Nucleic Acid Carriers Research Articles

Comparative evaluation of DNA synthesis for qPCR analysis from oral squamous cell carcinoma tissues - A rapid and robust isolation technique for gene expression studies

BackgroundDNA isolation from biological materials is the initial step in several bioanalytical processes, including the polymerase chain reaction (PCR). This procedure works best with pure DNA devoid of potential amplification reaction inhibitors. Since the quantity and quality of biological samples are limited, it is essential to extract as much DNA as possible from the original sample. The solid-phase extraction technique is frequently used to purify DNA. In this process, the DNA is adsorbed onto a solid support, any contaminants from the reaction are eliminated by washing, and the purified DNA is then eluted from the support. The quality and concentration of DNA have a direct effect on the gene analysis procedure. Therefore, before interpreting the results of PCR-based diagnostic assays, it is imperative to confirm the DNA preparation and integrity, particularly if no pathogenic DNA is identified. MethodsA comparative study was carried out using two standardized protocols for DNA synthesis in comparison with a test protocol incorporating carrier RNA and proteinase K from a viral detection kit. The quality and quantity of the synthesized DNA are assessed by qPCR analysis for gene amplification of metastasis suppressor genes NDRG1, RhoGDI, and KISS 1. Results and conclusionThe test protocol showed higher yields of DNA in comparison to the standard protocol. The concentration of DNA obtained was validated by the concentration of gene expressed from q PCR analysis. The gene expression was significantly higher when the test protocol method was followed for DNA synthesis. Thus the study validates the potential of nucleic acid carrier RNA molecules to improve DNA extraction processes used in tissue samples for gene analysis procedures.

Calixarene‐Guest Complexes: The Next Innovation in Delivery of Drugs and Biologics

AbstractCalixarenes are third generation of macrocyclic molecules with excellent biocompatibility currently being researched extensively for their diverse potential as therapeutic candidates and for delivery of drugs and biologics. This review discusses the unique structural features which allow them to selectively bind to a wide variety of guest molecules within their hydrophobic cavity, as well as complex with other molecules on their upper and lower rims to enable their application for encapsulation of drugs for targeted and controlled release, molecular carriers for antigens and nucleic acids, and as biomedical sensors. The calixarenes’ unique host–guest chemistry enables encapsulation of lipophilic drugs in the latter's cavity, while the head groups and side chains on the upper and lower rim can be functionalized readily with various targeting moieties as peptides and biological ligands which specifically recognize and bind to cancer cells via surface receptors. The design of calixarene constructs help incorporation of multiple functionalities into a single platform. This active targeting approach enhances the accumulation of the drug at the tumor site while reducing its distribution in healthy tissues, thereby minimizing side effects. Ongoing research in exploration and optimization of calixarenes for application as targeted drug and gene delivery agents has been discussed.

Lipid nanoparticles-based RNA therapies for breast cancer treatment

Breast cancer (BC) prevails as a major burden on global healthcare, being the most prevalent form of cancer among women. BC is a complex and heterogeneous disease, and current therapies, such as chemotherapy and radiotherapy, frequently fall short in providing effective solutions. These treatments fail to mitigate the risk of cancer recurrence and cause severe side effects that, in turn, compromise therapeutic responses in patients. Over the last decade, several strategies have been proposed to overcome these limitations. Among them, RNA-based technologies have demonstrated their potential across various clinical applications, notably in cancer therapy. However, RNA therapies are still limited by a series of critical issues like off-target effect and poor stability in circulation. Thus, novel approaches have been investigated to improve the targeting and bioavailability of RNA-based formulations to achieve an appropriate therapeutic outcome. Lipid nanoparticles (LNPs) have been largely proven to be an advantageous carrier for nucleic acids and RNA. This perspective explores the most recent advances on RNA-based technology with an emphasis on LNPs’ utilization as effective nanocarriers in BC therapy and most recent progresses in their clinical applications.Graphical

Engineering pH-sensitive dissolution of lipid-polymer nanoparticles by Eudragit integration impacts plasmid DNA (pDNA) transfection

