s)
- Weiming Ren
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Suyang Duan
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chao Dai
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chunbao Xie
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Lingxi Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 610072, China
- Department of Ophthalmology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
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7
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EGFR-Targeted Cellular Delivery of Therapeutic Nucleic Acids Mediated by Boron Clusters. Int J Mol Sci 2022; 23:ijms232314793. [PMID: 36499115 PMCID: PMC9740766 DOI: 10.3390/ijms232314793] [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: 10/17/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
New boron carriers with high boron content and targeted cancer-cell delivery are considered the first choice for boron neutron capture therapy (BNCT) for cancer treatment. Previously, we have shown that composites of antisense oligonucleotide and boron clusters are functional nanoparticles for the downregulation of expression of epidermal growth factor receptor (EGFR) and can be loaded into EGFR-overexpressing cancer cells without a transfection factor. In this study, we hypothesize that free cellular uptake is mediated by binding and activation of the EGFR by boron clusters. Proteomic analysis of proteins pulled-down from various EGFR-overexpressing cancer cells using short oligonucleotide probes, conjugated to 1,2-dicarba-closo-dodecaborane (1,2-DCDDB, [C2B10H12]) and [(3,3'-Iron-1,2,1',2'-dicarbollide)-] (FESAN, [Fe(C2B9H11)2]-), evidenced that boron cage binds to EGFR subdomains. Moreover, inductively coupled plasma mass spectrometry (ICP MS) and fluorescence microscopy analyses confirmed that FESANs-highly decorated B-ASOs were efficiently delivered and internalized by EGFR-overexpressing cells. Antisense reduction of EGFR in A431 and U87-MG cells resulted in decreased boron accumulation compared to control cells, indicating that cellular uptake of B-ASOs is related to EGFR-dependent internalization. The data obtained suggest that EGFR-mediated cellular uptake of B-ASO represents a novel strategy for cellular delivery of therapeutic nucleic acids (and possibly other medicines) conjugated to boron clusters.
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8
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Bano N, Ehlinger C, Yang TY, Swanson M, Allen S. Considerations in the Immunogenicity Assessment Strategy for Oligonucleotide Therapeutics (ONTs). AAPS J 2022; 24:93. [DOI: 10.1208/s12248-022-00741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
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9
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Zhu Y, Zhu L, Wang X, Jin H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis 2022; 13:644. [PMID: 35871216 PMCID: PMC9308039 DOI: 10.1038/s41419-022-05075-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto "undruggable" proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
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Affiliation(s)
- Yiran Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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10
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Tsunoda T, Tanoeyadi S, Proteau PJ, Mahmud T. The chemistry and biology of natural ribomimetics and related compounds. RSC Chem Biol 2022; 3:519-538. [PMID: 35656477 PMCID: PMC9092360 DOI: 10.1039/d2cb00019a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022] Open
Abstract
Natural ribomimetics represent an important group of specialized metabolites with significant biological activities. Many of the activities, e.g., inhibition of seryl-tRNA synthetases, glycosidases, or ribosomes, are manifestations of their structural resemblance to ribose or related sugars, which play roles in the structural, physiological, and/or reproductive functions of living organisms. Recent studies on the biosynthesis and biological activities of some natural ribomimetics have expanded our understanding on how they are made in nature and why they have great potential as pharmaceutically relevant products. This review article highlights the discovery, biological activities, biosynthesis, and development of this intriguing class of natural products.
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Affiliation(s)
- Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
| | - Samuel Tanoeyadi
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
| | - Philip J Proteau
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University Corvallis OR 97331 USA
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11
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Fitzmaurice O, Bartkowski M, Giordani S. Molecular Switches—Tools for Imparting Control in Drug Delivery Systems. Front Chem 2022; 10:859450. [PMID: 35433638 PMCID: PMC9008311 DOI: 10.3389/fchem.2022.859450] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
Cancer is a globally prevalent cause of premature mortality. Of growing interest is the development of novel anticancer therapies and the optimisation of associated risks. Major issues presently facing conventional anticancer therapies include systemic toxicity, poor solubility, membrane permeability, and multidrug resistance Nanocarriers have been employed to address these issues. Nanocarriers encapsulate anticancer drugs, enabling them to bypass biological barriers and minimise their adverse side effects. These drug delivery systems offer extensive benefits as they can be modified to gravitate towards specific environmental conditions. To further enhance the safety and efficacy of these drug carriers, modern developments have included incorporating a molecular switching mechanism into their structure. These molecular switches are responsive to endogenous and exogenous stimuli and may undergo reversible and repeatable conformational changes when activated. The incorporation of molecular switches can, therefore, impart stimuli-responsive drug-release control on a DDS. These stimuli can then be manipulated to offer precise dosage control over the drug release at a specific target site. This review discusses recent developments in the design of DDSs incorporating light and pH-responsive molecular switches as drug release controllers.
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12
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Tu MJ, Yi CM, Traber GM, Yu AM. Bioengineered RNA Therapy in Patient-Derived Organoids and Xenograft Mouse Models. Methods Mol Biol 2022; 2521:191-206. [PMID: 35732999 PMCID: PMC9484490 DOI: 10.1007/978-1-0716-2441-8_10] [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] [Indexed: 06/15/2023]
Abstract
Therapeutic RNAs, such as antisense oligonucleotides (ASOs), aptamers, small-interfering RNAs (siRNAs), microRNAs (miRs or miRNAs), messenger RNAs (mRNAs), and guide RNAs (gRNAs), represent a novel class of modalities that not only increase the molecular diversity of medications but also expand the range of druggable targets. To develop noncoding RNA therapeutics for the treatment of cancer diseases, we have established a novel robust RNA bioengineering platform to achieve high-yield and large-scale production of true biologic RNA agents, which are proven to be functional in the control of target gene expression and effective in the management of tumor progression in various models. Herein, we describe the methods for bioengineered RNA (BioRNA or BERA) therapy in patient-derived organoids (PDOs) in vitro and patient-derived xenograft (PDX) mouse models in vivo. The efficacy of a BioRNA, miR-1291, in the inhibition of pancreatic cancer PDO and PDX growth is exemplified in this chapter.
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Affiliation(s)
- Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Colleen M Yi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Gavin M Traber
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, USA.
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13
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Bibby G, Krasniqi B, Reddy I, Sekar D, Ross K. Capturing the RNA castle: Exploiting MicroRNA inhibition for wound healing. FEBS J 2021; 289:5137-5151. [PMID: 34403569 DOI: 10.1111/febs.16160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/14/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
The growing pipelines of RNA-based therapies herald new opportunities to deliver better patient outcomes for complex disorders such as chronic nonhealing wounds associated with diabetes. Members of the microRNA (miRNA) family of small noncoding RNAs have emerged as targets for diverse elements of cutaneous wound repair, and both miRNA enhancement with mimics or inhibition with antisense oligonucleotides represent tractable approaches for miRNA-directed wound healing. In this review, we focus on miRNA inhibition strategies to stimulate skin repair given advances in chemical modifications to enhance the performance of antisense miRNA (anti-miRs). We first explore miRNAs whose inhibition in keratinocytes promotes keratinocyte migration, an essential part of re-epithelialisation during wound repair. We then focus on miRNAs that can be targeted for inhibition in endothelial cells to promote neovascularisation for wound healing in the context of diabetic mouse models. The picture that emerges is that direct comparisons of different anti-miRNAs modifications are required to establish the most translationally viable options in the chronic wound environment, that direct comparisons of the impact of inhibition of different miRNAs are needed to quantify and rank their relative efficacies in promoting wound repair, and that a standardised human ex vivo model of the diabetic wound is needed to reduce reliance on mouse models that do not necessarily enhance mechanistic understanding of miRNA-targeted wound healing.
