RNA four-way junction (4WJ) for spontaneous cancer-targeting, effective tumor-regression, metastasis suppression, fast renal excretion and undetectable toxicity

Non-Viral RNA Therapies for Non-Small Cell Lung Cancer and Their Corresponding Clinical Trials

Ribonucleic acid (RNA)-based therapies represent a promising class of drugs for the treatment of non-small cell lung cancer (NSCLC) due to their ability to modulate gene expression. Therapies leveraging small interfering RNA (siRNA), messenger RNA (mRNA), microRNA (miRNA), and antisense oligonucleotides (ASOs) offer various advantages over conventional treatments, including the ability to target specific genetic mutations and the potential for personalized medicine approaches. However, the clinical translation of these therapeutics for the treatment of NSCLC faces challenges in delivery due to their immunogenicity, negative charge, and large size, which can be mitigated with delivery platforms. In this review, we provide a description of the pathophysiology of NSCLC and an overview of RNA-based therapeutics, specifically highlighting their potential application in the treatment of NSCLC. We discuss relevant classes of RNA and their therapeutic potential for NSCLC. We then discuss challenges in delivery and non-viral delivery strategies such as lipid- and polymer-based nanoparticles that have been developed to address these issues in preclinical models. Furthermore, we provide a summary table of clinical trials that leverage RNA therapies for NSCLC [which includes their National Clinical Trial (NCT) numbers] to highlight the current progress in NSCLC. We also discuss how these NSCLC therapies can be integrated with existing treatment modalities to enhance their efficacy and improve patient outcomes. Overall, we aim to highlight non-viral strategies that tackle RNA delivery challenges while showcasing RNA's potential as a next-generation therapy for NSCLC treatment.

Using aptamers for targeted delivery of RNA therapies

RNA-based treatments that can silence, introduce, or restore gene expression to target human diseases are emerging as a new class of therapeutics. Despite their potential for use in broad applications, their clinical translation has been hampered by a need for delivery to specific cells and tissues. Cell targeting based on the use of aptamers provides an approach for improving their delivery to the desired sites of action. Aptamers are nucleic acid oligonucleotides with structural conformations that provide a robust capacity for the recognition of cell surface molecules and that can be used for directed targeting. Aptamers can be directly conjugated to therapeutic RNA molecules, in the form of aptamer-oligonucleotide chimeras, or incorporated into nanoparticles used as vehicles for the delivery of these therapeutics. Herein, we discuss the use of aptamers for cell-directed RNA therapies, provide an overview of different types of aptamer-targeting RNA therapeutics, and review examples of their therapeutic applications. Challenges associated with manufacturing and scaling up production, and key considerations for their clinical implementation, are also outlined.

DNA/RNA hybrids avoid channel gating that leads to the continued packaging of numerous hybrids into the phi29 protein shell

Packaging of double-stranded DNA (dsDNA) into viral capsids is crucial in dsDNA viruses, including herpesviruses, adenoviruses, poxviruses, and bacteriophages. An ATPase motor compacts genomes. The phi29 DNA packaging motor, a model system, employs a hexameric pRNA (packaging RNA) ring and ATPase, sharing a revolving mechanism observed in herpesvirus genome packaging, bacterial DNA transport, Holliday junction resolution, and plasmid conjugation. Channel gating terminates translocation and readies a reversed pore for dsDNA exit; its mechanism is unclear. We report a packaging efficiency difference between dsDNA and RNA/DNA hybrids. Single-channel electrophysiology and sucrose gradient ultracentrifugation reveal that packaging fails if both ends are dsRNA, but succeeds if either 5' or 3' end is DNA. As long as one strand is DNA, RNA/DNA hybrids are packaged, with a higher copy number than dsDNA. Single-pore conductance assays show that this efficiency results from the absence of channel gating. The channel remains open during RNA/DNA translocation and does not close after hybrid packaging, implying dsDNA's role in gating and conformational changes. This gating arises from dsDNA's interaction with three flexible loops of the motor channel. These findings offer a structural and chemical foundation for designing containers to package RNA/DNA hybrids for gene/RNAi delivery, therapy, synthetic biology, nanotechnology, and single-particle sensing.

