Nucleic-acid based gene therapeutics: delivery challenges and modular design of nonviral gene carriers and expression cassettes to overcome intracellular barriers for sustained targeted expression

Tuning the Potency of Farnesol-Modified Polyethylenimine with Polyanionic Trans-Booster to Enhance DNA Delivery

Low molecular weight polyethylenimine (PEI) based lipopolymers become an attractive strategy to construct nonviral therapeutic carriers with promising transfection efficiency and minimal toxicity. Herein, this paper presents the design and synthesis of novel farnesol (Far) conjugated PEI, namely PEI1.2k-SA-Far7. The polymers had quick DNA complexation, effective DNA unpacking (dissociation), and cellular uptake abilities when complexed with plasmid DNA. However, they were unable to provide robust transfection in culture, indicating inability of Far grafting to improve the transfection efficacy significantly. To overcome this limitation, the commercially available polyanionic Trans-Booster additive, which is capable of displaying electrostatic interaction with PEI1.2k-SA-Far7, has been used to enhance the uptake of pDNA polyplexes and transgene expression. pDNA condensation was successfully achieved in the presence of the Trans-Booster with more stable polyplexes, and in vitro transfection efficacy of the polyplexes was improved to be comparable to that obtained with an established reference reagent. The PEI1.2k-SA-Far7/pDNA/Trans-Booster ternary complex exhibited good compatibility with cells and minimal hemolysis activity. This work demonstrates the exemplary potency of using additives in polyplexes and the potential of resultant ternary complexes for effective pDNA delivery.

Gene-editing technology, from macromolecule therapeutics to organ transplantation: Applications, limitations, and prospective uses

Gene editing technologies (GETs) could induce gene knockdown or gene knockout for biomedical applications. The clinical success of gene silence by RNAi therapies pays attention to other GETs as therapeutic approaches. This review aims to highlight GETs, categories, mechanisms, challenges, current use, and prospective applications. The different academic search engines, electronic databases, and bibliographies of selected articles were used in the preparation of this review with a focus on the fundamental considerations. The present results revealed that, among GETs, CRISPR/Cas9 has higher editing efficiency and targeting specificity compared to other GETs to insert, delete, modify, or replace the gene at a specific location in the host genome. Therefore, CRISPR/Cas9 is talented in the production of molecular, tissue, cell, and organ therapies. Consequently, GETs could be used in the discovery of innovative therapeutics for genetic diseases, pandemics, cancer, hopeless diseases, and organ failure. Specifically, GETs have been used to produce gene-modified animals to spare human organ failure. Genetically modified pigs are used in clinical trials as a source of heart, liver, kidneys, and lungs for xenotransplantation (XT) in humans. Viral, non-viral, and hybrid vectors have been utilized for the delivery of GETs with some limitations. Therefore, extracellular vesicles (EVs) are proposed as intelligent and future cargoes for GETs delivery in clinical applications. This study concluded that GETs are promising for the production of molecular, cellular, and organ therapies. The use of GETs as XT is still in the early stage as well and they have ethical and biosafety issues.

Nucleic acid therapies for CNS diseases: Pathophysiology, targets, barriers, and delivery strategies

Nucleic acid therapeutics have emerged as one of the very advanced and efficacious treatment approaches for debilitating health conditions, including those diseases affecting the central nervous system (CNS). Precise targeting with an optimal control over gene regulation confers long-lasting benefits through the administration of nucleic acid payloads via viral, non-viral, and engineered vectors. The current review majorly focuses on the development and clinical translational potential of non-viral vectors for treating CNS diseases with a focus on their specific design and targeting approaches. These carriers must be able to surmount the various intracellular and extracellular barriers, to ensure successful neuronal transfection and ultimately attain higher therapeutic efficacies. Additionally, the specific challenges associated with CNS administration also include the presence of blood-brain barrier (BBB), the complex pathophysiological and biochemical changes associated with different disease conditions and the existence of non-dividing cells. The advantages offered by lipid-based or polymeric systems, engineered proteins, particle-based systems coupled with various approaches of neuronal targeting have been discussed in the context of a variety of CNS diseases. The possibilities of rapid yet highly efficient gene modifications rendered by the breakthrough methodologies for gene editing and gene manipulation have also opened vast avenues of research in neuroscience and CNS disease therapy. The current review also underscores the extensive scientific efforts to optimize specialized, efficacious yet non-invasive and safer administration approaches to overcome the therapeutic delivery challenges specifically posed by the CNS transport barriers and the overall obstacles to clinical translation.

