Delivery of magic bullets: on the still rocky road to gene therapy

Combinatorial Polycation Synthesis and Causal Machine Learning Reveal Divergent Polymer Design Rules for Effective pDNA and Ribonucleoprotein Delivery

The development of polymers that can replace engineered viral vectors in clinical gene therapy has proven elusive despite the vast portfolios of multifunctional polymers generated by advances in polymer synthesis. Functional delivery of payloads such as plasmids (pDNA) and ribonucleoproteins (RNP) to various cellular populations and tissue types requires design precision. Herein, we systematically screen a combinatorially designed library of 43 well-defined polymers, ultimately identifying a lead polycationic vehicle (P38) for efficient pDNA delivery. Further, we demonstrate the versatility of P38 in codelivering spCas9 RNP and pDNA payloads to mediate homology-directed repair as well as in facilitating efficient pDNA delivery in ARPE-19 cells. P38 achieves nuclear import of pDNA and eludes lysosomal processing far more effectively than a structural analogue that does not deliver pDNA as efficiently. To reveal the physicochemical drivers of P38's gene delivery performance, SHapley Additive exPlanations (SHAP) are computed for nine polyplex features, and a causal model is applied to evaluate the average treatment effect of the most important features selected by SHAP. Our machine learning interpretability and causal inference approach derives structure-function relationships underlying delivery efficiency, polyplex uptake, and cellular viability and probes the overlap in polymer design criteria between RNP and pDNA payloads. Together, combinatorial polymer synthesis, parallelized biological screening, and machine learning establish that pDNA delivery demands careful tuning of polycation protonation equilibria while RNP payloads are delivered most efficaciously by polymers that deprotonate cooperatively via hydrophobic interactions. These payload-specific design guidelines will inform further design of bespoke polymers for specific therapeutic contexts.

Scaffold-Based microRNA Therapies in Regenerative Medicine and Cancer

microRNA-based therapies are an advantageous strategy with applications in both regenerative medicine (RM) and cancer treatments. microRNAs (miRNAs) are an evolutionary conserved class of small RNA molecules that modulate up to one third of the human nonprotein coding genome. Thus, synthetic miRNA activators and inhibitors hold immense potential to finely balance gene expression and reestablish tissue health. Ongoing industry-sponsored clinical trials inspire a new miRNA therapeutics era, but progress largely relies on the development of safe and efficient delivery systems. The emerging application of biomaterial scaffolds for this purpose offers spatiotemporal control and circumvents biological and mechanical barriers that impede successful miRNA delivery. The nascent research in scaffold-mediated miRNA therapies translates know-how learnt from studies in antitumoral and genetic disorders as well as work on plasmid (p)DNA/siRNA delivery to expand the miRNA therapies arena. In this progress report, the state of the art methods of regulating miRNAs are reviewed. Relevant miRNA delivery vectors and scaffold systems applied to-date for RM and cancer treatment applications are discussed, as well as the challenges involved in their design. Overall, this progress report demonstrates the opportunity that exists for the application of miRNA-activated scaffolds in the future of RM and cancer treatments.

Anionic nanoparticles based on Span 80 as low-cost, simple and efficient non-viral gene-transfection systems

The existing strategies in the design of non-viral vectors for gene therapy are primarily conceived for cationic systems. However, the safety concerns associated with the use of positively charged systems for nucleic acid delivery and several reports regarding the efficacy of negatively charged systems highlights the need for improved gene-delivery vectors. With these premises in mind, we investigated the development of new negatively charged nanoparticles based on Sorbitan esters (Span(®)) – extremely cheap excipients broadly used in the pharmaceutical industry – on the basis of a simple, one-step and easily scalable procedure. For their specific use in gene therapy, we have incorporated oleylamine (OA) or poly-L-arginine (PA) into these nanosystems. Thus, we used Sorbitan monooleate (Span(®) 80) to design Span(®) 80-oleylamine and Span(®) 80-poly-L-arginine nanosystems (SP-OA and SP-PA, respectively). These systems can associate with the model plasmid pEGFP-C3 and show mean particle sizes of 304 nm and 247 nm and surface charges of -13 mV and -17 mV, respectively. The nanoparticles developed were evaluated in terms of in vitro cell viability and transfection ability. Both systems exhibited an appropriate cell-toxicity profile and are able to transfect the plasmid effectively. Specifically, the nanosystems including OA among their components provided higher transfection levels than the SP-PA nanoparticles. In conclusion, anionic nanoparticles based on Span(®) 80 can be considered low-cost, simple and efficient non-viral anionic gene-transfection systems.

Non-viral gene-activated matrices: next generation constructs for bone repair

In the context of producing enhanced therapeutics for regenerative medicine, our laboratory develops gene-activated matrices (GAMs) using non-viral gene therapy (GT) in combination with collagen-based scaffolds engineered specifically for tissue repair. Non-viral vectors have been referred to as a minority pursuit in GT but considering the concerns associated with viral vectors and as transient gene expression is such a key consideration, further research is clearly warranted for tissue engineering (TE) applications. Mesenchymal stem cells (MSCs) are well regarded for their capability in bone regeneration but as primary cells, they are difficult to transfect. We have recently optimised the non-viral vector, polyethyleneimine (PEI), to achieve high transfection efficiencies in MSCs. Subsequently, a series of PEI-based GAMs were developed using collagen, collagen-glycosaminoglycan and collagen-nanohydroxyapatite (collagen-nHa) scaffolds whereby transgene expression was detected up to 21 d with the collagen-nHa scaffold providing the most prolonged expression. Moreover, all PEI-based GAMs contained a low plasmid DNA dose of 2 µg which is far below doses often required in previous GAMs. Having successfully developed these GAMs, the ephrinB2 gene has recently been incorporated to produce a novel therapeutic GAM for bone repair. Herein, we discuss our recent investigations in the development and application of non-viral GAMs.

Recent Findings Concerning PAMAM Dendrimer Conjugates with Cyclodextrins as Carriers of DNA and RNA

We have evaluated the potential use of various polyamidoamine (PAMAM) dendrimer [dendrimer, generation (G) 2-4] conjugates with cyclodextrins (CyDs) as novel DNA and RNA carriers. Among the various dendrimer conjugates with CyDs, the dendrimer (G3) conjugate with α-CyD having an average degree of substitution (DS) of 2.4 [α-CDE (G3, DS2)] displayed remarkable properties as DNA, shRNA and siRNA delivery carriers through the sensor function of α-CDEs toward nucleic acid drugs, cell surface and endosomal membranes. In an attempt to develop cell-specific gene transfer carriers, we prepared sugar-appended α-CDEs. Of the various sugar-appended α-CDEs prepared, galactose- or mannose-appended α-CDEs provided superior gene transfer activity to α-CDE in various cells, but not cell-specific gene delivery ability. However, lactose-appended α-CDE [Lac-α-CDE (G2)] was found to possess asialoglycoprotein receptor (AgpR)-mediated hepatocyte-selective gene transfer activity, both in vitro and in vivo. Most recently, we prepared folate-poly(ethylene glycol)-appended α-CDE [Fol-PαC (G3)] and revealed that Fol-PαC (G3) imparted folate receptor (FR)-mediated cancer cell-selective gene transfer activity. Consequently, α-CDEs bearing integrated, multifunctional molecules may possess the potential to be novel carriers for DNA, shRNA and siRNA.