RNA aptamer-mediated RNA nanotechnology for potential treatment of cardiopulmonary diseases

Ribonucleic acid (RNA) aptamers are single-stranded RNAs that bind to target proteins or other molecules with high specificity and affinity, modulating biological functions through distinct mechanisms. These aptamers can act n as antagonists to block pathological interactions, agonists to activate signaling pathways, or delivery vehicles for therapeutic cargos such as siRNAs and miRNAs. The advances in RNA nanotechnology further enhances the versatility of RNA aptamers, offering scalable platforms for engineering. In this review, we have summarized recent developments in RNA aptamer-mediated RNA nanotechnology and provide an overview of its potential in treating cardiovascular and respiratory disorders, including atherosclerosis, acute coronary syndromes, heart failure, lung cancer, pulmonary hypertension, asthma, chronic obstructive pulmonary disease (COPD), acute lung injury, viral respiratory infections, and pulmonary fibrosis. By integrating aptamer technologies with innovative delivery systems, RNA aptamers hold the potential to revolutionize the treatment landscape for cardiopulmonary diseases.

Engineered extracellular vesicles for combinatorial TNBC therapy: SR-SIM-guided design achieves substantial drug dosage reduction

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that has no therapeutic targets, relies on chemotherapeutics for treatment, and is in dire need of novel therapeutic approaches for improved patient outcomes. Extracellular vesicles (EVs) serve as intercellular communicators and have been proposed as ideal drug delivery vehicles. Here, EVs were engineered with RNA nanotechnology to develop TNBC tumor inhibitors. Using super resolved-structured illumination microscopy, EVs were optimized for precise Survivin small interfering RNA (siRNA) conjugated to chemotherapeutics loading and CD44 aptamer ligand decoration, thereby enhancing specificity toward TNBC cells. Conventional treatments typically employ chemotherapy drugs gemcitabine (GEM) and paclitaxel (PTX) at dosages on the order of mg/kg respectively, per injection (intravenous) in mice. In contrast, engineered EVs encapsulating these drugs saw functional tumor growth inhibition at significantly reduced concentrations: 2.2 μg/kg for GEM or 5.6 μg/kg for PTX, in combination with 21.5 μg/kg survivin-siRNA in mice. The result is a substantial decrease in the chemotherapeutic dose required, by orders of magnitude, compared with standard regimens. In vivo and in vitro evaluations in a TNBC orthotopic xenograft mouse model demonstrated the efficacy of this decreased dosage strategy, indicating the potential for decreased chemotherapy-associated toxicity.

RNA Nanotechnology for Codelivering High-Payload Nucleoside Analogs to Cancer with a Synergetic Effect

Nucleoside analogs are potent inhibitors for cancer treatment, but the main obstacles to their application in humans are their toxicity, nonspecificity, and lack of targeted delivery tools. Here, we report the use of RNA four-way junctions (4WJs) to deliver two nucleoside analogs, floxuridine (FUDR) and gemcitabine (GEM), with high payloads through routine and simple solid-state RNA synthesis and nanoparticle assembly. The design of RNA nanotechnology for the co-delivery of nucleoside analogs and the chemotherapeutic drug paclitaxel (PTX) resulted in synergistic effects and high efficacy in the treatment of Triple-Negative Breast Cancer (TNBC). The 4WJ-drug complexes were confirmed to have efficient tumor spontaneous targeting and no toxicity because the motility of RNA nanoparticles has been previously shown to enable these RNA-drug complexes to spontaneously accumulate in tumor blood vessels. The negative charge of RNA enables those RNA complexes that are not targeted to tumor vasculature to circulate in the blood and enter the urine through the kidney glomerulus, without accumulating in organs, therefore being nontoxic. Drug incorporation into RNA 4WJ can be precisely controlled with a defined loading amount, location, and ratio. The incorporation of nucleoside analogs into 4WJ only requires one step using nucleoside analogue phosphoramidites during solid-phase RNA synthesis, without the need for additional conjugation and purification processes.