Microfluidic production of mRNA-loaded lipid nanoparticles for vaccine applications

INTRODUCTION

During past years, lipid nanoparticles (LNPs) have emerged as promising carriers for RNA delivery, with several clinical trials focusing on both infectious diseases and cancer. More recently, the success of messenger RNA (mRNA) vaccines for the treatment of severe diseases such as acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is partially justified by the development of LNPs encapsulating mRNA for efficient cytosolic delivery.

AREAS COVERED

This review examines the production and formulation of LNPs by using microfluidic devices, the status of mRNA-loaded LNPs therapeutics and explores spray drying process, as a promising dehydration process to enhance LNP stability and provide alternative administration routes.

EXPERT OPINION

Microfluidic techniques for preparation of LNPs based on organic solvent injection method promotes the generation of stable, uniform, and monodispersed nanoparticles enabling higher encapsulation efficiency. In particular, the application of microfluidics for the fabrication of mRNA-loaded LNPs is based on rapid mixing of small volumes of ethanol solution containing lipids and aqueous solution containing mRNA. Control of operating parameters and formulation has enabled the optimization of nanoparticle physicochemical characteristics and encapsulation efficiency.

Long non-coding RNA LALTOP promotes non-small cell lung cancer progression by stabilizing topoisomerase IIα mRNA

The long noncoding RNAs (lncRNAs) have been shown to actively participate in various biological processes including cancer progression. However, most lncRNAs still have undefined functions. In current work, we identified a novel lncRNA named LALTOP which displayed an oncogenic function in non-small cell lung cancer (NSCLC). LALTOP expression is increased in NSCLC tissues and cell lines. Moreover, LALTOP strongly promoted proliferation and migration of A549 and H1793 cells. RNA-RNA interaction assay showed that LALTOP bound and stabilized topoisomerase II alpha (Top2α) mRNA. Positive correlation can be found between LALTOP and Top2α mRNA expressions in clinical specimens. ASOs targeting LALTOP could markedly inhibit malignant phenotypes of NSCLC. Collectively, LALTOP may serve as an oncogenic lncRNA and enhances NSCLC progression. Targeting LALTOP has therapeutic potential for eradicating lung cancer cells.

Limited expression of non-integrating CpG-free plasmid is associated with increased nucleosome enrichment

CpG-free pDNA was reported to facilitate sustained transgene expression with minimal inflammation in vivo as compared to CpG-containing pDNA. However, the expression potential and impact of CpG-free pDNA in in vitro model have never been described. Hence, in this study, we analyzed the transgene expression profiles of CpG-free pDNA in vitro to determine the influence of CpG depletion from the transgene. We found that in contrast to the published in vivo studies, CpG-free pDNA expressed a significantly lower level of luciferase than CpG-rich pDNA in several human cell lines. By comparing novel CpG-free pDNA carrying CpG-free GFP (pZGFP: 0 CpG) to CpG-rich GFP (pRGFP: 60 CpGs), we further showed that the discrepancy was not influenced by external factors such as gene transfer agent, cell species, cell type, and cytotoxicity. Moreover, pZGFP exhibited reduced expression despite having equal gene dosage as pRGFP. Analysis of mRNA distribution revealed that the mRNA export of pZGFP and pRGFP was similar; however, the steady state mRNA level of pZGFP was significantly lower. Upon further investigation, we found that the CpG-free transgene in non-integrating CpG-free pDNA backbone acquired increased nucleosome enrichment as compared with CpG-rich transgene, which may explain the observed reduced level of steady state mRNA. Our findings suggest that nucleosome enrichment could regulate non-integrating CpG-free pDNA expression and has implications on pDNA design.