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Affiliation(s)
- George Bibby
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Blerta Krasniqi
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Izaak Reddy
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
| | - Durairaj Sekar
- Dental Research Cell and Biomedical Research Unit (DRC-BRULAC), Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Science (SIMATS), Saveetha University, Chennai, India
| | - Kehinde Ross
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, UK
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14
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Yu AM, Tu MJ. Deliver the promise: RNAs as a new class of molecular entities for therapy and vaccination. Pharmacol Ther 2021; 230:107967. [PMID: 34403681 PMCID: PMC9477512 DOI: 10.1016/j.pharmthera.2021.107967] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
The concepts of developing RNAs as new molecular entities for therapies have arisen again and again since the discoveries of antisense RNAs, direct RNA-protein interactions, functional noncoding RNAs, and RNA-directed gene editing. The feasibility was demonstrated with the development and utilization of synthetic RNA agents to selectively control target gene expression, modulate protein functions or alter the genome to manage diseases. Rather, RNAs are labile to degradation and cannot cross cell membrane barriers, making it hard to develop RNA medications. With the development of viable RNA technologies, such as chemistry and pharmaceutics, eight antisense oligonucleotides (ASOs) (fomivirsen, mipomersen, eteplirsen, nusinersen, inotersen, golodirsen, viltolarsen and casimersen), one aptamer (pegaptanib), and three small interfering RNAs (siRNAs) (patisiran, givosiran and lumasiran) have been approved by the United States Food and Drug Administration (FDA) for therapies, and two mRNA vaccines (BNT162b2 and mRNA-1273) under Emergency Use Authorization for the prevention of COVID-19. Therefore, RNAs have become a great addition to small molecules, proteins/antibodies, and cell-based modalities to improve the public health. In this article, we first summarize the general characteristics of therapeutic RNA agents, including chemistry, common delivery strategies, mechanisms of actions, and safety. By overviewing individual RNA medications and vaccines approved by the FDA and some agents under development, we illustrate the unique compositions and pharmacological actions of RNA products. A new era of RNA research and development will likely lead to commercialization of more RNA agents for medical use, expanding the range of therapeutic targets and increasing the diversity of molecular modalities.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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15
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Wang P, Zhou Y, Richards AM. Effective tools for RNA-derived therapeutics: siRNA interference or miRNA mimicry. Theranostics 2021; 11:8771-8796. [PMID: 34522211 PMCID: PMC8419061 DOI: 10.7150/thno.62642] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
The approval of the first small interfering RNA (siRNA) drug Patisiran by FDA in 2018 marks a new era of RNA interference (RNAi) therapeutics. MicroRNAs (miRNA), an important post-transcriptional gene regulator, are also the subject of both basic research and clinical trials. Both siRNA and miRNA mimics are ~21 nucleotides RNA duplexes inducing mRNA silencing. Given the well performance of siRNA, researchers ask whether miRNA mimics are unnecessary or developed siRNA technology can pave the way for the emergence of miRNA mimic drugs. Through comprehensive comparison of siRNA and miRNA, we focus on (1) the common features and lessons learnt from the success of siRNAs; (2) the unique characteristics of miRNA that potentially offer additional therapeutic advantages and opportunities; (3) key areas of ongoing research that will contribute to clinical application of miRNA mimics. In conclusion, miRNA mimics have unique properties and advantages which cannot be fully matched by siRNA in clinical applications. MiRNAs are endogenous molecules and the gene silencing effects of miRNA mimics can be regulated or buffered to ameliorate or eliminate off-target effects. An in-depth understanding of the differences between siRNA and miRNA mimics will facilitate the development of miRNA mimic drugs.
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Affiliation(s)
- Peipei Wang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Yue Zhou
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
| | - Arthur M. Richards
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Medicine, National University Health System, 119228 Singapore
- Christchurch Heart Institute, Department of Medicine, University of Otago Christchurch, New Zealand
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16
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 PMCID: PMC8312718 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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17
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Butreddy A, Kommineni N, Dudhipala N. Exosomes as Naturally Occurring Vehicles for Delivery of Biopharmaceuticals: Insights from Drug Delivery to Clinical Perspectives. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1481. [PMID: 34204903 PMCID: PMC8229362 DOI: 10.3390/nano11061481] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Exosomes as nanosized vesicles are emerging as drug delivery systems for therapeutics owing to their natural origin, their ability to mediate intercellular communication, and their potential to encapsulate various biological molecules such as proteins and nucleic acids within the lipid bilayer membrane or in the lumen. Exosomes contain endogenous components (proteins, lipids, RNA) that could be used to deliver cargoes to target cells, offering an opportunity to diagnose and treat various diseases. Owing to their ability to travel safely in extracellular fluid and to transport cargoes to target cells with high efficacy, exosomes offer enhanced delivery of cargoes in vivo. However, several challenges related to the stabilization of the exosomes, the production of sufficient amounts of exosomes with safety and efficacy, the efficient loading of drugs into exosomes, the clearance of exosomes from circulation, and the transition from the bench scale to clinical production may limit their development and clinical use. For the clinical use of exosomes, it is important to understand the molecular mechanisms behind the transport and function of exosome vesicles. This review exploits techniques related to the isolation and characterization of exosomes and their drug delivery potential to enhance the therapeutic outcome and stabilization methods. Further, routes of administration, clinical trials, and regulatory aspects of exosomes will be discussed in this review.
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Affiliation(s)
- Arun Butreddy
- Formulation R&D, Biological E. Limited, IKP Knowledge Park, Shameerpet, Hyderabad 500078, Telangana State, India;
| | - Nagavendra Kommineni
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, USA;
| | - Narendar Dudhipala
- Depratment of Pharmaceutics, Vaagdevi College of Pharmacy, Warangal 506005, Telangana State, India
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18
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Flynn LL, Mitrpant C, Adams A, Pitout IL, Stirnweiss A, Fletcher S, Wilton SD. Targeted SMN Exon Skipping: A Useful Control to Assess In Vitro and In Vivo Splice-Switching Studies. Biomedicines 2021; 9:552. [PMID: 34069072 PMCID: PMC8156830 DOI: 10.3390/biomedicines9050552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 01/23/2023] Open
Abstract
The literature surrounding the use of antisense oligonucleotides continues to grow, with new disease and mechanistic applications constantly evolving. Furthermore, the discovery and advancement of novel chemistries continues to improve antisense delivery, stability and effectiveness. For each new application, a rational sequence design is recommended for each oligomer, as is chemistry and delivery optimization. To confirm oligomer delivery and antisense activity, a positive control AO sequence with well characterized target-specific effects is recommended. Here, we describe splice-switching antisense oligomer sequences targeting the ubiquitously expressed human and mouse SMN and Smn genes for use as control AOs for this purpose. We report two AO sequences that induce targeted skipping of SMN1/SMN2 exon 7 and two sequences targeting the Smn gene, that induce skipping of exon 5 and exon 7. These antisense sequences proved effective in inducing alternative splicing in both in vitro and in vivo models and are therefore broadly applicable as controls. Not surprisingly, we discovered a number of differences in efficiency of exon removal between the two species, further highlighting the differences in splice regulation between species.
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Affiliation(s)
- Loren L. Flynn
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (L.L.F.); (A.A.); (I.L.P.); (S.F.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia;
- Centre for Neuromuscular & Neurological Disorders, University of Western Australia, Crawley, WA 6009, Australia
- Black Swan Pharmaceuticals, Wake Forest, NC 27587, USA
| | - Chalermchai Mitrpant
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia;
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Abbie Adams
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (L.L.F.); (A.A.); (I.L.P.); (S.F.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia;
- Centre for Neuromuscular & Neurological Disorders, University of Western Australia, Crawley, WA 6009, Australia
| | - Ianthe L. Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (L.L.F.); (A.A.); (I.L.P.); (S.F.)
- PYC Therapeutics, Nedlands, WA 6009, Australia;
| | | | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (L.L.F.); (A.A.); (I.L.P.); (S.F.)
- Centre for Neuromuscular & Neurological Disorders, University of Western Australia, Crawley, WA 6009, Australia
- PYC Therapeutics, Nedlands, WA 6009, Australia;
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia; (L.L.F.); (A.A.); (I.L.P.); (S.F.)
