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  • 1.
    Dowaidar, Moataz
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Chimeric gene delivery vectors: Design, synthesis, and mechanisms from transcriptomics analysis2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    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.

  • 2.
    Dowaidar, Moataz
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    In-silico design of peptide-based transfection systems, in-vitro validation, and up-take pathways investigation2017Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cell-penetrating peptide-based transfection systems (PBTS) are a promising group of drug delivery vectors. Cell-penetrating peptides (CPPs) are short cationic peptides that are able of transporting cell non-permeant cargos into different cell types. Some CPPs can be used to form non-covalent complexes with oligonucleotides for gene delivery applications. For the potential use of CPPs as drug delivery tools, it is important to understand the mechanism of uptake. Here, a fragment quantitative structure–activity relationships (FQSAR) model is generated to predict novel peptides based on approved alpha helical conformers and assisted model construction with energy refinement molecular mechanics simulations of former peptides. The modeled peptides were examined for plasmid transfection efficiency and compared with their predicted biological activity. The best predicted peptides were efficient for plasmid transfection with significant enhancement compared to the former group of peptides. Our results confirm that FQSAR model refinement is an efficient method for optimizing PBTS for improved biological activity. Additionally, using RNA sequencing, we demonstrated the involvement of autophagy pathways in PBTS uptake.

  • 3.
    Dowaidar, Moataz
    et al.
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Abdelhamid, Hani Nasser
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hällbrink, Mattias
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Freimann, Krista
    Kurrikof, Kaido
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry. University of Tartu, Estonia.
    Magnetic Nanoparticle Assisted Self-assembly of Cell Penetrating Peptides-Oligonucleotides Complexes for Gene Delivery2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 9159Article in journal (Refereed)
    Abstract [en]

    Magnetic nanoparticles (MNPs, Fe3O4) incorporated into the complexes of cell penetrating peptides (CPPs)-oligonucleotides (ONs) promoted the cell transfection for plasmid transfection, splice correction, and gene silencing efficiencies. Six types of cell penetrating peptides (CPPs; PeptFect220 (denoted PF220), PF221, PF222, PF223, PF224 and PF14) and three types of gene therapeutic agents (plasmid (pGL3), splicing correcting oligonucleotides (SCO), and small interfering RNA (siRNA) were investigated. Magnetic nanoparticles incorporated into the complexes of CPPs-pGL3, CPPs-SCO, and CPPs-siRNA showed high cell biocompatibility and efficiently transfected the investigated cells with pGL3, SCO, and siRNA, respectively. Gene transfer vectors formed among PF14, SCO, and MNPs (PF14-SCO-MNPs) showed a superior transfection efficiency (up to 4-fold) compared to the noncovalent PF14-SCO complex, which was previously reported with a higher efficiency compared to commercial vector called Lipofectamine™2000. The high transfection efficiency of the new complexes (CPPs-SCO-MNPs) may be attributed to the morphology, low cytotoxicity, and the synergistic effect of MNPs and CPPs. PF14-pDNA-MNPs is an efficient complex for in vivo gene delivery upon systemic administration. The conjugation of CPPs-ONs with inorganic magnetic nanoparticles (Fe3O4) may open new venues for selective and efficient gene therapy.

  • 4.
    Dowaidar, Moataz
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Abdelhamid, Hani Nasser
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Assuit University, Egypt.
    Hällbrink, Mattias
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Chitosan enhances gene delivery of oligonucleotide complexes with magnetic nanoparticles–cell-penetrating peptide2018In: Journal of biomaterials applications, ISSN 0885-3282, E-ISSN 1530-8022, Vol. 33, no 3, p. 392-401Article in journal (Refereed)
    Abstract [en]

    Gene-based therapies, including the delivery of oligonucleotides, offer promising methods for the treatment of cancer cells. However, they have various limitations including low efficiency. Herein, cell-penetrating peptides (CPPs)-conjugated chitosan-modified iron oxide magnetic nanoparticles (CPPs-CTS@MNPs) with high biocompatibility as well as high efficiency were tested for the delivery of oligonucleotides such as plasmid pGL3, splice correction oligonucleotides, and small-interfering RNA. A biocompatible nanocomposite, in which CTS@MNPs was incorporated in non-covalent complex with CPPs-oligonucleotide, is developed. Modifying the surface of magnetic nanoparticles with cationic chitosan-modified iron oxide improved the performance of magnetic nanoparticles-CPPs for oligonucleotide delivery. CPPs-CTS@MNPs complexes enhance oligonucleotide transfection compared to CPPs@MNPs or CPPs. The hydrophilic character of CTS@MNPs improves complexation with plasmid pGL3, splice correction oligonucleotides, and small-interfering RNA payload, which consequently resulted in not only strengthening the colloidal stability of the constructed complex but also improving their biocompatibility. Transfection using PF14-splice correction oligonucleotides-CTS@MNPs showed sixfold increase of the transfection compared to splice correction oligonucleotides-PF14 that showed higher transfection than the commercially available lipid-based vector Lipofectamine™ 2000. Nanoscaled CPPs-CTS@MNPs comprise a new family of biomaterials that can circumvent some of the limitations of CPPs or magnetic nanoparticles.