High Throughput and Highly Controllable Methods for In Vitro Intracellular Delivery

In vitro and ex vivo intracellular delivery methods hold the key for releasing the full potential of tissue engineering, drug development, and many other applications. In recent years, there has been significant progress in the design and implementation of intracellular delivery systems capable of delivery at the same scale as viral transfection and bulk electroporation but offering fewer adverse outcomes. This review strives to examine a variety of methods for in vitro and ex vivo intracellular delivery such as flow-through microfluidics, engineered substrates, and automated probe-based systems from the perspective of throughput and control. Special attention is paid to a particularly promising method of electroporation using micro/nanochannel based porous substrates, which expose small patches of cell membrane to permeabilizing electric field. Porous substrate electroporation parameters discussed include system design, cells and cargos used, transfection efficiency and cell viability, and the electric field and its effects on molecular transport. The review concludes with discussion of potential new innovations which can arise from specific aspects of porous substrate-based electroporation platforms and high throughput, high control methods in general.

Cell-Based Therapy Manufacturing in Stirred Suspension Bioreactor: Thoughts for cGMP Compliance

Cell-based therapy (CBT) is attracting much attention to treat incurable diseases. In recent years, several clinical trials have been conducted using human pluripotent stem cells (hPSCs), and other potential therapeutic cells. Various private- and government-funded organizations are investing in finding permanent cures for diseases that are difficult or expensive to treat over a lifespan, such as age-related macular degeneration, Parkinson’s disease, or diabetes, etc. Clinical-grade cell manufacturing requiring current good manufacturing practices (cGMP) has therefore become an important issue to make safe and effective CBT products. Current cell production practices are adopted from conventional antibody or protein production in the pharmaceutical industry, wherein cells are used as a vector to produce the desired products. With CBT, however, the “cells are the final products” and sensitive to physico- chemical parameters and storage conditions anywhere between isolation and patient administration. In addition, the manufacturing of cellular products involves multi-stage processing, including cell isolation, genetic modification, PSC derivation, expansion, differentiation, purification, characterization, cryopreservation, etc. Posing a high risk of product contamination, these can be time- and cost- prohibitive due to maintenance of cGMP. The growing demand of CBT needs integrated manufacturing systems that can provide a more simple and cost-effective platform. Here, we discuss the current methods and limitations of CBT, based upon experience with biologics production. We review current cell manufacturing integration, automation and provide an overview of some important considerations and best cGMP practices. Finally, we propose how multi-stage cell processing can be integrated into a single bioreactor, in order to develop streamlined cGMP-compliant cell processing systems.

Antisense Oligonucleotide (AS-ODN) Technology: Principle, Mechanism and Challenges

Recently, there is a hopefully tremendous interest in antisense therapeutics for clinical purposes. Single-stranded synthetic antisense oligonucleotides (As-ODNs) with monomers of chemically modified 18-21 deoxynucleotides complement the mRNA sequence in target gene. The target gene expression can be blocked because of created cleavage or disability of the mRNA by binding the As-ODNs to cognate mRNA sequences via sequence-specific hybridization. The idea of antisense therapy has become particular concerning that any sequence longer than a minimal number of nucleotides (17 for DNA and 13 for RNA) can be observed only once within the human genome. The mRNA is omnipresent more probably to manipulate compared to DNA, which results in multiple in vitro and in vivo applications for As-ODNs in the field of regulatory mechanisms of biological processes, cancer, viral infections and hereditary impairments. Although, there are uncertain clinical outcomes on the ability of this approach in treatment procedures despite achieving promising findings based on previous investigations. Accordingly, the efficacy, off-target effects, delivery are issues that should be investigated to obtain satisfactory results. In this review, we will explain the mechanism of action of As-ODNs and various types of modifications and their therapeutic purposes. This article is protected by copyright. All rights reserved.

