Muscular Dystrophy (MD) is a progressive muscle wasting disease which currently has no cure, and is caused by the mutation of the dystrophin gene. A multitude of approaches for the improvement of the muscular pathology caused by this condition are being investigated, one of which is gene therapy. This approach is used to deliver vectors containing therapeutic transgenes such as dystrophin to target muscle cells. One method of gene delivery utilises viral vectors, and although this has resulted in systemic delivery and efficient transgene expression, there are many safety implications which have led to the development of non-viral approaches, such as the direct delivery of naked plasmid DNA. However, the shortcomings of these vectors include an inability to replicate within host cells, resulting in the loss of vector as cells replicate, and the silencing of transgene expression. In an effort to overcome such limitations, a novel system called the ‘pEPI vector' has been developed. Here, the inclusion of the β-IFN scaffold/matrix-attachment region (S/MAR) element into the open reading frame of an actively transcribed transgene has been found to lead to sustained, long term transgene expression, and to allow the episomal propagation and maintenance of the vector in dividing cells over many generations. The aim of this thesis was to investigate the potential of this vector for use as a gene therapy vector in muscle cells in order to treat MD. In this study, the long-term expression of the eGFP reporter transgene inserted into the pEPI vector was evaluated, and the pEPI vector's episomal/integrant status was investigated, in C2C12 murine myoblasts, HeLa, and HepG2 cell lines. 60 days after transfection the vector was found not to have integrated into the host genomes of any of the cell lines. Transgene expression had declined to nearly undetectable levels in fast-replicating C2C12 and HeLa cells, but was at high levels in the relatively slow-dividing HepG2 cells. An attempt to improve long term transgene expression in C2C12 cells by changing the promoter from CMV to CAGG still led to low transgene expression after 60 days. To address this issue, this study focused on the development of a novel approach to ameliorate long-term transgene expression, based upon the origin of replication and nuclear matrix attachment properties of the S/MAR element, as well as the results obtained from testing the vector in the HeLa and HepG2 cells. It involved the arrest of C2C12 cells in the G0/G1 phase of the cell cycle post transfection with the pEPI vector in order to allow these fast-dividing cells an extended period of time to epigenetically mark pEPI prior to selection. The findings indicated that this novel method of pEPI vector establishment was superior to that which utilises selection alone. However, in spite of the improvement in long-term episomal transgene expression observed using this novel method of establishment of the pEPI vector, transgene expression levels were still relatively low after 35 days of cell proliferation, which led to the conclusion that further development of this vector is essential in order for it to be able to elicit a significant restoration of muscle function in MD patients. Additionally, two other S/MAR vectors were tested in C2C12 cells. One vector contained the ‘mini-S/MAR', a shorter version of the β-IFN S/MAR, and the other contained a novel S/MAR derived from the c-myc proto-oncogene. Transgene expression by either vector was nearly undetectable after several weeks of proliferation, and both were found to integrate into the C2C12 host genome, leading to the conclusion that not all S/MAR elements inserted within a plasmid vector can lead to long-term transgene expression, nor confer protection from vector integration.