Lipid-polymer nanoparticles offer a promising strategy for improving gene nanomedicines by combining the benefits of biocompatibility and stability associated with the individual systems. However, research to date has focused on poly-lactic-co-glycolic acid (PLGA) and resulted in inefficient transfection. In this study, biocompatible Eudragit constructs E100 and RS100 were formulated as lipid-polymer nanoparticles loaded with pDNA expressing red fluorescent protein (RFP) as a model therapeutic. Using a facile nanoprecipitation technique, a core–shell structure stabilised by lipid-polyethylene glycol (PEG) surfactant was produced and displayed resistance to ultracentrifugation. Both cationic polymers E100 (pH-sensitive dissolution at 5) and RS100 (pH-insensitive dissolution) produced 150–200 nm sized particles with a small positive surface charge (+3–5 mV) and high pDNA encapsulation efficiencies (EE) of 75–90%. The dissolution properties of the Eudragit polymers significantly impacted the biological performance in human embryonic kidney cells (HEK293T). Nanoparticles composed of polymer RS100 resulted in consistently high cell viability (80–100%), whereas polymer E100 demonstrated dose-dependent behaviour (20–90% cell viability). The low dissolution of polymer RS100 over the full pH range and the resulting nanoparticles failed to induce RFP expression in HEK293T cells. In contrast, polymer E100-constructed nanoparticles resulted in reproducible and gradually increasing RFP expression of 26–42% at 48–72 h. Intraperitoneal (IP) injection of the polymer E100-based nanoparticles in C57BL/6 mice resulted in targeted RFP expression in mouse testes with favourable biocompatibility one-week post-administration. These findings predicate Eudragit based lipid-polymer nanoparticles as a novel and effective carrier for nucleic acids, which could facilitate pre-clinical evaluation and translation of gene nanomedicines.

Acrylic acid and vinylamine copolymers: Anomalous acidity and association with short polyacids

Acrylic acid and vinylamine copolymers represent one of the simplest polyampholyte structures. The acid-base and solution properties of these copolymers are hardly studied, and there are no works devoted to the synthesis of a set of copolymers with different compositions. We have synthesized a set of acrylic acid and vinylamine copolymers containing from 21 to 95 mol% acrylic acid units. The copolymers show the hydrodynamic properties and solubility of typical polyampholytes. Potentiometric titration revealed unusual acid-base properties of the new copolymers. The addition of HCl to the copolymers in the form of sodium/potassium salt results in only partial protonation of carboxyl anions and amine groups, including the acidic range (pH 2.5). This abnormally high acidity of acrylic acid and vinylamine copolymers is probably due to the formation of strong intra- and intermolecular hydrogen or ionic bonds between partially protonated and protonated groups: ∼COO−+H3N∼, COOH∙∙∙:NH2∼, ∼H2N:∙∙∙ +H3N∼. Poly(vinylamine) and copolymers are able to stabilize curcumin in aqueous medium, significantly increasing its concentration in the neutral pH range. Polymers with high content of amine groups prevent curcumin degradation, probably by converting it to a more stable anionic form. New copolymers are promising substances for the creation of nucleic acid carriers for gene therapy and genetic engineering. The copolymer containing 21 % acrylic acid is comparable to poly(vinylamine) in terms of interaction with oligonucleotides, but yields more homogeneous polyplexes without the impurity of positively charged and potentially toxic particles.

Membrane-Cloaked Nanoparticles for RNA Interference of β-Catenin in Triple-Negative Breast Cancer.

There is an outstanding need for targeted therapies for triple-negative breast cancer (TNBC), an aggressive breast cancer subtype. Since TNBC's rapid growth and metastasis are driven by hyperactive Wnt signaling, suppressing the key-pathway mediator β-catenin through RNA interference may improve patient outcomes. However, small interfering ribonucleic acid (siRNA) molecules require a carrier to elicit targeted gene silencing. Here, we show that 4T1 cancer cell membrane wrapped poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) can deliver siRNA into TNBC cells, silence β-catenin expression, and reduce the cells' tumorigenic qualities. Compared to unwrapped and nontargeted NPs, the cancer cell membrane wrapped nanoparticles (CCNPs) exhibit dramatically improved uptake by TNBC cells versus breast epithelial cells and greater gene silencing at mRNA and protein levels. Congruently, β-catenin siRNA-loaded CCNPs significantly activate senescence in 2D cultured TNBC cells and reduce proliferation in 3D spheroids. This work advances the development of nucleic acid carriers for targeted RNA interference therapy.