Therapeutic applications of RNA nanostructures

RNA-based therapeutics have gained wide public interest in recent years. RNA is a versatile molecule that exists in many forms including mRNA, siRNA, miRNA, ribozymes, and other non-coding RNAs and is primarily applied for gene therapy. RNA is also used as a modular building block to construct RNA nanostructures. The programmable nature of RNA nanostructures enables the generation of simple, modulable, and multi-functional RNA-based therapeutics. Although the therapeutic application of RNA may be limited due to its structural instability, advances in RNA nanotechnology have improved the stability of RNA nanostructures for greater application. Various strategies have been developed to enhance the stability of RNA nanostructures enabling their application in vivo. In this review, we examine the therapeutic applications of RNA nanostructures. Non-immunogenic RNA nanostructures can be rationally designed with functional RNA molecules to modulate gene expression for gene therapy. On the other hand, nucleic acids can be sensed by cellular receptors to elicit an innate immune response, for which certain DNA and RNA motifs can function as adjuvants. Taking advantage of this adjuvant potential, RNA nanostructures can be used for immunotherapy and be designed for cancer vaccines. Thus, we examine the therapeutic application of immunogenic RNA nanostructures for cancer immunotherapy. RNA nanostructures represent promising platforms to design new nanodrugs, gene therapeutics, immunotherapeutic adjuvants, and cancer vaccines. Ongoing research in the field of RNA nanotechnology will continue to empower the development of RNA nanostructure-based therapeutics with high efficacy and limited toxicity.

The Effects of the Carrier and Ligand Spatial Conformation on RNA Nanodrug Cell Delivery

Small interfering RNA (siRNA) highlights the immense therapeutic potential for cancer treatment. The major challenge in siRNA therapy is the effective RNA nanodrug delivery system, which is facilitated by the ligand and the carrier. In this study, we analyzed the binding specificity of linear RGD and circular RGD to αVβ3 integrins by mapping the morphology using super-resolution direct stochastic optical reconstruction microscopy. Meanwhile, the binding dynamics was investigated using single-molecule force spectroscopy. Then, the effects of the ligand and carrier on RNA nanodrug cell entry dynamic parameters were evaluated at the single particle level by the force tracing technique. Furthermore, the delivery efficiency of RNA nanodrugs was assessed using AFM-based nanoindentation at the single cell level. This report will provide valuable insights for rational design strategies aiming to achieve improved efficiency for nanodrug delivery systems.

Enhancing X-Ray Sensitization with Multifunctional Nanoparticles

In the progression of X-ray-based radiotherapy for the treatment of cancer, the incorporation of nanoparticles (NPs) has a transformative impact. This study investigates the potential of NPs, particularly those comprised of high atomic number elements, as radiosensitizers. This aims to optimize localized radiation doses within tumors, thereby maximizing therapeutic efficacy while preserving surrounding tissues. The multifaceted applications of NPs in radiotherapy encompass collaborative interactions with chemotherapeutic, immunotherapeutic, and targeted pharmaceuticals, along with contributions to photodynamic/photothermal therapy, imaging enhancement, and the integration of artificial intelligence technology. Despite promising preclinical outcomes, the paper acknowledges challenges in the clinical translation of these findings. The conclusion maintains an optimistic stance, emphasizing ongoing trials and technological advancements that bolster personalized treatment approaches. The paper advocates for continuous research and clinical validation, envisioning the integration of NPs as a revolutionary paradigm in cancer therapy, ultimately enhancing patient outcomes.

RNA nanotechnology on the horizon: Self-assembly, chemical modifications, and functional applications

RNA nanotechnology harnesses the unique chemical and structural properties of RNA to build nanoassemblies and supramolecular structures with dynamic and functional capabilities. This review focuses on design and assembly approaches to building RNA structures, the RNA chemical modifications used to enhance stability and functionality, and modern-day applications in therapeutics, biosensing, and bioimaging.

Cracking the Code: Enhancing Molecular Tools for Progress in Nanobiotechnology

Nature continually refines its processes for optimal efficiency, especially within biological systems. This article explores the collaborative efforts of researchers worldwide, aiming to mimic nature's efficiency by developing smarter and more effective nanoscale technologies and biomaterials. Recent advancements highlight progress and prospects in leveraging engineered nucleic acids and proteins for specific tasks, drawing inspiration from natural functions. The focus is developing improved methods for characterizing, understanding, and reprogramming these materials to perform user-defined functions, including personalized therapeutics, targeted drug delivery approaches, engineered scaffolds, and reconfigurable nanodevices. Contributions from academia, government agencies, biotech, and medical settings offer diverse perspectives, promising a comprehensive approach to broad nanobiotechnology objectives. Encompassing topics from mRNA vaccine design to programmable protein-based nanocomputing agents, this work provides insightful perspectives on the trajectory of nanobiotechnology toward a future of enhanced biomimicry and technological innovation.