BACKGROUND: Spondyloarthritis is a family of related inflammatory diseases including psoriatic arthritis and ankylosing spondylitis. The cytokine IL-23 is known to play an important role in spondyloarthritis development. Overexpression of IL-23 using IL-23 minicircle DNA in B10.RIII mice results in the development of a spondyloarthritis-like disease. B10.RIII is a major histocompatibility complex (MHC) congenic mouse strain that is susceptible to a number of autoimmune and autoinflammatory diseases. Contaminating regions outside the congenic interval from the donor strain, RIII, have been previously detected. While B10.RIII mice develop collagen-induced arthritis (CIA) and collagen antibody induced arthritis (CAIA), the background strain, C57BL/10 (B10) does not. The MHC region is known to play a role in the susceptibility of B10.RIII mice to CIA, but not in CAIA development, so other regions must be involved in arthritis development as well. These contaminating RIII-derived regions may control susceptibility to IL-23 minicircle induced arthritis in B10.RIII mice. OBJECTIVE: This study aimed to identify RIII-derived regions in the genome of B10.RIII mice and begin to interrogate their effects on IL-23 minicircle induced arthritis. METHODS: A systematic literature review was conducted using Pubmed and Web of Science. Articles using B10.RIII mice to study inflammatory disease models were included and data about year of publication, inbred mouse strains used, disease model, and inbred strain notation were extracted. Genome sequences of B10.RIII(71NS)/Sn, C57BL/10SnJ, and C57BL/10J were compared to identify RIII-derived clusters of variation in the B10.RIII genome. B10.RIII mice were crossed with B10 mice and subsequently backcrossed to B10.RIII mice to introduce the B10 allele at chromosome 15. Chr15b/b, Chr15b/r, and Chr15r/r B10.RIII mice were hydrodynamically injected with IL-23 minicircles, and arthritis development was monitored every other day for two weeks. RESULTS: The systematic literature review yielded 8 studies that compared arthritis development in B10.RIII to RIII or B10. These studies identified three arthritis susceptibility regions: Cia5/Eae3 on chromosome 3, Eae2 on chromosome 15, and Eae39 on chromosome 5. Eae2 is further split into four sub-regions: Cia30, Cia31, Cia32, and Cia26. Genome sequence comparison identified RIII-derived clusters in B10.RIII mice on chromosomes 10, 14, 15, and 17. The chromosome 15 region overlaps with the Eae2 susceptibility region for approximately 17 Mbp and includes the arthritis susceptibility loci Cia26 and Cia32. When this region was interrogated in vivo, Chr15r/r and Chr15b/r B10.RIII mice developed IL-23 minicircle arthritis, while Chr15b/b mice did not. CONCLUSION: The B10.RIII(71NS)/Sn strain contains several large RIII/WySn-derived regions outside the congenic MHC region. One of these clusters on chromosome 15 includes the arthritis susceptibility loci Cia26 and Cia32 and appears to determine susceptibility to IL-23 minicircle induced arthritis. Future studies will interrogate the role of the chromosome 15 RIII-derived region in arthritis development in more detail and aim to identify the specific gene variants that control arthritis susceptibility. / 2023-01-28T00:00:00Z

Krebs gehört zu den häufigsten Todesursachen weltweit. Ein großer Hoffnungsträger für die Behandlung maligner Tumore ist die Gentherapie. Die nicht-virale Gentherapie gilt als sicherere Alternative zur viralen Gentherapie. Für den nicht viralen Gentransfer sind sowohl Vektor als auch Gentransfertechnologie von entscheidender Bedeutung. Im Rahmen dieser Arbeit wurde die Gentransfereffizienz und Sicherheit der Jet-Injektion in einer klinischen Phase I Gentransferstudie mit Hilfe des Swiss-Injektors untersucht. Es konnte gezeigt werden, dass diese Technologie sicher klinisch angewendet werden kann, dass jedoch die Sicherheit der Vektoren und vor allem die Gentransfereffizienz weiter optimiert werden müssen. Ausgehend von diesen Ergebnissen wurden optimierte nicht-virale Vektoren (Minicircle, MIDGE) miteinander und mit ihren parentalen Plasmiden verglichen. Mit Hilfe des MIDGE Vektors konnte die höchste Transgenexpression aufgrund einer erhöhten Transkription erzielt werden. In Vorbereitung der klinischen Anwendung des MIDGE-Vektors wurde die Kombination von hTNF-alpha Gentransfer und Vindesin Chemotherapie untersucht. Auch hier zeigte der MIDGE-Vektor eine erhöhte in vitro Genexpression, die in vitro zu einer erhöhten Zytotoxizität von Vindesin aufgrund einer verstärkten Aktivierung der Apoptose führte. Auch in vivo konnte die verbesserte hTNF-alpha-Genexpression des MIDGE-Vektors nach Jet-Injektion gezeigt werden. Dies führte in Kombination mit Vindesin zu einem signifikant reduzierten Tumorwachstum. Durch Analyse der systemischen Vektorverteilung im Blut und in den Organen sowie in einer präklinischen toxikologischen Untersuchung konnte die sichere Anwendung des MIDGE-Vektors bestätigt werden. Abschließend wurden weitere Anwendungsmöglichkeiten des MIDGE-Vektors für die stabile Genexpression und für die Verwendung in kombinierten Gentransferprotokollen untersucht. / Cancer is one leading causes of death worldwide. Gene therapy belongs to the promising options for treatment of malignant tumors. The non-viral gene therapy is known as safer alternative to the viral gene therapy. For non-viral gene transfer the vector and the transfer technology are of crucial importance. As part of this work a clinical trial was performed to assess efficiency and safety of the non-viral jet-injection. It was shown, that this technology can be used safely in a clinical setting. As a result of this clinical trial we concluded, that vector safety and especially efficiency need further improvements. Based on this optimized non-viral vectors (minicircle, MIDGE) were compared with each other and their respective parental plasmids. The MIDGE vector showed the highest transgene expression due to increased transcription. In preparation of a clinical trial the combined treatment of hTNF-alpha gene transfer and Vindesine chemotherapy was analyzed. Again, the MIDGE vector showed the highest transgene expression. This expression led to an increased cytotoxicity of Vindesine in vitro due to an elevated apoptosis signaling. Furthermore, these results could be assigned to an in vivo model. The increased hTNF-alpha expression after MIDGE vector jet-injection in combination with Vindesine led to a significant decrease in tumor growth. Detailed analysis of systemic vector distribution in the blood and organs as well as the preclinical toxicity evaluation showed the safety of the non-viral MIDGE vector. Initial experiments were performed to show further options for stable gene expression and combined gene transfer protocols using the MIDGE vector.