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia;
- Centre for Neuromuscular & Neurological Disorders, University of Western Australia, Crawley, WA 6009, Australia
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19
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Schlick T, Portillo-Ledesma S, Myers CG, Beljak L, Chen J, Dakhel S, Darling D, Ghosh S, Hall J, Jan M, Liang E, Saju S, Vohr M, Wu C, Xu Y, Xue E. Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field. Annu Rev Biophys 2021; 50:267-301. [PMID: 33606945 PMCID: PMC8105287 DOI: 10.1146/annurev-biophys-091720-102019] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We reassess progress in the field of biomolecular modeling and simulation, following up on our perspective published in 2011. By reviewing metrics for the field's productivity and providing examples of success, we underscore the productive phase of the field, whose short-term expectations were overestimated and long-term effects underestimated. Such successes include prediction of structures and mechanisms; generation of new insights into biomolecular activity; and thriving collaborations between modeling and experimentation, including experiments driven by modeling. We also discuss the impact of field exercises and web games on the field's progress. Overall, we note tremendous success by the biomolecular modeling community in utilization of computer power; improvement in force fields; and development and application of new algorithms, notably machine learning and artificial intelligence. The combined advances are enhancing the accuracy andscope of modeling and simulation, establishing an exemplary discipline where experiment and theory or simulations are full partners.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, New York University, New York, New York 10003, USA;
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
| | | | - Christopher G Myers
- Department of Chemistry, New York University, New York, New York 10003, USA;
| | - Lauren Beljak
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Justin Chen
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sami Dakhel
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Daniel Darling
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sayak Ghosh
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Joseph Hall
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Mikaeel Jan
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Emily Liang
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Sera Saju
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Mackenzie Vohr
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Chris Wu
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Yifan Xu
- College of Arts and Science, New York University, New York, New York 10003, USA
| | - Eva Xue
- College of Arts and Science, New York University, New York, New York 10003, USA
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20
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Zou M, Du Y, Liu R, Zheng Z, Xu J. Nanocarrier-delivered small interfering RNA for chemoresistant ovarian cancer therapy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1648. [PMID: 33682310 DOI: 10.1002/wrna.1648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022]
Abstract
Ovarian cancer is the fifth leading cause of cancer-related death in women in the United States. Because success in early screening is limited, and most patients with advanced disease develop resistance to multiple treatment modalities, the overall prognosis of ovarian cancer is poor. Despite the revolutionary role of surgery and chemotherapy in curing ovarian cancer, recurrence remains a major challenge in treatment. Thus, improving our understanding of the pathogenesis of ovarian cancer is essential for developing more effective treatments. In this review, we analyze the underlying molecular mechanisms leading to chemotherapy resistance. We discuss the clinical benefits and potential challenges of using nanocarrier-delivered small interfering RNA to treat chemotherapy-resistant ovarian cancer. We aim to elicit collaborative studies on nanocarrier-delivered small interfering RNA to improve the long-term survival rate and quality of life of patients with ovarian cancer. This article is categorized under: RNA Methods > RNA Nanotechnology Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.
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Affiliation(s)
- Mingyuan Zou
- Medical School of Southeast University, Nanjing, Jiangsu, China
| | - Yue Du
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruizhen Liu
- The First People's Hospital of Wu'an, Wu'an, Hebei, China
| | - Zeliang Zheng
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jian Xu
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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21
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Salim L, Goss E, Desaulniers JP. Synthesis and evaluation of modified siRNA molecules containing a novel glucose derivative. RSC Adv 2021; 11:9285-9289. [PMID: 35423452 PMCID: PMC8698894 DOI: 10.1039/d1ra00922b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 11/21/2022] Open
Abstract
Chemical modifications are critical for the development of safe and effective siRNAs for downstream applications. In this study, we report the synthesis of a novel glucose phosphoramidite, a triazole-linked to uracil at position one, for incorporation into oligonucleotides. Biological testing revealed that the glucose derivative at key positions within the sense or antisense strand can lead to potent gene-silencing activity, thus highlighting its tolerance in both sense and antisense positions. Furthermore, the A-form helical formation was maintained with this modification. Overall, placing the modification at the 3' end and at key internal positions led to effective RNAi gene-silencing activity.
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Affiliation(s)
- Lidya Salim
- University of Ontario Institute of Technology, Faculty of Science 2000 Simcoe Street North Oshawa ON L1G 0C5 Canada
| | - Eva Goss
- Synthose Inc. 50 Viceroy Road Unit 7 Concord ON L4K 3A7 Canada
| | - Jean-Paul Desaulniers
- University of Ontario Institute of Technology, Faculty of Science 2000 Simcoe Street North Oshawa ON L1G 0C5 Canada
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22
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Petrek H, Yan Ho P, Batra N, Tu MJ, Zhang Q, Qiu JX, Yu AM. Single bioengineered ncRNA molecule for dual-targeting toward the control of non-small cell lung cancer patient-derived xenograft tumor growth. Biochem Pharmacol 2021; 189:114392. [PMID: 33359565 DOI: 10.1016/j.bcp.2020.114392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Lung cancer remains the leading cause of cancer deaths worldwide and accounts for more than 22% of all cancer-related deaths in the US. Developing new therapies is essential to combat against deadly lung cancer, especially the most common type, non-small cell lung cancer (NSCLC). With the discovery of genome-derived functional small noncoding RNA (ncRNA), namely microRNAs (miRNA or miR), restoration of oncolytic miRNAs lost or downregulated in NSCLC cells represents a new therapeutic strategy. Very recently, we have developed a novel technology that achieves in vivo fermentation production of bioengineered miRNA agents (BERA) for research and development. In this study, we aimed at simultaneously introducing two miRNAs into NSCLC cells by using single recombinant "combinatorial BERA" (CO-BERA) molecule. Our studies show that single CO-BERA molecule (e.g., let-7c/miR-124) was successfully processed to two miRNAs (e.g., let-7c-5p and miR-124-3p) to combinatorially regulate the expression of multiple targets (e.g., RAS, VAMP3 and CDK6) in human NSCLC cells, exhibiting greater efficacy than respective BERA miRNAs in the inhibition of cell viability and colony formation. Furthermore, we demonstrate that CO-BERA let-7c/miR-124-loaded lipopolyplex nanomedicine was the most effective among tested RNAs in the control of tumor growth in NSCLC patient-derived xenograft mouse models. The anti-tumor activity of CO-BERA let-7c/miR-124 was associated with the suppression of RAS and CDK6 expression, and enhancement of apoptosis. These results support the concept to use single ncRNA agent for dual-targeting and offer insight into developing new RNA therapeutics for the treatment of lethal NSCLC.
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Affiliation(s)
- Hannah Petrek
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Pui Yan Ho
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Qianyu Zhang
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Jing-Xin Qiu
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
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23
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Tu MJ, Wright HK, Batra N, Yu AM. Expression and Purification of tRNA/ pre-miRNA-Based Recombinant Noncoding RNAs. Methods Mol Biol 2021; 2323:249-265. [PMID: 34086286 PMCID: PMC9516694 DOI: 10.1007/978-1-0716-1499-0_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Research on RNA function and therapeutic potential is dominated by the use of chemoengineered RNA mimics. Recent efforts have led to the establishment of novel technologies for the production of recombinant or bioengineered RNA molecules, which should better recapitulate the structures, functions and safety profiles of natural RNAs because both are produced and folded in living cells. Herein, we describe a robust approach for reproducible fermentation production of bioengineered RNA agents (BERAs) carrying warhead miRNAs, siRNAs, aptamers, or other forms of small RNAs, based upon an optimal hybrid tRNA/pre-miRNA carrier. Target BERA/sRNAs are readily purified by fast protein liquid chromatography (FPLC) to a high degree of homogeneity (>97%). This approach offers a consistent high-level expression (>30% of total bacterial RNAs) and large-scale production of ready-to-use BERAs (multiple to tens milligrams from 1 L bacterial culture).
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24
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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25
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Kim T, Viard M, Afonin KA, Gupta K, Popov M, Salotti J, Johnson PF, Linder C, Heldman E, Shapiro BA. Characterization of Cationic Bolaamphiphile Vesicles for siRNA Delivery into Tumors and Brain. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:359-372. [PMID: 32200271 PMCID: PMC7090283 DOI: 10.1016/j.omtn.2020.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/19/2019] [Accepted: 02/23/2020] [Indexed: 12/27/2022]
Abstract
Small interfering RNAs (siRNAs) are potential therapeutic substances due to their gene silencing capability as exemplified by the recent approval by the US Food and Drug Administration (FDA) of the first siRNA therapeutic agent (patisiran). However, the delivery of naked siRNAs is challenging because of their short plasma half-lives and poor cell penetrability. In this study, we used vesicles made from bolaamphiphiles (bolas), GLH-19 and GLH-20, to investigate their ability to protect siRNA from degradation by nucleases while delivering it to target cells, including cells in the brain. Based on computational and experimental studies, we found that GLH-19 vesicles have better delivery characteristics than do GLH-20 vesicles in terms of stability, binding affinity, protection against nucleases, and transfection efficiency, while GLH-20 vesicles contribute to efficient release of the delivered siRNAs, which become available for silencing. Our studies with vesicles made from a mixture of the two bolas (GLH-19 and GLH-20) show that they were able to deliver siRNAs into cultured cancer cells, into a flank tumor and into the brain. The vesicles penetrate cell membranes and the blood-brain barrier (BBB) by endocytosis and transcytosis, respectively, mainly through the caveolae-dependent pathway. These results suggest that GLH-19 strengthens vesicle stability, provides protection against nucleases, and enhances transfection efficiency, while GLH-20 makes the siRNA available for gene silencing.