Additive Polyplexes to Undertake siRNA Therapy against CDC20 and Survivin in Breast Cancer Cells

Small interfering RNA (siRNA) delivered to silence overexpressed genes associated with malignancies is a promising targeted therapy to decrease the uncontrolled growth of malignant cells. To create potent delivery agents for siRNA, here we formulated additive polyplexes of siRNA using linoleic acid-substituted polyethylenimine and additive polymers (hyaluronic acid, poly(acrylic acid), dextran sulfate, and methyl cellulose) and characterized their physicochemical properties and effectiveness. Incorporating polyanionic polymer along with anionic siRNA in polyplexes was found to decrease the ζ-potential of polyplexes but enhance the cellular delivery of siRNA. The CDC20 and survivin siRNAs delivered by additive polyplexes showed promising efficacy in breast cancer MDA-MB-231, SUM149PT, MDA-MB-436, and MCF7 cells. However, the side effects of the siRNA delivery were observed in nonmalignant cells, and a careful formulation of siRNA/polymer polyplexes was needed to minimize side effects on normal cells. Because the efficacy of siRNA delivery by additive polyplexes was independent of breast cancer phenotypes used in this study, these polyplexes could be further developed to treat a wide range of breast cancers.

An Integrated Approach toward the Biomanufacturing of Engineered Cell Therapy Products in a Stirred-Suspension Bioreactor

Recent advances in stem cell biology have accelerated the pre-clinical development of cell-based therapies for degenerative and chronic diseases. The success of this growing area hinges upon the concomitant development of scalable manufacturing platforms that can produce clinically relevant quantities of cells for thousands of patients. Current biomanufacturing practices for cell therapy products are built on a model previously optimized for biologics, wherein stable cell lines are established first, followed by large-scale production in the bioreactor. This “two-step” approach can be costly, labor-intensive, and time-consuming, particularly for cell therapy products that must be individually sourced from patients or compatible donors. In this report, we describe a “one-step” integrated approach toward the biomanufacturing of engineered cell therapy products by direct transfection of primary human fibroblast in a continuous stirred-suspension bioreactor. We optimized the transfection efficiency by testing rate-limiting factors, including cell seeding density, agitation rate, oxygen saturation, microcarrier type, and serum concentration. By combining the genetic modification step with the large-scale expansion step, this not only removes the need for manual handing of cells in planar culture dishes, but also enables the biomanufacturing process to be streamlined and automated in one fully enclosed bioreactor.

Key to Delivery: The (Epi-)genome Editing Vector Toolbox

Curing a genetic disease by repairing the underlying genetic defect is a fascinating concept that has been addressed so far by gene compensation therapy. For this, a functional copy of the gene in question together with elements controlling its expression is produced as a vector and introduced ex vivo into the patient's own cells that subsequently are reinfused. Alternatively, vectors are administered directly in vivo. Although this strategy resulted in impressive therapeutic benefits for patients, the ultimate goal of gene therapy, i.e., a cure by repairing the actual genetic or epigenetic defect, remained an unresolved task. With the advent of designer DNA-binding domains, this goal is coming into reach. These domains are either combined with nucleases and used as molecular precision scissors for introducing DNA breaks at defined sites in the cell's genome preparing for position-selective DNA repair, or they are used as programmable DNA-binding units for positioning epigenome-modifying domains to predefined target sequences. However, for reaching its full potential, these components need to be delivered into cells in an efficient and safe manner. Here, we summarize current viral and non-viral delivery approaches applicable for genome and epigenome editing and discuss their respective advantages and limitations.