BACKGROUND: Spondyloarthritis is a subset of inflammatory rheumatic diseases that includes ankylosing spondyloarthritis, psoriatic arthritis, undifferentiated spondyloarthritis, and arthritis related to inflammatory bowel. The IL-23 cytokine has been implicated in the pathogenesis of spondyloarthritis. B10.RIII mice hydrodynamically injected with IL-23 minicircle overexpress the IL-23 cytokine, which leads to the development of spondyloarthritis-like disease. It is important to note that B10.RIII is a major histocompatibility complex (MHC) congenic mouse strain that is susceptible to autoimmune and autoinflammatory diseases where the background strain, C57BL/10 (B10), or the MHC donor strain, RIIIS/J, is resistant. For instance, the B10.RIII strain of mice is susceptible to IL-23-induced arthritis, while the B10 background strain is not. Large contaminating RIII-derived regions outside of the selected congenic interval on chromosome 17 were identified on chromosomes 10, 14, 15, and 17. Genetic variations in these intervals may contribute to the susceptibility of the B10.RIII mice to arthritis induced by IL-23 minicircle. OBJECTIVE: This study aimed to interrogate the arthritis phenotype after IL-23 minicircle injection in Chr17 subcongenic B10.RIII mice. In addition, chromosome 17 RIII-derived Ilrun gene and its role in regulating the Interferon signaling pathway between the B10.RIII and B10 mice were investigated. METHOD: Chromosome 17 subcongenic mice were generated by crossing B10.RIII mice with B10 mice and backcrossing the offspring to the B10.RIII mice. Offspring heterozygous b/r for the Chr17 region were then intercrossed to generate B10.RIII mice that are identical to the B10.RIII mice, except at chromosome 17, where they had the genotypes Chr17b/b, Chr17b/r, or Chr17r/r. These mice were then hydrodynamically injected with IL-23 minicircle DNA, and disease development was monitored every other day for two weeks using two parameters: clinical arthritis score and paw swelling. Bone marrow-derived macrophages were differentiated in vitro from B10.RIII and B10 mice. Cells were stimulated with TLR agonists (Pam3CSK4, Poly (I:C), LPS) that induce either the Ilrun-regulated Interferon signaling pathway or the NF-kB signaling pathway. Gene expression changes of NF-kB and Interferon-induced genes were measured using real-time quantitative PCR. TNF protein concentration in the supernatant was measured by ELISA. RESULTS: Upon IL-23 minicircle injection, Chr17r/r and Chr17b/r B10.RIII mice developed arthritis while Chr17b/b B10.RIII mice did not. In addition, the disease severity increased with the number of r alleles as the Chr17r/r B10.RIII mice had a higher clinical score and paw swelling when compared to the heterozygote Chr17b/r mice. Gene expression analysis of NF-kB and Interferon response genes revealed that there was no difference in the induction of NF-kB and Interferon response genes in bone marrow-derived macrophages from B10.RIII and B10 mice. In addition, there was also no difference in the induction of the Ilrun gene in bone marrow-derived macrophages from B10.RIII and B10 mice. CONCLUSION: The B10.RIII(71NS)/Sn strain contains three major RIII/WySn-derived regions outside of the congenic MHC region. The chromosome 17 cluster appears to play a role in susceptibility to IL-23 minicircle-induced arthritis. In vitro studies with bone marrow-derived macrophages failed to show functional differences in Ilrun between the B10.RIII and B10 mice. Future studies will interrogate chromosome 17 RIII-derived regions in arthritis development in more detail and investigate the role of Ilrun in immune responses using Ilrun knock-out mice. / 2025-02-28T00:00:00Z