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Affiliation(s)
- Taejin Kim
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kshitij Gupta
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mary Popov
- Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | | | | | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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26
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Landmesser U, Haghikia A, Leiter LA, Wright RS, Kallend D, Wijngaard P, Stoekenbroek R, Kastelein JJ, Ray KK. Effect of inclisiran, the small-interfering RNA against proprotein convertase subtilisin/kexin type 9, on platelets, immune cells, and immunological biomarkers: a pre-specified analysis from ORION-1. Cardiovasc Res 2020; 117:284-291. [PMID: 32243492 DOI: 10.1093/cvr/cvaa077] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/29/2020] [Indexed: 01/21/2023] Open
Abstract
AIMS Small-interfering RNA (siRNA)-based targeting of proprotein convertase subtilisin/kexin type 9 (PCSK9) represents a novel therapeutic approach that may provide a convenient, infrequent, and safe dosing schedule to robustly lower low-density lipoprotein cholesterol (LDL-C). Given the long duration of action, however, establishing safety in particular with respect to immunogenicity is of paramount importance. In earlier clinical studies of other RNA-targeted treatment approaches (antisense oligonucleotide therapy) immunological and haematological adverse effects, in particular thrombocytopenia and pro-inflammatory effects, have been reported. Here, we present the pre-specified safety analysis from ORION-1 evaluating platelets, immune cells, immunological markers, antidrug antibodies, and clinical immunogenicity adverse events (AEs) under PCSK9 siRNA treatment with inclisiran. METHODS AND RESULTS The pre-specified safety analysis from ORION-1 was performed in six different inclisiran dosing regimens in patients at high risk of cardiovascular disease with elevated LDL-C levels. Patients received either a single dose (SD: 200 mg, n = 60; 300 mg, n = 62 or 500 mg, n = 66) or double-dose starting regimen (DD: 100 mg, n = 62; 200 mg, n = 63; or 300 mg, n = 61 on days 1 and 90) of inclisiran or placebo (SD: n = 65; DD: n = 62). The effects of inclisiran on haematological parameters including platelet counts, lymphocytes, and monocytes as well as on the immune markers interleukin 6 (IL-6) and tumour necrosis factor-α (TNF-α) were examined after 180 days. Immunogenicity was further evaluated by analysis of anti-drug-antibodies (ADAs) towards inclisiran in 6068 study samples and by careful analysis of immunogenicity AEs as part of the pharmacovigilance strategy. At day 180, no significant alterations of platelet counts were observed in any of the dosing groups (change from baseline, SD: 200 mg: 0.8%; 300 mg: -0.5%; 500 mg: -1.8%; DD: 100 mg: 1.3%; 200 mg: -0.5%; 300 mg: 1.0%; no significant difference for any group as compared with placebo). No significant effects on other immune cells, including leucocytes, monocytes, or neutrophils were detected. Notably, no significant increase of inflammatory biomarkers (IL-6 or TNF-α) with either the SD or DD regimen became evident. There was no evidence for immunogenicity based on ADA level analysis and careful review of clinical immunogenicity AEs in none of the treatment regimens. CONCLUSION In this pre-specified safety analysis of ORION-1 for the siRNA therapeutic inclisiran, no adverse effects on measures of inflammation or immune activation nor adverse effects on platelets or clinical immunogenicity AEs were observed over at least 6-month treatment. These safety findings in the largest analysis of an RNAi study in humans to date provide strong reassurance about the safety of inclisiran and the potential of cardiovascular RNA-targeted therapies.
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Affiliation(s)
- Ulf Landmesser
- Department of Cardiology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany.,Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Arash Haghikia
- Department of Cardiology, Charité-Universitätsmedizin Berlin, 12203 Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 10785 Berlin, Germany.,Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Lawrence A Leiter
- The Li Ka Shing Knowledge Institute, Departments of Medicine and Nutritional Sciences, St. Michael's Hospital, University of Toronto, M5B 1W8 Toronto, Canada
| | - R Scott Wright
- Department of Cardiology, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | - John Jp Kastelein
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Kausik K Ray
- Imperial Centre for Cardiovascular Disease Prevention, Department of Primary Care and Public Health, Imperial College London, SW7 2AZ London, UK
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Segal M, Biscans A, Gilles ME, Anastasiadou E, De Luca R, Lim J, Khvorova A, Slack FJ. Hydrophobically Modified let-7b miRNA Enhances Biodistribution to NSCLC and Downregulates HMGA2 In Vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:267-277. [PMID: 31855835 PMCID: PMC6926262 DOI: 10.1016/j.omtn.2019.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) have increasingly been shown to be involved in human cancer, and interest has grown about the potential use of miRNAs for cancer therapy. miRNA levels are known to be altered in cancer cells, including in non-small cell lung cancer (NSCLC), a subtype of lung cancer that is the most prevalent form of cancer worldwide and that lacks effective therapies. The let-7 miRNA is involved in the regulation of oncogene expression in cells and directly represses cancer growth in the lung. let-7 is therefore a potential molecular target for tumor therapy. However, applications of RNA interference for cancer research have been limited by a lack of simple and efficient methods to deliver oligonucleotides (ONs) to cancer cells. In this study, we have used in vitro and in vivo approaches to show that HCC827 cells internalize hydrophobically modified let-7b miRNAs (hmiRNAs) added directly to the culture medium without the need for lipid formulation. We identified functional let-7b hmiRNAs targeting the HMGA2 mRNA, one of the let-7 target genes upregulated in NSCLC, and show that direct uptake in HCC827 cells induced potent and specific gene silencing in vitro and in vivo. Thus, hmiRNAs constitute a novel class of ONs that enable functional studies of genes involved in cancer biology and are potentially therapeutic molecules.
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Affiliation(s)
- Meirav Segal
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Annabelle Biscans
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Maud-Emmanuelle Gilles
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Eleni Anastasiadou
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Roberto De Luca
- HMS Initiative for RNA Medicine, Department of Neurology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Jihoon Lim
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, USA.
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28
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Yu AM, Batra N, Tu MJ, Sweeney C. Novel approaches for efficient in vivo fermentation production of noncoding RNAs. Appl Microbiol Biotechnol 2020; 104:1927-1937. [PMID: 31953559 PMCID: PMC7385725 DOI: 10.1007/s00253-020-10350-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/26/2019] [Accepted: 01/03/2020] [Indexed: 01/07/2023]
Abstract
Genome-derived noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs), play an essential role in the control of target gene expression underlying various cellular processes, and dysregulation of ncRNAs is involved in the pathogenesis and progression of various diseases in virtually all species including humans. Understanding ncRNA biology has opened new avenues to develop novel RNA-based therapeutics. Presently, ncRNA research and drug development is dominated by the use of ncRNA mimics that are synthesized chemically in vitro and supplemented with extensive and various types of artificial modifications and thus may not necessarily recapitulate the properties of natural RNAs generated and folded in living cells in vivo. Therefore, there are growing interests in developing novel technologies for in vivo production of RNA molecules. The two most recent major breakthroughs in achieving an efficient, large-scale, and cost-effective fermentation production of recombinant or bioengineered RNAs (e.g., tens of milligrams from 1 L of bacterial culture) are (1) using stable RNA carriers and (2) direct overexpression in RNase III-deficient bacteria, while other approaches offer a low yield (e.g., nano- to microgram scales per liter). In this article, we highlight these novel microbial fermentation-based technologies that have shifted the paradigm to the production of true biological ncRNA molecules for research and development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA.