Evaluating Cationic Nanoparticles as Carriers of Antiviral Nucleic Acids.

Nanoparticle carriers enable the multivalent delivery of nucleic acids to cells and protect them from degradation. In this chapter, we present a comprehensive overview of four methodologies: electrophoretic mobility shift assay (EMSA), alamarBlue/CFDA-AM cell viability dyes, fluorescence microscopy, and antiviral assays, which collectively are tools to explore interactions between nucleic acids and nanoparticles, and their biological efficacy. These assays provide insights into binding potential, cytotoxicity, and antiviral efficacy of nucleic acid-based nanoparticle treatments furthering the development of effective antiviral therapeutics.

Polymer design via SHAP and Bayesian machine learning optimizes pDNA and CRISPR ribonucleoprotein delivery.

We present the facile synthesis of a clickable polymer library with systematic variations in length, binary composition, pKa, and hydrophobicity (clog P) to optimize intracellular pDNA and CRISPR-Cas9 ribonucleoprotein (RNP) performance. We couple physicochemical characterization and machine learning to interpret quantitative structure-property relationships within the combinatorial design space. For the first time, we reveal unexpected disparate design parameters for nucleic acid carriers; via explainable machine learning on 432 formulations, we discover that lower polymer pKa and higher percentages of benzimidazole ethanethiol enhance pDNA delivery, yet polymer length and captamine cation identity improve RNP delivery. Closed-loop Bayesian optimization of 552 formulation ratios further enhances in vitro performance. The top three polymers yield a higher signal and stable transgene expression over 20 days in vivo, and a 1.7-fold enhancement over controls. Our facile coupling of synthesis, characterization, and machine analysis provides powerful tools to quantitate performance parameters accelerating next-generation vehicles for nucleic acid medicines.

Modulating efficacy and cytotoxicity of lipoamino fatty acid nucleic acid carriers using disulfide or hydrophobic spacers.

Double pH-responsive xenopeptides comprising polar ionizable succinoyl tetraethylene pentamine (Stp) motifs and lipophilic ionizable lipoamino fatty acids (LAFs) were recently found to efficiently transfect mRNA and pDNA at low doses. However, potency was often accompanied with cytotoxicity at higher doses. Insertion of bioreducible disulfide building blocks (ssbb) or non-reducible hydrophobic spacers between polar and apolar ionizable domains of LAF-Stp carriers should mitigate toxicity of xenopeptides. Carriers showed stable nucleic acid complexation and endosomal pH-dependent lytic activities, both of which were abolished after reductive cleavage of ssbb-containing carriers. For pDNA, U-shaped carriers with one Stp and two LAF units or bundle carriers with two Stps and four LAFs displayed highest potency. For mRNA, best transfection was achieved with bundle carriers with one Stp and four LAFs. Both the ssbb and hydrophobic spacer containing analogs displayed improved metabolic activity, reduced membrane damage, and improved cell growth. The ssbb carriers were most beneficial regarding living cell count and low apoptosis rates. Mechanistically, inserted spacers decelerated the transfection kinetics and altered the requirement of endosomal protonation. Overall, mRNA and pDNA carriers with improved biocompatibility have been designed, with their high potency illustrated in transfection of various cell lines including low passage number colon carcinoma cells.

Zwitterionic materials for nucleic acid delivery and therapeutic applications

Nucleic acid therapeutics have demonstrated substantial potential in combating various diseases. However, challenges persist, particularly in the delivery of multifunctional nucleic acids. To address this issue, numerous gene delivery vectors have been developed to fully unlock the potential of gene therapy. The advancement of innovative materials with exceptional delivery properties is critical to propel the clinical translation of nucleic acid drugs. Cationic vector materials have received extensive attention, while zwitterionic materials remain relatively underappreciated in delivery. In this review, we outline a diverse range of zwitterionic material nucleic acid carriers, predominantly encompassing zwitterionic lipids, polymers and peptides. Their respective chemical structures, synthesis approaches, properties, advantages, and therapeutic applications are summarized and discussed. Furthermore, we highlight the challenges and future opportunities associated with the development of zwitterionic vector materials. This review will aid to understand the zwitterionic materials in aiding gene delivery, contributing to the continual progress of nucleic acid therapeutics.