En thérapie génique, la stratégie du leurre moléculaire consiste à utiliser un acide nucléique courtcontenant une séquence spécifiquement reconnue par un facteur de transcription cible, ce qui permetson piégeage intracellulaire et conduit à inhiber l’expression des gènes sous sa dépendance.L’efficacité thérapeutique de cette stratégie est notamment liée à la biostabilité de l’acide nucléique età la possibilité de multicibler des facteurs de transcription qui coopèrent dans des dérégulationscellulaires à l’origine de nombreuses pathologies. Nous avons développé une technologie deproduction in vitro de minicercles d’ADN de moins de 250 paires de base pour interagir avec plusieursprotéines, fonctionnalisables chimiquement et résistants aux exonucléases. Un double ciblage dufacteur de transcription NF-κB par un minicercle permet l’inhibition in cellulo d’un système rapporteurde la transcription NF-κB dépendante, en faveur d’une activité leurre moléculaire du minicercle.Le cisplatine est une molécule anticancéreuse dont la cible pharmacologique est l’ADN. Dansplusieurs lignées cellulaires cancéreuses, la baisse d’activité transcriptionnelle de NF-κB a été reliée àune augmentation de la sensibilité des cellules au cisplatine. Nous avons étudié in cellulo si lemécanisme d’inhibition de NF-κB par le cisplatine pouvait dépendre de la platination de son siteconsensus à l’aide d’une application originale de la stratégie leurre moléculaire. Nous montrons queles adduits du cisplatine contrairement à ceux du transplatine (isomère inactif) diminuent lareconnaissance de NF-κB pour son site consensus in vitro et in cellulo.La stratégie leurre moléculaire de multiciblage avec un minicercle d’ADN sera développée au niveaucellulaire pour faire la preuve de concept de cette approche et démontrer son efficacité biologique. / In gene therapy, decoy strategy consists in using short nucleic acid containing a sequence specificallyrecognized by a transcription factor in order to trap it and in turn to inhibit the expression of genesunder its control. The therapeutic efficacy of this strategy is related to the biostability of the nucleicacid and the possibility to target several transcription factors that cooperate to induce cellderegulations responsible in human diseases. We have developed a technology to product in vitroDNA minicircle less than 250 base pairs which can interact with several proteins, chemicallyfunctionalizable and resistant to exonucleases. A dual targeting of the transcription factor NF-κB by aminicircle allows inhibition in cellulo of a NF-κB-dependent transcription reporter system consistentwith a decoy activity induced by the minicircle.Cisplatin is an anticancer drug whose pharmacological target is DNA. In several cancer cell lines, thedecrease of transcriptional activity of NF-κB has been linked to an increase in the sensitivity of cells tocisplatin. We studied in cellulo whether the mechanism of inhibition of NF-κB by cisplatin could dependon the platination of its consensus sequence using a novel application of the decoy strategy. We showthat cisplatin adducts, unlike those of transplatin (inactive isomer), decreases recognition of NF-κB toits consensus sequence in vitro and in cellulo.Decoy strategy with minicircle DNA will be developed to make the proof of concept of this approach atthe cellular level and further to demonstrate its biological effectiveness.

The RNA polymerase T7 is utilized as a component of motor complexes in DNA nanotechnology due to its high promotor specificity, the lack of external transcription factors and its very high processivity, but there is no experience of its application on small double stranded DNA circles. Circular templates from 210 to 126 bp in circumference sharing a common promotor termination motif were synthesized and transcription was monitored at end point on gel and in real time with a 2’ O methyl RNA molecular beacon. The RNAP T7 was found to be able to utilize circular dsDNA templates down to 126 bp with moderate impact on transcription rate for saturated systems and rolling circle transcription products were evident with denaturizing PAGE gel electrophoresis for templates down to 167 bp.

