Rapid and facile quantitation of polyplex endocytic trafficking

Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods

Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.

Polymeric Delivery of Therapeutic Nucleic Acids

The advent of genome editing has transformed the therapeutic landscape for several debilitating diseases, and the clinical outlook for gene therapeutics has never been more promising. The therapeutic potential of nucleic acids has been limited by a reliance on engineered viral vectors for delivery. Chemically defined polymers can remediate technological, regulatory, and clinical challenges associated with viral modes of gene delivery. Because of their scalability, versatility, and exquisite tunability, polymers are ideal biomaterial platforms for delivering nucleic acid payloads efficiently while minimizing immune response and cellular toxicity. While polymeric gene delivery has progressed significantly in the past four decades, clinical translation of polymeric vehicles faces several formidable challenges. The aim of our Account is to illustrate diverse concepts in designing polymeric vectors towards meeting therapeutic goals of in vivo and ex vivo gene therapy. Here, we highlight several classes of polymers employed in gene delivery and summarize the recent work on understanding the contributions of chemical and architectural design parameters. We touch upon characterization methods used to visualize and understand events transpiring at the interfaces between polymer, nucleic acids, and the physiological environment. We conclude that interdisciplinary approaches and methodologies motivated by fundamental questions are key to designing high-performing polymeric vehicles for gene therapy.

Separation-related rapid nuclear transport of DNA/RNA heteroduplex oligonucleotide: unveiling distinctive intracellular trafficking

DNA/RNA heteroduplex oligonucleotide (HDO), composed of DNA/locked nucleic acid (LNA) antisense oligonucleotide (ASO) and complementary RNA, is a next-generation antisense therapeutic agent. HDO is superior to the parental ASO in delivering to target tissues, and it exerts a more potent gene-silencing effect. In this study, we aimed to elucidate the intracellular trafficking mechanism of HDO-dependent gene silencing. HDO was more preferably transferred to the nucleus after transfection compared to the parental ASO. To determine when and where HDO is separated into the antisense strand (AS) and complementary strand (CS), we performed live-cell time-lapse imaging and fluorescence resonance energy transfer (FRET) assays. These assays demonstrated that HDO had a different intracellular trafficking mechanism than ASO. After endocytosis, HDO was separated in the early endosomes, and both AS and CS were released into the cytosol. AS was more efficiently transported to the nucleus than CS. Separation, endosomal release, and initiation of nuclear transport were a series of time-locked events occurring at a median of 30 s. CS cleavage was associated with efficient nuclear distribution and gene silencing in the nucleus. Understanding the unique intracellular silencing mechanisms of HDO will help us design more efficient drugs and might also provide insight into innate DNA/RNA cellular biology.

Boronic acid copolymers for direct loading and acid-triggered release of Bis-T-23 in cultured podocytes

We report an acid-reversible linker for triggered release of Bis-T-23, an experimental small molecule drug for kidney disease treatment that restores podocyte morphology during disease. Bis-T-23 contains catechols, which form an acid-reversible, covalent boronate ester bond with boronic acids. We synthesized phenylboronic acid-containing polymers using reversible addition-fragmentation chain transfer polymerization that were able to directly load and solubilize Bis-T-23. Because of the reversibility of the boronic ester bond, drug was released in its native form in a pH-dependent manner. The polymers rapidly trafficked into acidic compartments and did not exhibit cytotoxicity, and polymer-drug conjugates successfully delivered Bis-T-23 into cultured podocytes.

Quantitative colocalization analysis of DNA delivery by PEI-mediated cationic polymers in mammalian cells

Although cationic polymers are widely used for DNA delivery, the relationship between the properties of the formed complexes and their biological activity is not fully understood. Here, we propose a novel procedure consisting of superresolved images coupled with quantitative colocalization to analyse DNA release in living cells. This work compares the different workflows available in a quantitative colocalization study of DNA delivery using polyethylenimine as transfection reagent. A nimble workflow with deconvolution in three-dimensional images was developed. Among the different colocalization coefficients, Manders' colocalization coefficient was the best to track the complexes. Results showed that DNA/polyethylenimine complexes were tightly interacting at the time of transfection and their disassembly was observed between 2 and 10 h after their uptake. Heterogenicity was found in the intracellular fate of each complex. At 24 h, some complexes were still present underneath the nuclear envelope. Overall, this study opens the door for particle tracking assessment with three-dimensional imaging at intracellular level. LAY DESCRIPTION: DNA delivery technologies in living cells are of high relevance in the biotechnology field. The transient expression of a gene of interest enables the production of a wide range of new therapeutic candidates for clinical purposes. However, the introduction of an exogenous DNA construct into a cell culture requires the use of certain vehicles that protect the DNA from host cell DNases and deliver it into the cell nucleus. From the different systems available, polyethylenimine (PEI) has been extensively used in transient gene expression strategies for the last three decades. However, the intracellular fate of the formed DNA/PEI complexes and the DNA release from the complexes is still poorly understood. In this work, we propose the application of combined superresolved images through mathematical deconvolution to colocalization studies of DNA/PEI complexes evolution in living mammalian cell cultures. Both specimens were covalently labelled with Cy3 and Cy5 dye, respectively, and the kinetics of its disassembly process within the cells was tracked over the time. Because of the specific features of the formed-complexes, a comparative study of the different colocalization coefficients was performed towards optimizing the analysis of these particles with confocal microscopy. Besides, the 3D imaging of the process allowed the direct visualization of a partial DNA/PEI complexes disassembly and the location of those complexes underneath the nuclear envelope during the cell production phase (24 h after the uptake).

Intracellular Trafficking and Endosomal Release of Oligonucleotides: What We Know and What We Don't

Understanding the cellular uptake and intracellular trafficking of oligonucleotides provides an important basic underpinning for the developing field of oligonucleotide-based therapeutics. Whether delivered as "free" oligonucleotides, as ligand-oligonucleotide conjugates, or in association with various nanocarriers, all forms of oligonucleotide enter cells by endocytosis and are initially ensconced within membrane-limited vesicles. Accordingly, the locus and extent of release to the cytosol and nucleus are key determinants of the pharmacological actions of oligonucleotides. A number of recent studies have explored the intracellular trafficking of various forms of oligonucleotides and their release from endomembrane compartments. These studies reveal a surprising convergence on an early-intermediate compartment in the trafficking pathway as the key locus of release for oligonucleotides administered in "free" form as well as those delivered with lipid complexes. Thus, oligonucleotide release from multivesicular bodies or from late endosomes seems to be the crucial endogenous process for attaining pharmacological effects. This intrinsic process of oligonucleotide release may be amplified by delivery agents such as lipid complexes or small molecule enhancers.

The great escape: how cationic polyplexes overcome the endosomal barrier

Endo-lysosomal escape strategies of cationic polymer-mediated gene delivery at a glance.