Peptide carriers as delivery vehicles for therapeutic nucleic acids. Мechanisms and potential applications in medicine

Currently, a significant number of drugs based on therapeutic nucleic acids are being under development for the treatment of oncological, inflammatory, infectious diseases, and metabolic disorders. A growing number of approved nucleic acid therapeutics demonstrate the potential of gene therapy approaches. Therapeutic nucleic acids realize their biological effect in the cytoplasm, while plasma membrane is the main barrier to their intracellular delivery. Therefore, specially designed carriers are often used during the development of such drugs. The optimal carrier should not only facilitate the internalization of nucleic acids, but also exhibit no toxic effects, provide stabilization, and must be suitable for large scale production at low cost. Cell penetrating peptides (CPPs) match all these requirements. CPPs are effective and low-toxic carriers of nucleic acids. They usually represent basic peptides with a positive charge at physiological pH that capable to form nanostructures with negatively charged nucleic acids. Numerous preclinical studies in which CPP has been used as a carrier have shown promising results. In some cases, CPP-containing drugs successfully passed through clinical trials and the implemented into clinical practice. In this review, we consider the variety of therapeutic nucleic acids and summarize the experience of using CPP for their intracellular delivery. In addition, the classification and mechanisms of CPP cellular uptake are discussed, the understanding of which will accelerate the development of new gene therapy drugs.

Lipid Nanoparticles Optimized for Targeting and Release of Nucleic Acid.

Lipid nanoparticles (LNPs) are currently the most promising clinical nucleic acids drug delivery vehicles. LNPs prevent the degradation of cargo nucleic acids during blood circulation. Upon entry into the cell, specific components of the lipid nanoparticles can promote the endosomal escape of nucleic acids. These are the basic properties of lipid nanoparticles as nucleic acid carriers. As LNPs exhibit hepatic aggregation characteristics, enhancing targeting out of the liver is a crucial way to improve LNPs administrated in vivo. Meanwhile, endosomal escape of nucleic acids loaded in LNPs is often considered inadequate, and therefore, much effort is devoted to enhancing the intracellular release efficiency of nucleic acids. Here, different strategies to efficiently deliver nucleic acid delivery from LNPs are concluded and their mechanisms are investigated. In addition, based on the information on LNPs that are in clinical trials or have completed clinical trials, the issues that are necessary to be approached in the clinical translation of LNPs are discussed, which it is hoped will shed light on the development of LNP nucleic acid drugs.

EXTH-14. MRNA-LOADED EXOSOMES FOR TARGETED GLIOBLASTOMA IMMUNOTHERAPY

Abstract Recent successes of mRNA therapeutics against pathogenic infections have increased interest in their investigations for other human diseases including cancer. However, precisely delivering the genetic cargo to cells and tissues of interest remains challenging. Extracellular vesicles such as exosomes have gained increased interest recently as potential nucleic acid and drug carriers given their favorable immunogenic profile, long circulatory half-life, and ability to cross biological barriers such as blood-brain barrier. Here, we show an adaptive strategy that enables the docking of different targeting ligands onto the surface of mRNA-loaded exosomes. This was achieved using a microfluidic electroporation approach where a combination of nano- and milli-second pulse electroporations produced a large quantity of IFN-γ mRNA-loaded exosomes with CD64 overexpressed on their surface. The CD64 molecule serves as an adaptor to dock targeting ligands, such as anti-CD71 and anti-programmed cell death-ligand 1 (PD-L1) antibodies. The resulting immunogenic exosomes (imExo) selectively targeted glioblastoma cells and generated potent antitumor activities in vivo, including against tumors intrinsically resistant to immunotherapy. Together, these results provide a new adaptive approach to engineering mRNA-loaded exosomes with targeting functionality and pave the way for their adoption in cancer immunotherapy applications.