Backround: Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs may also harbor extra copies of genes or recently activated transposable elements. As eccDNAs occur in all eukaryotes investigated so far and likely play roles in stress, cancer, and aging, they have been prime targets in recent research—with their investigation limited by the scarcity of computational tools. Results: Here, we present the ECCsplorer, a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing techniques. Following Illumina-sequencing of amplified circular DNA (circSeq), the ECCsplorer enables an easy and automated discovery of eccDNA candidates. The data analysis encompasses two major procedures: first, read mapping to the reference genome allows the detection of informative read distributions including high coverage, discordant mapping, and split reads. Second, reference-free comparison of read clusters from amplified eccDNA against control sample data reveals specifically enriched DNA circles. Both software parts can be run separately or jointly, depending on the individual aim or data availability. To illustrate the wide applicability of our approach, we analyzed semi-artificial and published circSeq data from the model organisms Homo sapiens and Arabidopsis thaliana, and generated circSeq reads from the non-model crop plant Beta vulgaris. We clearly identified eccDNA candidates from all datasets, with and without reference genomes. The ECCsplorer pipeline specifically detected mitochondrial mini-circles and retrotransposon activation, showcasing the ECCsplorer’s sensitivity and specificity. Conclusion: The ECCsplorer (available online at https://github.com/crimBubble/ECCsplorer) is a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing data. The derived eccDNA targets are valuable for a wide range of downstream investigations—from analysis of cancer-related eccDNAs over organelle genomics to identification of active transposable elements.

Delivery of siRNAs for the treatment of tumors critically depends on the development of efficient nucleic acid carrier systems. The complexation of dendritic polymers (dendrimers) results in nanoparticles, called dendriplexes, that protect siRNA from degradation and mediate non-specific cellular uptake of siRNA. However, large siRNA doses are required for in vivo use due to accumulation of the nanoparticles in sinks such as the lung, liver, and spleen. This suggests the exploration of targeted nanoparticles for enhancing tumor cell specificity and achieving higher siRNA levels in tumors. In this work, we report on the targeted delivery of a therapeutic siRNA specific for BIRC5/Survivin in vitro and in vivo to tumor cells expressing the surface marker prostate stem cell antigen (PSCA). For this, polyplexes consisting of single-chain antibody fragments specific for PSCA conjugated to siRNA/maltose-modified poly(propylene imine) dendriplexes were used. These polyplexes were endocytosed by PSCA-positive 293TPSCA/ffLuc and PC3PSCA cells and caused knockdown of reporter gene firefly luciferase and Survivin expression, respectively. In a therapeutic study in PC3PSCA xenograft-bearing mice, significant anti-tumor effects were observed upon systemic administration of the targeted polyplexes. This indicates superior anti-tumor efficacy when employing targeted delivery of Survivin-specific siRNA, based on the additive effects of siRNA-mediated Survivin knockdown in combination with scFv-mediated PSCA inhibition. Among non-viral vectors, cationic polymers, such as poly(propylene imine) (PPI), play also a prominent role in plasmid DNA delivery. However, limitations of polycationic polymer-based DNA delivery systems are (i) insufficient target specificity, (ii) unsatisfactory transgene expression, and (iii) undesired transfer of therapeutic DNA into non-target cells. We developed single-chain antibody fragment (scFv)-directed hybrid polyplexes for targeted gene therapy of prostate stem cell antigen (PSCA)-positive tumors. Besides mono-biotinylated PSCA-specific single-chain antibodies (scFv(AM1-P-BAP)) conjugated to neutravidin, the hybrid polyplexes comprise β cyclodextrin-modified PPI as well as biotin/maltose-modified PPI as carriers for minicircle DNAs encoding for Sleeping Beauty transposase and a transposon encoding the gene of interest. The PSCA-specific hybrid polyplexes efficiently delivered a GFP gene in PSCA-positive tumor cells, whereas control hybrid polyplexes showed low gene transfer efficiency. In an experimental gene therapy approach, targeted transposition of a codon-optimized p53 into p53 deficient HCT116p53-/-/PSCA cells demonstrated decreased clonogenic survival when compared to mock controls. Noteworthily, p53 transposition in PTEN-deficient H4PSCA glioma cells caused nearly complete loss of clonogenic survival. These results demonstrate the feasibility of combining tumor-targeting hybrid polyplexes and Sleeping Beauty gene transposition, which, due to the modular design, can be extended to other target genes and tumor entities.