In Vitro and In Vivo Evaluation of the Pathology and Safety Aspects of Three- and Four-Way Junction RNA Nanoparticles

RNA therapeutics has advanced into the third milestone in pharmaceutical drug development, following chemical and protein therapeutics. RNA itself can serve as therapeutics, carriers, regulators, or substrates in drug development. Due to RNA's motile, dynamic, and deformable properties, RNA nanoparticles have demonstrated spontaneous targeting and accumulation in cancer vasculature and fast excretion through the kidney glomerulus to urine to prevent possible interactions with healthy organs. Furthermore, the negatively charged phosphate backbone of RNA results in general repulsion from negatively charged lipid cell membranes for further avoidance of vital organs. Thus, RNA nanoparticles can spontaneously enrich tumor vasculature and efficiently enter tumor cells via specific targeting, while those not entering the tumor tissue will clear from the body quickly. These favorable parameters have led to the expectation that RNA has low or little toxicity. RNA nanoparticles have been well characterized for their anticancer efficacy; however, little detail on RNA nanoparticle pathology and safety is known. Here, we report the in vitro and in vivo assessment of the pathology and safety aspects of different RNA nanoparticles including RNA three-way junction (3WJ) harboring 2'-F modified pyrimidine, folic acid, and Survivin siRNA, as well as the RNA four-way junction (4WJ) harboring 2'-F modified pyrimidine and 24 copies of SN38. Both animal models and patient serum were investigated. In vitro studies include hemolysis, platelet aggregation, complement activation, plasma coagulation, and interferon induction. In vivo studies include hematoxylin and eosin (H&E) staining, hematological and biochemical analysis as the serum profiling, and animal organ weight study. No significant toxicity, side effect, or immune responses were detected during the extensive safety evaluations of RNA nanoparticles. These results further complement previous cancer inhibition studies and demonstrate RNA nanoparticles as an effective and safe drug delivery vehicle for future clinical translations.

Conversion of Chemical Drugs into Targeting Ligands on RNA Nanoparticles and Assessing Payload Stoichiometry for Optimal Biodistribution in Cancer Treatment

Active targeting-mediated nanodelivery takes advantages of ligand-receptor specificity to avoid non-specific distribution, holding great promise for the treatment of a spectrum of diseases. RNA nanoparticles have demonstrated rapid spontaneous tumor targeting and very little organ accumulation due to rapid renal clearance of non-tumor accumulated RNA nanoparticles. However available ligands for specific cells are limited, yet many chemical entities possess receptor targeting capability and remains unexplored. To provide specific tumor accumulation, a multivalent targeting strategy on RNA nanoparticles to control their in vivo fate is implemented. Methotrexate (MTX), a clinically approved chemotherapy was used as a tumor-targeting ligand through conjugation to our RNA nanoparticle with controlled conjugation of various copy numbers. As copies of conjugated MTX increased on the nanoparticle, the specific binding to overexpressed folate receptor was enhanced as demonstrated by flow cytometry analysis and confocal microscopy imaging. Increasing the amounts of conjugated MTX did not significantly change the nanoparticle size, Zeta potential, or cytokine induction. Increased amounts of conjugated MTX resulted in improved cell inhibition due to MTX release following cell internalization. However, increasing conjugated MTX to the RNA nanoparticles reduced the melting temperature of RNA nanoparticles and increased in vitro serum protein binding to the nanoparticles. Thus, in vivo biodistribution profiles of RNA nanoparticles revealed different behaviors based on MTX conjugation in cancer targeting and clearance. Increased copies of MTX changed the ability of nanoparticles to target tumors, accumulate in healthy organs, and rapidly clear through the urine. Nanoparticle design must be closely considered for optimized cancer targeting and therapy, providing the rationale for a proper design of RNA nanodelivery in cancer treatment.

pH-responsive bond as a linker for the release of chemical drugs from RNA-drug complexes in endosome or lysosome

