Chimeric gene delivery vectors : Design, synthesis, and mechanisms from transcriptomics analysis

Abstract: Delivery of nucleic acid is a promising approach for genetic diseases/disorders. However, gene therapy using oligonucleotides (ONs) suffers from low transfection efficacy due to negative charges, weak cellular permeability, and enzymatic degradation. Thus, cell-penetrating peptide (CPP), is a short cationic peptide, is used to improve the cell transfection. In this thesis, new strategies for gene transfection using the CPP vectors in complex with ONs without and with nanoparticles, such as magnetic nanoparticles (MNPs, Fe3O4), and graphene oxide (GO), are investigated. Furthermore, the possible CPP uptake signalling pathways are also discussed.A fragment quantitative structure-activity relationship (FQSAR) model is applied to predict new effective peptides for plasmid DNA transfection. The best-predicted peptides were able to transfect plasmids with significant enhancement compared to the other peptides. CPPs (PeptFect220 (denoted PF220), PF221, PF222, PF223, PF224) generated from the FQSAR, and standard PF14 were able to form self-assembled complexes with MNPs and GO. The formed new hybrid vectors improved the cell transfection for plasmid (pGL3), splicing correcting oligonucleotides (SCO), and small interfering RNA (siRNA). These vectors showed high cell biocompatibility and offered high transfection efficiency (> 4-fold for MNPs, 10–25-fold for GO) compared to PF14/SCO complex, which was before reported with a higher efficacy compared to the commercial lipid-based transfection vector Lipofectamine™2000. The high transfection efficiency of the novel complexes (CPP/ON/MNPs and CPP/ON/GO) may be due to their low cytotoxicity, and the synergistic effect of MNPs, GO, and CPPs. In vivo gene delivery using PF14/pDNA/MNPs was also reported. The assembly of CPPs/ON with MNPs or GO is promising and may open new venues for potent and selective gene therapy using external stimuli. The uptake signaling pathways using CPPs vectors, the RNA expression profile for PF14, with and without ON were investigated using RNA sequencing and qPCR analysis. Data showed that the signaling pathways are due to the regulation of autophagy-related genes. Our study revealed that the autophagy regulating proteins are concentration-dependent. Confocal microscopy and transmission electron microscopy have demonstrated the autophagy initiation and colocalization of ON with autophagosomes. Results showed that the cellular uptake of CPP-based transfection activates the autophagy signaling pathway. These findings may open new opportunities to use autophagy modifiers in gene therapy.