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
| | - Colleen Sweeney
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA, 95817, USA
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29
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Kotikam V, Viel JA, Rozners E. Synthesis and Biological Activity of Short Interfering RNAs Having Several Consecutive Amide Internucleoside Linkages. Chemistry 2020; 26:685-690. [PMID: 31693228 PMCID: PMC6980941 DOI: 10.1002/chem.201903754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/01/2019] [Indexed: 02/06/2023]
Abstract
The success of RNA interference (RNAi) as a research tool and potential therapeutic approach has reinvigorated interest in chemical modifications of RNA. Replacement of the negatively charged phosphates with neutral amides may be expected to improve bioavailability and cellular uptake of small interfering RNAs (siRNAs) critical for in vivo applications. In this study, we introduced up to seven consecutive amide linkages at the 3'-end of the guide strand of an siRNA duplex. Modified guide strands having four consecutive amide linkages retained high RNAi activity when paired with a passenger strand having one amide modification between its first and second nucleosides at the 5'-end. Further increase in the number of modifications decreased the RNAi activity; however, siRNAs with six and seven amide linkages still showed useful target silencing. While an siRNA duplex having nine amide linkages retained some silencing activity, the partial reduction of the negative charge did not enable passive uptake in HeLa cells. Our results suggest that further chemical modifications, in addition to amide linkages, are needed to enable cellular uptake of siRNAs in the absence of transfection agents.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Julien A Viel
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
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30
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Salim L, Islam G, Desaulniers JP. Targeted delivery and enhanced gene-silencing activity of centrally modified folic acid-siRNA conjugates. Nucleic Acids Res 2020; 48:75-85. [PMID: 31777918 PMCID: PMC6943128 DOI: 10.1093/nar/gkz1115] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
One of the major hurdles in RNAi research has been the development of safe and effective delivery systems for siRNAs. Although various chemical modifications have been proposed to improve their pharmacokinetic behaviour, their delivery to target cells and tissues presents many challenges. In this work, we implemented a receptor-targeting strategy to selectively deliver siRNAs to cancer cells using folic acid as a ligand. Folic acid is capable of binding to cell-surface folate receptors with high affinity. These receptors have become important molecular targets for cancer research as they are overexpressed in numerous cancers despite being expressed at low levels in normal tissues. Employing a post-column copper-catalyzed alkyne-azide cycloaddition (CuAAC), we report the synthesis of siRNAs bearing folic acid modifications at different positions within the sense strand. In the absence of a transfection carrier, these siRNAs were selectively taken up by cancer cells expressing folate receptors. We show that centrally modified folic acid-siRNAs display enhanced gene-silencing activity against an exogenous gene target (∼80% knockdown after 0.75 μM treatment) and low cytotoxicity. In addition, these siRNAs achieved potent dose-dependent knockdown of endogenous Bcl-2, an important anti-apoptotic gene.
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Affiliation(s)
- Lidya Salim
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1G 0C5, Canada
| | - Golam Islam
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1G 0C5, Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1G 0C5, Canada
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31
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Halman JR, Kim KT, Gwak SJ, Pace R, Johnson MB, Chandler MR, Rackley L, Viard M, Marriott I, Lee JS, Afonin KA. A cationic amphiphilic co-polymer as a carrier of nucleic acid nanoparticles (Nanps) for controlled gene silencing, immunostimulation, and biodistribution. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2020; 23:102094. [PMID: 31669854 PMCID: PMC6942546 DOI: 10.1016/j.nano.2019.102094] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022]
Abstract
Programmable nucleic acid nanoparticles (NANPs) provide controlled coordination of therapeutic nucleic acids (TNAs) and other biological functionalities. Beyond multivalence, recent reports demonstrate that NANP technology can also elicit a specific immune response, adding another layer of customizability to this innovative approach. While the delivery of nucleic acids remains a challenge, new carriers are introduced and tested continuously. Polymeric platforms have proven to be efficient in shielding nucleic acid cargos from nuclease degradation while promoting their delivery and intracellular release. Here, we venture beyond the delivery of conventional TNAs and combine the stable cationic poly-(lactide-co-glycolide)-graft-polyethylenimine with functionalized NANPs. Furthermore, we compare several representative NANPs to assess how their overall structures influence their delivery with the same carrier. An extensive study of various formulations both in vitro and in vivo reveals differences in their immunostimulatory activity, gene silencing efficiency, and biodistribution, with fibrous NANPs advancing for TNA delivery.
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Affiliation(s)
- Justin R Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ki-Taek Kim
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - So-Jung Gwak
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Richard Pace
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, USA
| | - Morgan R Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Lauren Rackley
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mathias Viard
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, USA
| | - Jeoung Soo Lee
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA.
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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32
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Lai CH, Chen RY, Hsieh HP, Tsai SJ, Chang KC, Yen CJ, Huang YC, Liu YW, Lee JC, Lai YC, Hung LY, Lin BW. A selective Aurora-A 5'-UTR siRNA inhibits tumor growth and metastasis. Cancer Lett 2019; 472:97-107. [PMID: 31875524 DOI: 10.1016/j.canlet.2019.12.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 01/08/2023]
Abstract
Many Aurora-A inhibitors have been developed for cancer therapy; however, the specificity and safety of Aurora-A inhibitors remain uncertain. The Aurora-A mRNA yields nine different 5'-UTR isoforms, which result from mRNA alternative splicing. Interestingly, we found that the exon 2-containing Aurora-A mRNA isoforms are predominantly expressed in cancer cell lines as well as human colorectal cancer tissues, making the Aurora-A mRNA exon 2 a promising treatment target in Aurora-A-overexpressing cancers. In this study, a selective siRNA, siRNA-2, which targets Aurora-A mRNA exon 2, was designed to translationally inhibit the expression of Aurora-A in cancer cells but not normal cells; locked nucleic acid (LNA)-modified siRNA-2 showed improved efficacy in inhibiting Aurora-A mRNA translation and tumor growth. Xenograft animal models combined with noninvasion in vivo imaging system (IVIS) analysis further confirmed the anticancer effect of LNA-siRNA-2 with improved efficiency and safety and reduced side effects. Mice orthotopically injected with colorectal cancer cells, LNA-siRNA-2 treatment not only inhibited the tumor growth but also blocked liver and lung metastasis. The results of our study suggest that LNA-siRNA-2 has the potential to be a novel therapeutic agent for cancer treatment.
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Affiliation(s)
- Chien-Hsien Lai
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Ruo-Yu Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli County, 35053, Taiwan
| | - Shaw-Jenq Tsai
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Kung-Chao Chang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chia-Jui Yen
- Division of Hematology and Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yu-Chuan Huang
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yao-Wen Liu
- Department of Pathology, Kuo General Hospital, Tainan, 70054, Taiwan
| | - Jenq-Chang Lee
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yi-Chien Lai
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Liang-Yi Hung
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan; Ph.D. Program for Cancer Molecular Biology and drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| | - Bo-Wen Lin
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
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Ning B, Yu D, Yu AM. Advances and challenges in studying noncoding RNA regulation of drug metabolism and development of RNA therapeutics. Biochem Pharmacol 2019; 169:113638. [PMID: 31518552 PMCID: PMC6802278 DOI: 10.1016/j.bcp.2019.113638] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/06/2019] [Indexed: 01/13/2023]
Abstract
Accumulating evidence has demonstrated that genome-derived noncoding RNAs (ncRNAs) play important roles in modulating inter-individual variations observed in drug metabolism and disposition by controlling the expression of genes coding drug metabolizing enzymes and transporters (DMETs) and relevant nuclear receptors (NRs). With the understanding of novel ncRNA regulatory mechanisms and significance in the control of disease initiation and progression, RNA-based therapies are under active investigation that may expand the druggable targets from conventional proteins to RNAs and the genome for the treatment of human diseases. Herein we provide an overview of research strategies, approaches and their limitations in biochemical and pharmacological studies pertaining to ncRNA functions in the regulation of drug and nutrient metabolism and disposition, and discussion on the promise and challenges in developing RNA therapeutics.