Tumor targeted siRNA delivery by adenosine receptor-specific curdlan nanoparticles

Aminated curdlan derivatives are highly effective nucleic acid carriers. Previously, we proved that the ligand-functionalized curdlan derivatives have greatly enhanced cell type specificity induced by receptor-mediated internalization in vitro. In this study, to improve biocompatibility and enhance tumor-targeting efficacy of the curdlan derivative, we pegylated the adenosine functionalized amino curdlan derivative (denoted by pAVC polymer). We confirmed that the uptake of pAVC polymer carrying siRNA by tumor cells was adenosine receptor (AR)-dependent and was specifically inhibited by AMP but not by GMP. The pAVC polymers not only preserved the receptor recognition and exhibited significantly decreased cytotoxicity but also showed remarkable tumor targeting efficiency in vivo. The nanoparticles formulated from siRNA (against STAT3) and pAVC4 polymer, which bears the highest degree of PEG substitution, delivered siRNA highly specifically to tumor tissue, knocked down STAT3, and inhibited tumor growth. The pAVC polymers may be a promising carrier for tumor specific delivery of nucleic acid drugs.

A Review of Labeling Approaches Used in Small Extracellular Vesicles Tracing and Imaging.

Small extracellular vesicles (sEVs), a subset of extracellular vesicles (EVs) originating from the endosomal compartment, are a kind of lipid bilayer vesicles released by almost all types of cells, serving as natural carriers of nucleic acids, proteins, and lipids for intercellular communication and transfer of bioactive molecules. The current findings suggest their vital role in physiological and pathological processes. Various sEVs labeling techniques have been developed for the more advanced study of the function, mode of action, bio-distribution, and related information of sEVs. In this review, we summarize the existing and emerging sEVs labeling techniques, including fluorescent labeling, radioisotope labeling, nanoparticle labeling, chemical contrast agents labeling, and label-free technique. These approaches will pave the way for an in-depth study of sEVs. We present a systematic and comprehensive review of the principles, advantages, disadvantages, and applications of these techniques, to help promote applications of these labeling approaches in future research on sEVs.

Polymeric-Micelle-Based Delivery Systems for Nucleic Acids.

Nucleic acids can modulate gene expression specifically. They are increasingly being utilized and show huge potential for the prevention or treatment of various diseases. However, the clinical translation of nucleic acids faces many challenges due to their rapid clearance after administration, low stability in physiological fluids and limited cellular uptake, which is associated with an inability to reach the intracellular target site and poor efficacy. For many years, tremendous efforts have been made to design appropriate delivery systems that enable the safe and effective delivery of nucleic acids at the target site to achieve high therapeutic outcomes. Among the different delivery platforms investigated, polymeric micelles have emerged as suitable delivery vehicles due to the versatility of their structures and the possibility to tailor their composition for overcoming extracellular and intracellular barriers, thus enhancing therapeutic efficacy. Many strategies, such as the addition of stimuli-sensitive groups or specific ligands, can be used to facilitate the delivery of various nucleic acids and improve targeting and accumulation at the site of action while protecting nucleic acids from degradation and promoting their cellular uptake. Furthermore, polymeric micelles can be used to deliver both chemotherapeutic drugs and nucleic acid therapeutics simultaneously to achieve synergistic combination treatment. This review focuses on the design approaches and current developments in polymeric micelles for the delivery of nucleic acids. The different preparation methods and characteristic features of polymeric micelles are covered. The current state of the art of polymeric micelles as carriers for nucleic acids is discussed while highlighting the delivery challenges of nucleic acids and how to overcome them and how to improve the safety and efficacy of nucleic acids after local or systemic administration.

Plant-Derived Extracellular Vesicles and Their Exciting Potential as the Future of Next-Generation Drug Delivery.