Enhancing the Therapeutic Delivery of Oligonucleotides by Chemical Modification and Nanoparticle Encapsulation

Oligonucleotide (ON) drugs, including small interfering RNA (siRNA), microRNA (miRNA) and antisense oligonucleotides, are promising therapeutic agents. However, their low membrane permeability and sensitivity to nucleases present challenges to in vivo delivery. Chemical modifications of the ON offer a potential solution to improve the stability and efficacy of ON drugs. Combined with nanoparticle encapsulation, delivery at the site of action and gene silencing activity of chemically modified ON drugs can be further enhanced. In the present review, several types of ON drugs, selection of chemical modification, and nanoparticle-based delivery systems to deliver these ON drugs are discussed.

Tumor-selective lipopolyplex encapsulated small active RNA hampers colorectal cancer growth in vitro and in orthotopic murine

Small active RNA (saRNA)-induced gene activation (RNAa) is a novel strategy to treat cancer. Our previous work proved that the p21-saRNA-322 successfully hindered colorectal cancer growth by activating p21 gene. However, the barrier for successful saRNA therapy is lack of efficient drug delivery. In the present study, a rectal delivery system entitled p21-saRNA-322 encapsulated tumor-selective lipopolyplex (TSLPP-p21-saRNA-322) which consist of PEI/p21-saRNA-322 polyplex core and hyaluronan (HA) modulated lipid shell was developed to treat colorectal cancer. Our results showed that this system maintained at the rectum for more than 6 h and preferentially accumulated at tumor site. CD44 knock down experiment instructed that the superb cellular uptake of TSLPP-p21-saRNA-322 attributed to HA-CD44 recognition. An orthotopic model of bio-luminescence human colorectal cancer in mice was developed using microsurgery and TSLPP-p21-saRNA-322 demonstrated a superior antitumor efficacy in vitro and in vivo. Our results provide preclinical proof-of-concept for a novel method to treat colorectal cancer by rectal administration of TSLPP formulated p21-saRNA-322.

Hydrophobically modified polyethylenimine-based ternary complexes for targeting brain tumor: stability, in vitro and in vivo studies

Hydrophobic modification of low molecular weight polyethylenimine (PEI 2 kDa) by cholic acid (ChA) was done to obtain PEI2-ChA. The nanoplexes of PEI2-ChA with gWIZ-GFP demonstrated increase transfection efficiency (∼27%) in NT8e cell lines. The cell-cycle analysis of NT8e cells (p53 mutant) treated with transferrin containing nanoplexes showed increased apoptosis of cells. In vitro protein expression revealed expression of exogenous p53 protein. In vivo imaging of mice showed localized signal for GFP protein in brain region. The tumors of mice treated with transferrin containing nanoplexes of PEI2-ChA were ∼5 times smaller in size than the tumor of untreated animals.

Critical Length of PEG Grafts on lPEI/DNA Nanoparticles for Efficient in Vivo Delivery

Nanoparticle-mediated gene delivery is a promising alternative to viral methods; however, its use in vivo, particularly following systemic injection, has suffered from poor delivery efficiency. Although PEGylation of nanoparticles has been successfully demonstrated as a strategy to enhance colloidal stability, its success in improving delivery efficiency has been limited, largely due to reduced cell binding and uptake, leading to poor transfection efficiency. Here we identified an optimized PEGylation scheme for DNA micellar nanoparticles that delivers balanced colloidal stability and transfection activity. Using linear polyethylenimine (lPEI)-g-PEG as a carrier, we characterized the effect of graft length and density of polyethylene glycol (PEG) on nanoparticle assembly, micelle stability, and gene delivery efficiency. Through variation of PEG grafting degree, lPEI with short PEG grafts (molecular weight, MW 500–700 Da) generated micellar nanoparticles with various shapes including spherical, rodlike, and wormlike nanoparticles. DNA micellar nanoparticles prepared with short PEG grafts showed comparable colloidal stability in salt and serum-containing media to those prepared with longer PEG grafts (MW 2 kDa). Corresponding to this trend, nanoparticles prepared with short PEG grafts displayed significantly higher in vitro transfection efficiency compared to those with longer PEG grafts. More importantly, short PEG grafts permitted marked increase in transfection efficiency following ligand conjugation to the PEG terminal in metastatic prostate cancer-bearing mice. This study identifies that lPEI-g-PEG with short PEG grafts (MW 500–700 Da) is the most effective to ensure shape control and deliver high colloidal stability, transfection activity, and ligand effect for DNA nanoparticles in vitro and in vivo following intravenous administration.