  • 5.
    Dowaidar, Moataz
    et al.
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Abdelhamid, Hani Nasser
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hällbrink, Mattias
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Zou, Xiaodong
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Graphene oxide nanosheets in complex with cell penetrating peptides for oligonucleotides delivery2017In: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1861, no 9, p. 2334-2341Article in journal (Refereed)
    Abstract [en]

    A new strategy for gene transfection using the nanocarrier of cell penetrating peptides (CPPs; PepFect14 (PF14) or PepFect14 (PF14) (PF221)) in complex with graphene oxide (GO) is reported. GO complexed with CPPs and plasmid (pGL3), splice correction oligonucleotides (SCO) or small interfering RNA (siRNA) are performed. Data show adsorption of CPPs and oligonucleotides on the top of the graphenic lamellar without any observed change of the particle size of GO. GO mitigates the cytotoxicity of CPPs and improves the material biocompatibility. Complexes of GO-pGL3-CPPs (CPPs; PF14 or PF221) offer 2.1–2.5 fold increase of the cell transfection compared to pGL3-CPPs (CPPs; PF14 or PF221). GO-SCO-PF14 assemblies effectively transfect the cells with an increase of > 10–25 fold compared to the transfection using PF14. The concentration of GO plays a significant role in the material nanotoxicity and the transfection efficiency. The results open a new horizon in the gene treatment using CPPs and offer a simple strategy for further investigations.

  • 6.
    Dowaidar, Moataz
    et al.
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Gestin, Maxime
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Cerrato, Carmine Pasquale
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Jafferali, Mohammed Hakim
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Margus, Helerin
    Kivistik, Paula Ann
    Ezzat, Kariem
    Hallberg, Einar
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Pooga, Margus
    Hällbrink, Mattias
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry. University of Tartu, Estonia.
    Role of autophagy in cell-penetrating peptide transfection model2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 12635Article in journal (Refereed)
    Abstract [en]

    Cell-penetrating peptides (CPPs) uptake mechanism is still in need of more clarification to have a better understanding of their action in the mediation of oligonucleotide transfection. In this study, the effect on early events (1 h treatment) in transfection by PepFect14 (PF14), with or without oligonucleotide cargo on gene expression, in HeLa cells, have been investigated. The RNA expression profile was characterized by RNA sequencing and confirmed by qPCR analysis. The gene regulations were then related to the biological processes by the study of signaling pathways that showed the induction of autophagy-related genes in early transfection. A ligand library interfering with the detected intracellular pathways showed concentration-dependent effects on the transfection efficiency of splice correction oligonucleotide complexed with PepFect14, proving that the autophagy process is induced upon the uptake of complexes. Finally, the autophagy induction and colocalization with autophagosomes have been confirmed by confocal microscopy and transmission electron microscopy. We conclude that autophagy, an inherent cellular response process, is triggered by the cellular uptake of CPP-based transfection system. This finding opens novel possibilities to use autophagy modifiers in future gene therapy.

  • 7.
    Dowaidar, Moataz
    et al.
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Gestin, Maxime
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Cerrato, Carmine Pasquale
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Margus, Helerin
    Kivistik, Paula Ann
    Pooga, Margus
    Hällbrink, Mattias
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Role of autophagy in PepFect14 transfection2017Manuscript (preprint) (Other academic)
    Abstract [en]

    Cell-penetrating peptides (CPP) uptake mechanism is still to be clarified to have a better understanding of their action in the mediation of oligonucleotide transfection. In this study, the effect on early events (1 h treatment) in transfection by Pepfect 14, with or without oligonucleotide cargo on gene expression, on HeLa cells, have been investigated. The RNA expression profile was characterized by RNA sequencing and confirmed with qPCR analysis. The gene regulations were then related to the biological process by the study of signaling pathways that showed the induction of autophagy-related genes in early transfection. A ligand library interfering with the detected intracellular pathways showed concentration-dependent effects on the transfection of splice correction oligonucleotide complexed with Pepfect 14 confirming the induction of autophagy process by the uptake of complexes. Finally, colocalization of nucleic acid cargo and autophagosomes, as well as the autophagosome production induced by the treatment, have been shown by confocal microscopy and transmission electron microscopy. We conclude that autophagy is an important response process triggered by the cellular uptake of CPP-based transfection system. This conclusion opens a possibility to use autophagy modifiers in future gene therapy.

  • 8.
    Dowaidar, Moataz
    et al.
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Regberg, Jakob
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Dobchev, Dimitar A.
    Lehto, Tõnis
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Hällbrink, Mattias
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Karelson, Mati
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry. University of Tartu, Estonia.
    Refinement of a Quantitative Structure–Activity Relationship Model for Prediction of Cell-Penetrating Peptide Based Transfection Systems2017In: International Journal of Peptide Research and Therapeutics, E-ISSN 1573-3904, Vol. 23, no 1, p. 91-100Article in journal (Refereed)
    Abstract [en]

    Cell-penetrating peptide (CPP) based transfection systems (PBTS) are a promising class of drug delivery vectors. CPPs are short mainly cationic peptides capable of delivering cell non-permeant cargo to the interior of the cell. Some CPPs have the ability to form non-covalent complexes with oligonucleotides for gene therapy applications. In this study, we use quantitative structure–activity relationships (QSAR), a statistical method based on regression data analysis. Here, a fragment QSAR (FQSAR) model is developed to predict new peptides based on standard alpha helical conformers and Assisted Model Building with Energy Refinement molecular mechanics simulations of previous peptides. These new peptides were examined for plasmid transfection efficiency and compared with their predicted biological activity. The best predicted peptides were capable of achieving plasmid transfection with significant improvement compared to the previous generation of peptides. Our results demonstrate that FQSAR model refinement is an efficient method for optimizing PBTS for improved biological activity.

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