Plant cells release tiny membranous vesicles called extracellular vesicles (EVs), which are rich in lipids, proteins, nucleic acids, and pharmacologically active compounds. These plant-derived EVs (PDEVs) are safe and easily extractable and have been shown to have therapeutic effects against inflammation, cancer, bacteria, and aging. They have shown promise in preventing or treating colitis, cancer, alcoholic liver disease, and even COVID-19. PDEVs can also be used as natural carriers for small-molecule drugs and nucleic acids through various administration routes such as oral, transdermal, or injection. The unique advantages of PDEVs make them highly competitive in clinical applications and preventive healthcare products in the future. This review covers the latest methods for isolating and characterizing PDEVs, their applications in disease prevention and treatment, and their potential as a new drug carrier, with special attention to their commercial viability and toxicological profile, as the future of nanomedicine therapeutics. This review champions the formation of a new task force specializing in PDEVs to address a global need for rigor and standardization in PDEV research.

Molecular Chameleon Carriers for Nucleic Acid Delivery: The Sweet Spot between Lipoplexes and Polyplexes.

Taking advantage of effective intracellular delivery mechanisms of both cationizable lipids and polymers, highly potent double pH-responsive nucleic acid carriers are generated by combining at least two lipo amino fatty acids (LAFs) as hydrophobic cationizable motifs with hydrophilic cationizable aminoethylene units into novel sequence-defined molecules. The pH-dependent tunable polarity of the LAF is successfully implemented by inserting a central tertiary amine, which disrupts the hydrophobic character once protonated, resulting in pH-dependent structural and physical changes. This "molecular chameleon character" turns out to be advantageous for dynamic nucleic acid delivery via lipopolyplexes. By screening different topologies (blocks, bundles, T-shapes, U-shapes), LAF types, and LAF/aminoethylene ratios, highly potent pDNA, mRNA, and siRNA carriers are identified, which are up to several 100-fold more efficient than previous carrier generations and characterized by very fast transfection kinetics. mRNA lipopolyplexes maintain high transfection activity in cell culture even in the presence of ≥90% serum at an ultra-low mRNA dose of 3 picogram (≈2 nanoparticles/cell), and thus are comparable in potency to viral nanoparticles. Importantly, they show great in vivo performance with high expression levels especially in spleen, tumor, lungs, and liver upon intravenous administration of 1-3µg luciferase-encoding mRNA in mice.

Extracellular Vesicles for Therapeutic Nucleic Acid Delivery: Loading Strategies and Challenges.

Extracellular vesicles (EVs) are membrane vesicles released into the extracellular milieu by cells of various origins. They contain different biological cargoes, protecting them from degradation by environmental factors. There is an opinion that EVs have a number of advantages over synthetic carriers, creating new opportunities for drug delivery. In this review, we discuss the ability of EVs to function as carriers for therapeutic nucleic acids (tNAs), challenges associated with the use of such carriers in vivo, and various strategies for tNA loading into EVs.

Long RNA Profiles of Human Brain Extracellular Vesicles Provide New Insights into the Pathogenesis of Alzheimer's Disease.

Alzheimer's disease (AD) is the most common neurodegenerative disorder. Extracellular vesicles (EVs), carriers of nucleic acids, lipids, and proteins, are known to play significant roles in neurodegenerative pathogenesis. Studies have shown that EVs from AD human brain tissue contain toxic proteins that may lead to neuron cell damage and loss. However, the potential contribution of EV long RNAs (exLR) to AD pathobiology is less well known, and their biochemical functions and molecular properties remain obscure. Here, EVs were isolated from the frontal cortex of normal control (NC; N = 10) and AD (N = 8) brain tissue donors. We performed exLR profiling on the isolated EVs followed by pathway analysis and weighted gene co-expression network analysis (WGCNA). A total of 1012 mRNAs, 320 long non-coding RNAs (lncRNAs), and 119 circular RNAs (circRNAs) were found to be differentially expressed (DE) in AD-EVs compared with NC-EVs. Functional analysis of the DEmRNAs revealed that metal ion transport, calcium signaling, and various neuronal processes were enriched. To investigate the possible functions of the identified DElncRNAs and DEcircRNAs, competing endogenous RNA (ceRNA) networks were constructed and subjected to WGCNA, in which two gene modules were identified to be significantly correlated with AD. Moreover, we discovered that NC-EVs were more effective than AD-EVs in promoting cytokine expression, phagocytosis, and induction of calcium signaling in microglia. Our study provides an in-depth characterization of brain tissue exLR and identifies several RNAs that correlate with the pathogenesis of AD.