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Affiliation(s)
- Baitang Ning
- National Center for Toxicological Research (NCTR), US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
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Su C, Weir JD, Zhang F, Yan H, Wu T. ENTRNA: a framework to predict RNA foldability. BMC Bioinformatics 2019; 20:373. [PMID: 31269893 PMCID: PMC6610807 DOI: 10.1186/s12859-019-2948-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particular, RNA secondary structures, is critical for elucidating biological functions. Existing literature has focused on RNA design as either an RNA structure prediction problem or an RNA inverse folding problem where free energy has played a key role. RESULTS In this research, we propose a Positive-Unlabeled data- driven framework termed ENTRNA. Other than free energy and commonly studied sequence and structural features, we propose a new feature, Sequence Segment Entropy (SSE), to measure the diversity of RNA sequences. ENTRNA is trained and cross-validated using 1024 pseudoknot-free RNAs and 1060 pseudoknotted RNAs from the RNASTRAND database respectively. To test the robustness of the ENTRNA, the models are further blind tested on 206 pseudoknot-free and 93 pseudoknotted RNAs from the PDB database. For pseudoknot-free RNAs, ENTRNA has 86.5% sensitivity on the training dataset and 80.6% sensitivity on the testing dataset. For pseudoknotted RNAs, ENTRNA shows 81.5% sensitivity on the training dataset and 71.0% on the testing dataset. To test the applicability of ENTRNA to long structural-complex RNA, we collect 5 laboratory synthetic RNAs ranging from 1618 to 1790 nucleotides. ENTRNA is able to predict the foldability of 4 RNAs. CONCLUSION In this article, we reformulate the RNA design problem as a foldability prediction problem which is to predict the likelihood of the co-existence of a sequence-structure pair. This new construct has the potential for both RNA structure prediction and the inverse folding problem. In addition, this new construct enables us to explore data-driven approaches in RNA research.
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Affiliation(s)
- Congzhe Su
- School of Computing, Informatics, Decision Systems Engineering, Arizona State University, Tempe, AZ 85281 USA
| | - Jeffery D. Weir
- Department of Operational Sciences, Graduate School of Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, Dayton, OH 45433 USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ 85281 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ 85281 USA
| | - Teresa Wu
- School of Computing, Informatics, Decision Systems Engineering, Arizona State University, Tempe, AZ 85281 USA
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Xu J, Sun J, Ho PY, Luo Z, Ma W, Zhao W, Rathod SB, Fernandez CA, Venkataramanan R, Xie W, Yu AM, Li S. Creatine based polymer for codelivery of bioengineered MicroRNA and chemodrugs against breast cancer lung metastasis. Biomaterials 2019; 210:25-40. [PMID: 31054369 PMCID: PMC6538300 DOI: 10.1016/j.biomaterials.2019.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 04/05/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023]
Abstract
Metastasis is the major cause for breast cancer related mortality. The combination of miRNA-based therapy and chemotherapy represents a promising approach against breast cancer lung metastasis. The goal of this study is to develop an improved therapy that co-delivers a novel bioengineered miRNA prodrug (tRNA-mir-34a) and doxorubicin (DOX) via a multifunctional nanomicellar carrier that is based on a conjugate of amphiphilic copolymer POEG-VBC backbone with creatine, a naturally occurring cationic molecule. Co-delivery of DOX leads to more effective processing of tRNA-mir-34a into mature miR-34a and down-regulation of target genes. DOX + tRNA-mir-34a/POEG-PCre exhibits potent synergistic anti-tumor and anti-metastasis activity in vitro and in vivo. Interestingly, the enhanced immune response contributes to the overall antitumor efficacy. POEG-PCre may represent a safe and effective delivery system for an optimal chemo-gene combination therapy.
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Affiliation(s)
- Jieni Xu
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jingjing Sun
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Pui Yan Ho
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California-Davis, Sacramento, CA 96817, USA
| | - Zhangyi Luo
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Weina Ma
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wenchen Zhao
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sanjay B Rathod
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Christian A Fernandez
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Raman Venkataramanan
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wen Xie
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California-Davis, Sacramento, CA 96817, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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Formulation of RNA interference-based drugs for pulmonary delivery: challenges and opportunities. Ther Deliv 2019; 9:731-749. [PMID: 30277138 DOI: 10.4155/tde-2018-0029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
With recent advances in the field of RNAi-based therapeutics, it is possible to make any target gene 'druggable', at least in principle. The present review focuses on aspects critical for pulmonary delivery of formulations of nucleic acid-based drugs. The first part introduces the therapeutic potential of RNAi-based drugs for the treatment of lung diseases. Subsequently, we discuss opportunities for formulation-enabled pulmonary delivery of RNAi drugs in light of key physicochemical properties and physiological barriers. In the following section, an overview is included of methodologies for imparting inhalable characteristics to nucleic acid formulations. Finally, we review one of the bottlenecks in the early preclinical testing of inhalable nucleic acid-based formulations, in other words, devices suitable for pulmonary administration of powder-based formulations in rodents.
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Bioengineering of a single long noncoding RNA molecule that carries multiple small RNAs. Appl Microbiol Biotechnol 2019; 103:6107-6117. [PMID: 31187211 DOI: 10.1007/s00253-019-09934-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs), regulate target gene expression and can be used as tools for understanding biological processes and identifying new therapeutic targets. Currently, ncRNA molecules for research and therapeutic use are limited to ncRNA mimics made by chemical synthesis. We have recently established a high-yield and cost-effective method of producing bioengineered or biologic ncRNA agents (BERAs) through bacterial fermentation, which is based on a stable tRNA/pre-miR-34a carrier (~ 180 nt) that accommodates target small RNAs. Nevertheless, it remains a challenge to heterogeneously express longer ncRNAs (e.g., > 260 nt), and it is unknown if single BERA may carry multiple small RNAs. To address this issue, we hypothesized that an additional human pre-miR-34a could be attached to the tRNA/pre-miR-34a scaffold to offer a new tRNA/pre-miR-34a/pre-miR-34a carrier (~ 296 nt) for the accommodation of multiple small RNAs. We thus designed ten different combinatorial BERAs (CO-BERAs) that include different combinations of miRNAs, siRNAs, and antagomirs. Our data showed that all target CO-BERAs were successfully expressed in Escherichia coli at high levels, greater than 40% in total bacterial RNAs. Furthermore, recombinant CO-BERAs were purified to a high degree of homogeneity by fast protein liquid chromatography methods. In addition, CO-BERAs exhibited strong anti-proliferative activities against a variety of human non-small cell lung cancer cell lines. These results support the production of long ncRNA molecules carrying different warhead small RNAs for multi-targeting which may open avenues for developing new biologic RNAs as experimental, diagnostic, and therapeutic tools.
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Andersen VL, Vinther M, Kumar R, Ries A, Wengel J, Nielsen JS, Kjems J. A self-assembled, modular nucleic acid-based nanoscaffold for multivalent theranostic medicine. Am J Cancer Res 2019; 9:2662-2677. [PMID: 31131060 PMCID: PMC6525989 DOI: 10.7150/thno.32060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
Rationale: Within the field of personalized medicine there is an increasing focus on designing flexible, multifunctional drug delivery systems that combine high efficacy with minimal side effects, by tailoring treatment to the individual. Methods: We synthesized a chemically stabilized ~4 nm nucleic acid nanoscaffold, and characterized its assembly, stability and functional properties in vitro and in vivo. We tested its flexibility towards multifunctionalization by conjugating various biomolecules to the four modules of the system. The pharmacokinetics, targeting capability and bioimaging properties of the structure were investigated in mice. The role of avidity in targeted liver cell internalization was investigated by flow cytometry, confocal microscopy and in vivo by fluorescent scanning of the blood and organs of the animals. Results: We have developed a nanoscaffold that rapidly and with high efficiency can self-assemble four chemically conjugated functionalities into a stable, in vivo-applicable system with complete control of stoichiometry and site specificity. The circulation time of the nanoscaffold could be tuned by functionalization with various numbers of polyethylene glycol polymers or with albumin-binding fatty acids. Highly effective hepatocyte-specific internalization was achieved with increasing valencies of tri-antennary galactosamine (triGalNAc) in vitro and in vivo. Conclusion: With its facile functionalization, stoichiometric control, small size and high serum- and thermostability, the nanoscaffold presented here constitutes a novel and flexible platform technology for theranostics.