Emerging phenomena have signaled that RNA therapeutics will be the third milestone in pharmaceutical drug development. RNA nanoparticles display motile and deformable properties that lead to (1) fast and efficient tumor accumulation via both spontaneous and active targeting, and (2) fast renal excretion of non-tumor-accumulated nanoparticles due to RNA's negative charge and dynamic property; thus, undetectable toxicity. Here, we report the use of RNA nanoparticles to harbor the cancer-targeting ligand and chemical drugs and the design of the pH-responsive bond as a linker for the release of chemical drugs from RNA-drug complexes in endosomes or lysosomes. RNA nanoparticles constructed from a three-way junction (3WJ) core of bacteriophage phi29 packaging RNA (pRNA) offer an advanced strategy for receptor-selective drug delivery into cancer cells and has the potential to enhance the efficacy of anti-cancer therapies while mitigating dose-limiting toxicity in patients with colorectal cancer (CRC). We investigated conjugation of small-molecule drugs targeting the PI3K/mTOR pathway to 3WJ RNA nanoparticles and confirmed intracellular drug delivery by 3WJ RNA nanoparticles into CRC cells. 3WJ a, a single strand of 3WJ nanoparticle, was constructed with a pH-sensitive linkage conjugated to a dual PI3K/mTOR inhibitor, PI-103-azide. We demonstrated PI-103 conjugation to RNA under normal physiologic pH conditions and rapid pH-dependent drug release in an acidic environment. Next, we assembled FA-3WJ-PI103 nanoparticles from three single-stranded RNA, 3WJ a-PI-103, 3WJ b and 3WJ c-folate, to specifically target folate receptor alpha (FRα). Our tests demonstrated receptor-mediated uptake of FA-pRNA-PI-103 nanoparticles, pH-responsive PI-103 drug release from lysosomes and inhibition of the PI3K/mTOR pathway in CRC cells and tumor spheroids. These results confirm receptor-mediated cytosolic drug delivery by pH-responsive RNA nanoparticles and demonstrate potential of the 3WJ-drug complex as a novel strategy for receptor-selective drug delivery to cancer cells with high FRα expression.

Targeted Delivery of Potent Chemical Drugs and RNAi to Drug-Resistant Breast Cancer Using RNA-Nanotechnology and RNA-Ligand Displaying Extracellular vesicles

This review describes a new technology to treat breast-cancer-drug-resistance by targeting the ABC as the multi-homo-subunit ATPase, enlightening by the Christmas-lighting budge with serial circuit and the asymmetrical homo-hexamer of the phi29 DNA packaging motor with sequential revolving mechanism. Chemotherapeutics has been widely used in breast cancer treatments, but drug resistance has raised a serious concern. RNA therapeutics has emerged as the third milestone in pharmaceutical drug development. RNA nanoparticles are dynamic, mild, and deformative, resulting in spontaneous, rapid, and efficient accumulation in tumor vasculature after IV injection. Their negative charge and favorable size bypass the nonspecific targeting of vital organs and normal cells. This motile and deformable nature also led to the fast passing of glomerular filters and their movement into the urine for rapid body clearance for those non-tumor-accumulated nanoparticles, resulting in undetectable toxicity. Extracellular vesicles have shown potential as a delivery system for RNAi and chemotherapeutic drugs in vivo, contributing to the efficacy of cancer remission. However, the lack of cell-targeting ligands on extracellular vesicles and the nonspecific entry into healthy cells has led to safety concerns. This review addresses how to apply RNA nanotechnology and RNA-ligand displaying extracellular vesicles for specific delivery to breast cancer. The particular focus is on using and combining the RNA and extracellular vesicle technology to deal with breast cancer drug resistance. The targeting capabilities and drug safety can be improved through extracellular vesicle engineering techniques, such as affixing ligands on the extracellular vesicle surface utilizing arrow-tail RNA nanoparticles, ultimately addressing off-target effects and toxicity. Using RNA ligands for specific targeting and the efficient membrane fusion of extracellular vesicles has enabled the development of ligand-displayed extracellular vesicles capable of delivering both RNAi and chemical drugs to cells with precision, effectively inhibiting tumor growth. The negative charge inherent in the vesicles results in electrostatic repulsion, reducing non-specific binding to healthy cells that contain negatively charged lipid membranes. By leveraging the principles of RNA nanotechnology, the engineering of extracellular vesicles offers a promising avenue for addressing breast cancer drug resistance. This review also discusses applying the series of circuit mechanisms in Christmas-decorating-lighting to develop effective therapeutics to combat breast cancer chemoresistance by targeting the ABC drug transporter and breast cancer surface receptors.