Apoferritin applications in nanomedicine

Nanomedicine as a continuously evolving discipline is still looking for a structure with perfect properties that is usable as a multifunctional transporter. Great potential is attributed to synthetic materials such as fullerenes, porous hollow silica nanoparticles and single-wall nanotubes, among others. However, materials that are natural to the human body are more acceptable by the organism, and thus become an attractive approach in this field of research. Ferritins are proteins that naturally occur in most living organisms throughout evolution and may be a possible transporter choice. Numerous applications have demonstrated the possibilities of iron-free ferritins, called apoferritins, serving as platforms for various nanomedical purposes This article summarizes the advantages and disadvantages of these proteins and discusses their practical applications and future perspectives.

Delivery of oligonucleotides with lipid nanoparticles

Since their inception in the 1980s, oligonucleotide-based (ON-based) therapeutics have been recognized as powerful tools that can treat a broad spectrum of diseases. The discoveries of novel regulatory methods of gene expression with diverse mechanisms of action are still driving the development of novel ON-based therapeutics. Difficulties in the delivery of this class of therapeutics hinder their in vivo applications, which forces drug delivery systems to be a prerequisite for clinical translation. This review discusses the strategy of using lipid nanoparticles as carriers to deliver therapeutic ONs to target cells in vitro and in vivo. A discourse on how chemical and physical properties of the lipid materials could be utilized during formulation and the resulting effects on delivery efficiency constitutes the major part of this review.

Peptide vectors for gene delivery: from single peptides to multifunctional peptide nanocarriers

The therapeutic use of nucleic acids relies on the availability of sophisticated delivery systems for targeted and intracellular delivery of these molecules. Such a gene delivery should possess essential characteristics to overcome several extracellular and intracellular barriers. Peptides offer an attractive platform for nonviral gene delivery, as several functional peptide classes exist capable of overcoming these barriers. However, none of these functional peptide classes contain all the essential characteristics required to overcome all of the barriers associated with successful gene delivery. Combining functional peptides into multifunctional peptide vectors will be pivotal for improving peptide-based gene delivery systems. By using combinatorial strategies and high-throughput screening, the identification of multifunctional peptide vectors will accelerate the optimization of peptide-based gene delivery systems.

Influence of pDNA availability on transfection efficiency of polyplexes in non-proliferative cells

We succeeded in visualizing plasmid DNA (pDNA) in the nucleus and cytosol of non-proliferative cells after transfection with linear polyethylenemine (lPEI) and histidinylated lPEI (His16-lPEI). This was possible with confocal microscope by using pDNA labelled with quantum dots. Indeed pDNA labelled with Cy3 leads to false positive nuclear localization because the saturation of the fluorescence signal overestimated the volume occupied by Cy3-pDNA. Moreover, Cy3 brightness was too weak to detect low amount of pDNA. About 20 to 40 pDNA copies were detected in the nucleus after the transfection of pDNA labelled with quantum dots. Transfection efficiency and cellular imaging data suggested that the cytosolic availability of pDNA, including endosome escape and/or polyplexes dissociation, is crucial for its nuclear delivery. In vitro transcription assay and transfection of cells allowing cytosolic gene expression concluded to better cytosolic availability of pDNA within His16-lPEI polyplexes. Cryo-TEM analyses revealed that His16-lPEI polyplexes exhibited a spherical shape and an amorphous internal structure which differed from the high degree of order of lPEI polyplexes. Altogether, this comparative study indicated that the high transfection efficiency of non-proliferative cells with His16-lPEI polyplexes was related to the amorphous structure and the facilitated dissociation of the assemblies.