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Abstract
Small-molecule and protein/antibody drugs mainly act on genome-derived proteins to exert pharmacological effects. RNA based therapies hold the promise to expand the range of druggable targets from proteins to RNAs and the genome, as evidenced by several RNA drugs approved for clinical practice and many others under active trials. While chemo-engineered RNA mimics have found their success in marketed drugs and continue dominating basic research and drug development, these molecules are usually conjugated with extensive and various modifications. This makes them completely different from cellular RNAs transcribed from the genome that usually consist of unmodified ribonucleotides or just contain a few posttranscriptional modifications. The use of synthetic RNA mimics for RNA research and drug development is also in contrast with the ultimate success of protein research and therapy utilizing biologic or recombinant proteins produced and folded in living cells instead of polypeptides or proteins synthesized in vitro. Indeed, efforts have been made recently to develop RNA bioengineering technologies for cost-effective and large-scale production of biologic RNA molecules that may better capture the structures, functions, and safety profiles of natural RNAs. In this article, we provide an overview on RNA therapeutics for the treatment of human diseases via RNA interference mechanisms. By illustrating the structural differences between natural RNAs and chemo-engineered RNA mimics, we focus on discussion of a novel class of bioengineered/biologic RNA agents produced through fermentation and their potential applications to RNA research and drug development.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Chao Jian
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Allan H Yu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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Gatta AK, Hariharapura RC, Udupa N, Reddy MS, Josyula VR. Strategies for improving the specificity of siRNAs for enhanced therapeutic potential. Expert Opin Drug Discov 2018; 13:709-725. [PMID: 29902093 DOI: 10.1080/17460441.2018.1480607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION RNA interference has become a tool of choice in the development of drugs in various therapeutic areas of Post Transcriptional Gene Silencing (PTGS). The critical element in developing successful RNAi therapeutics lies in designing small interfering RNA (siRNA) using an efficient algorithm satisfying the designing criteria. Further, translation of siRNA from bench-side to bedside needs an efficient delivery system and/or chemical modification. Areas covered: This review emphasizes the importance of dicer, the criteria for efficient siRNA design, the currently available algorithms and strategies to overcome off-target effects, immune stimulatory effects and endosomal trap. Expert opinion: Specificity and stability are the primary concerns for siRNA therapeutics. The design criteria and algorithms should be chosen rationally to have a siRNA sequence that binds to the corresponding mRNA as it happens in the Watson and Crick base pairing. However, it must evade a few more hurdles (Endocytosis, Serum stability etc.) to be functional in the cytosol.
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Affiliation(s)
- Aditya Kiran Gatta
- a Cell and Molecular Biology lab, Department of Pharmaceutical Biotechnology , Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Raghu Chandrashekhar Hariharapura
- a Cell and Molecular Biology lab, Department of Pharmaceutical Biotechnology , Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Nayanabhirama Udupa
- b Research Directorate of Health Sciences , Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Meka Sreenivasa Reddy
- c Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences , Manipal Academy of Higher Education , Manipal , Karnataka , India
| | - Venkata Rao Josyula
- a Cell and Molecular Biology lab, Department of Pharmaceutical Biotechnology , Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education , Manipal , Karnataka , India
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Ho PY, Duan Z, Batra N, Jilek JL, Tu MJ, Qiu JX, Hu Z, Wun T, Lara PN, DeVere White RW, Chen HW, Yu AM. Bioengineered Noncoding RNAs Selectively Change Cellular miRNome Profiles for Cancer Therapy. J Pharmacol Exp Ther 2018; 365:494-506. [PMID: 29602831 DOI: 10.1124/jpet.118.247775] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/28/2018] [Indexed: 12/16/2022] Open
Abstract
Noncoding RNAs (ncRNAs) produced in live cells may better reflect intracellular ncRNAs for research and therapy. Attempts were made to produce biologic ncRNAs, but at low yield or success rate. Here we first report a new ncRNA bioengineering technology using more stable ncRNA carrier (nCAR) containing a pre-miR-34a derivative identified by rational design and experimental validation. This approach offered a remarkable higher level expression (40%-80% of total RNAs) of recombinant ncRNAs in bacteria and gave an 80% success rate (33 of 42 ncRNAs). New FPLC and spin-column based methods were also developed for large- and small-scale purification of milligrams and micrograms of recombinant ncRNAs from half liter and milliliters of bacterial culture, respectively. We then used two bioengineered nCAR/miRNAs to demonstrate the selective release of target miRNAs into human cells, which were revealed to be Dicer dependent (miR-34a-5p) or independent (miR-124a-3p), and subsequent changes of miRNome and transcriptome profiles. miRNA enrichment analyses of altered transcriptome confirmed the specificity of nCAR/miRNAs in target gene regulation. Furthermore, nCAR assembled miR-34a-5p and miR-124-3p were active in suppressing human lung carcinoma cell proliferation through modulation of target gene expression (e.g., cMET and CDK6 for miR-34a-5p; STAT3 and ABCC4 for miR-124-3p). In addition, bioengineered miRNA molecules were effective in controlling metastatic lung xenograft progression, as demonstrated by live animal and ex vivo lung tissue bioluminescent imaging as well as histopathological examination. This novel ncRNA bioengineering platform can be easily adapted to produce various ncRNA molecules, and biologic ncRNAs hold the promise as new cancer therapeutics.
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Affiliation(s)
- Pui Yan Ho
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Zhijian Duan
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Joseph L Jilek
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Jing-Xin Qiu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Zihua Hu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Theodore Wun
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Primo N Lara
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Ralph W DeVere White
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Hong-Wu Chen
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine (P.Y.H., Z.D., N.B., J.L.J., M.-J.T., H.-W.C., A.-M.Y.), Division of Hematology Oncology (T.W.), Department of Internal Medicine (P.N.L.), and Department of Urology (R.W.D.W.), UC Davis School of Medicine, Sacramento, California; Department of Pathology, Roswell Park Cancer Institute, Buffalo, New York (J.-X.Q.); and Center for Computational Research, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York (Z.H.)
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Lozada-Delgado EL, Grafals-Ruiz N, Vivas-Mejía PE. RNA interference for glioblastoma therapy: Innovation ladder from the bench to clinical trials. Life Sci 2017; 188:26-36. [PMID: 28864225 PMCID: PMC5617340 DOI: 10.1016/j.lfs.2017.08.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common and deadliest type of primary brain tumor with a prognosis of 14months after diagnosis. Current treatment for GBM patients includes "total" tumor resection, temozolomide-based chemotherapy, radiotherapy or a combination of these options. Although, several targeted therapies, gene therapy, and immunotherapy are currently in the clinic and/or in clinical trials, the overall survival of GBM patients has hardly improved over the last two decades. Therefore, novel multitarget modalities are urgently needed. Recently, RNA interference (RNAi) has emerged as a novel strategy for the treatment of most cancers, including GBM. RNAi-based therapies consist of using small RNA oligonucleotides to regulate protein expression at the post-transcriptional level. Despite the therapeutic potential of RNAi molecules, systemic limitations including short circulatory stability and low release into the tumor tissue have halted their progress to the clinic. The effective delivery of RNAi molecules through the blood-brain barrier (BBB) represents an additional challenge. This review focuses on connecting the translational process of RNAi-based therapies from in vitro evidence to pre-clinical studies. We delineate the effect of RNAi in GBM cell lines, describe their effectiveness in glioma mouse models, and compare the proposed drug carriers for the effective transport of RNAi molecules through the BBB to reach the tumor in the brain. Furthermore, we summarize the most important obstacles to overcome before RNAi-based therapy becomes a reality for GBM treatment.
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Affiliation(s)
- Eunice L Lozada-Delgado
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00927, United States; Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States
| | - Nilmary Grafals-Ruiz
- Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Physiology, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States
| | - Pablo E Vivas-Mejía
- Comprehensive Cancer Center, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States; Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR 00935, United States.
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Mutisya D, Hardcastle T, Cheruiyot SK, Pallan PS, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E. Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic Acids Res 2017; 45:8142-8155. [PMID: 28854734 PMCID: PMC5737567 DOI: 10.1093/nar/gkx558] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/18/2017] [Indexed: 12/21/2022] Open
Abstract
While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA-DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs.
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Affiliation(s)
- Daniel Mutisya
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
| | | | - Samwel K Cheruiyot
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
| | - Pradeep S Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
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Jedrzejczyk D, Gendaszewska-Darmach E, Pawlowska R, Chworos A. Designing synthetic RNA for delivery by nanoparticles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:123001. [PMID: 28004640 DOI: 10.1088/1361-648x/aa5561] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rapid development of synthetic biology and nanobiotechnology has led to the construction of various synthetic RNA nanoparticles of different functionalities and potential applications. As they occur naturally, nucleic acids are an attractive construction material for biocompatible nanoscaffold and nanomachine design. In this review, we provide an overview of the types of RNA and nucleic acid's nanoparticle design, with the focus on relevant nanostructures utilized for gene-expression regulation in cellular models. Structural analysis and modeling is addressed along with the tools available for RNA structural prediction. The functionalization of RNA-based nanoparticles leading to prospective applications of such constructs in potential therapies is shown. The route from the nanoparticle design and modeling through synthesis and functionalization to cellular application is also described. For a better understanding of the fate of targeted RNA after delivery, an overview of RNA processing inside the cell is also provided.
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Affiliation(s)
- Dominika Jedrzejczyk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Tai W, Gao X. Functional peptides for siRNA delivery. Adv Drug Deliv Rev 2017; 110-111:157-168. [PMID: 27530388 PMCID: PMC5305781 DOI: 10.1016/j.addr.2016.08.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/21/2016] [Accepted: 08/05/2016] [Indexed: 11/19/2022]
Abstract
siRNA is considered as a potent therapeutic agent because of its high specificity and efficiency in suppressing genes that are overexpressed during disease development. For nearly two decades, a significant amount of efforts has been dedicated to bringing the siRNA technology into clinical uses. However, only limited success has been achieved to date, largely due to the lack of a cell type-specific, safe, and efficient delivery technology to carry siRNA into the target cells' cytosol where RNA interference takes place. Among the emerging candidate nanocarriers for siRNA delivery, peptides have gained popularity because of their structural and functional diversity. A variety of peptides have been discovered for their ability to translocate siRNA into living cells via different mechanisms such as direct penetration through the cellular membrane, endocytosis-mediated cell entry followed by endosomolysis, and receptor-mediated uptake. This review is focused on the multiple roles played by peptides in siRNA delivery, such as membrane penetration, endosome disruption, targeting, as well as the combination of these functionalities.
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Affiliation(s)
- Wanyi Tai
- Department of Bioengineering, University of Washington, William H Foege Building N561, Seattle, WA 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, William H Foege Building N561, Seattle, WA 98195, USA.
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47
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Martins AN, Ke W, Jawahar V, Striplin M, Striplin C, Freed EO, Afonin KA. Intracellular Reassociation of RNA-DNA Hybrids that Activates RNAi in HIV-Infected Cells. Methods Mol Biol 2017; 1632:269-283. [PMID: 28730446 PMCID: PMC6941940 DOI: 10.1007/978-1-4939-7138-1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human immunodeficiency virus Type 1 (HIV-1) is the major cause of acquired immune deficiency syndrome (AIDS). In 2014, it was estimated that 1.2 million people died from AIDS-related illnesses. RNA interference-based therapy to block HIV replication is a field that, as of now, is without any FDA-approved drugs available for clinical use. In this chapter we describe a protocol for testing and utilizing a new approach that relies on reassociation of RNA-DNA hybrids activating RNAi and blocking HIV replication in human cells.
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Affiliation(s)
- Angelica N Martins
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, 28223, USA
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Vaishnavi Jawahar
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, 28223, USA
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Morriah Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Caryn Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Eric O Freed
- HIV Dynamics and Replication Program, NCI, Frederick, MD, 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA.
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA.
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Fujino T, Suzuki T, Okada K, Kogashi K, Yasumoto KI, Sogawa K, Isobe H. Chimeric RNA Oligonucleotides Incorporating Triazole-Linked Trinucleotides: Synthesis and Function as mRNA in Cell-Free Translation Reactions. J Org Chem 2016; 81:8967-8976. [PMID: 27579606 DOI: 10.1021/acs.joc.6b01618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A method for the synthesis of chimeric oligonucleotides was developed to incorporate purine nucleobases and multiple triazole linkers in natural, phosphate-linked structures of RNA. A solution-phase synthesis method for triazole-linked RNA oligomers via copper-catalyzed azide-alkyne cycloaddition reaction was optimized and tolerated purine nucleobases and protecting groups for further transformations. Three TLRNA trinucleotides with 5'-protected hydroxy and 3'-phosphoramidite groups were prepared, and one congener with a representative sequence was subjected to automated, solid-phase phosphoramidite synthesis. The synthesis allowed the efficient preparation of 13-mer chimeric RNA oligonucleotides with two triazole linkers, ten phosphate linkers and purine/pyrimidine nucleobases. The chimeric oligonucleotide was found applicable to a cell-free translation system as mRNA and provided the genetic code for dipeptide production.
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Affiliation(s)
- Tomoko Fujino
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Takeru Suzuki
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Koudai Okada
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Kanako Kogashi
- Department of Chemistry, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Ken-Ichi Yasumoto
- Department of Biomolecular Sciences, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Kazuhiro Sogawa
- Department of Biomolecular Sciences, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Hiroyuki Isobe
- JST ERATO, Isobe Degenerate π-Integration Project and Advanced Institute for Materials Research, Tohoku University , Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, The University of Tokyo , Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Kelley ML, Strezoska Ž, He K, Vermeulen A, Smith AVB. Versatility of chemically synthesized guide RNAs for CRISPR-Cas9 genome editing. J Biotechnol 2016; 233:74-83. [PMID: 27374403 DOI: 10.1016/j.jbiotec.2016.06.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/31/2016] [Accepted: 06/10/2016] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas9 system has become the most popular and efficient method for genome engineering in mammalian cells. The Streptococcus pyogenes Cas9 nuclease can function with two types of guide RNAs: the native dual crRNA and tracrRNA (crRNA:tracrRNA) or a chimeric single guide RNA (sgRNA). Although sgRNAs expressed from a DNA vector are predominant in the literature, guide RNAs can be rapidly generated by chemical synthesis and provide equivalent functionality in gene editing experiments. This review highlights the attributes and advantages of chemically synthesized guide RNAs including the incorporation of chemical modifications to enhance gene editing efficiencies in certain applications. The use of synthetic guide RNAs is also uniquely suited to genome-scale high throughput arrayed screening, particularly when using complex phenotypic assays for functional genomics studies. Finally, the use of synthetic guide RNAs along with DNA-free sources of Cas9 (mRNA or protein) allows for transient CRISPR-Cas9 presence in the cell, thereby resulting in a decreased probability of off-target events.
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Affiliation(s)
| | | | - Kaizhang He
- Dharmacon, part of GE Healthcare, Lafayette, CO, 80026, USA
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Dar SA, Gupta AK, Thakur A, Kumar M. SMEpred workbench: A web server for predicting efficacy of chemicallymodified siRNAs. RNA Biol 2016; 13:1144-1151. [PMID: 27603513 DOI: 10.1080/15476286.2016.1229733] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chemical modifications have been extensively exploited to circumvent shortcomings in therapeutic applications of small interfering RNAs (siRNAs). However, experimental designing and testing of these siRNAs or chemically modified siRNAs (cm-siRNAs) involves enormous resources. Therefore, in-silico intervention in designing cm-siRNAs would be of utmost importance. We developed SMEpred workbench to predict the efficacy of normal siRNAs as well as cm-siRNAs using 3031 heterogeneous cm-siRNA sequences from siRNAmod database. These include 30 frequently used chemical modifications on different positions of either siRNA strand. Support Vector Machine (SVM) was employed to develop predictive models utilizing various sequence features namely mono-, di-nucleotide composition, binary pattern and their hybrids. We achieved highest Pearson Correlation Coefficient (PCC) of 0.80 during 10-fold cross validation and similar PCC value in independent validation. We have provided the algorithm in the 'SMEpred' pipeline to predict the normal siRNAs from the gene or mRNA sequence. For multiple modifications, we have assembled 'MultiModGen' module to design multiple modifications and further process them to evaluate their predicted efficacies. SMEpred webserver will be useful to scientific community engaged in use of RNAi-based technology as well as for therapeutic development. Web server is available for public use at following URL address: http://bioinfo.imtech.res.in/manojk/smepred .
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Affiliation(s)
- Showkat Ahmad Dar
- a Bioinformatics Center, Institute of Microbial Technology, Council of Scientific and Industrial Research , Chandigarh , India
| | - Amit Kumar Gupta
- a Bioinformatics Center, Institute of Microbial Technology, Council of Scientific and Industrial Research , Chandigarh , India
| | - Anamika Thakur
- a Bioinformatics Center, Institute of Microbial Technology, Council of Scientific and Industrial Research , Chandigarh , India
| | - Manoj Kumar
- a Bioinformatics Center, Institute of Microbial Technology, Council of Scientific and Industrial Research , Chandigarh , India
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