Mutations in the DMD gene are causative for Duchenne muscular dystrophy (DMD). Antisense oligonucleotide (AON) mediated exon skipping to restore disrupted dystrophin reading frame is a therapeutic... Show moreMutations in the DMD gene are causative for Duchenne muscular dystrophy (DMD). Antisense oligonucleotide (AON) mediated exon skipping to restore disrupted dystrophin reading frame is a therapeutic approach that allows production of a shorter but functional protein. As DMD causing mutations can affect most of the 79 exons encoding dystrophin, a wide variety of AONs are needed to treat the patient population. Design of AONs is largely guided by trial-and-error, and it is yet unclear what defines the skippability of an exon. Here, we use a library of phosphorodiamidate morpholino oligomer (PMOs) AONs of similar physical properties to test the skippability of a large number of DMD exons. The DMD transcript is non-sequentially spliced, meaning that certain introns are retained longer in the transcript than downstream introns. We tested whether the relative intron retention time has a significant effect on AON efficiency, and found that targeting an out-of-frame exon flanked at its 5'-end by an intron that is retained in the transcript longer ('slow' intron) leads to overall higher exon skipping efficiency than when the 5'-end flanking intron is 'fast'. Regardless of splicing speed of flanking introns, we find that positioning an AON closer to the 5'-end of the target exon leads to higher exon skipping efficiency opposed to targeting an exons 3'-end. The data enclosed herein can be of use to guide future target selection and preferential AON binding sites for both DMD and other disease amenable by exon skipping therapies. Show less
Kuijper, E.C.; Overzier, M.; Suidgeest, E.; Dzyubachyk, O.; Maguin, C.; Pérot, J.B.; ... ; Roon-Mom, W. van 2023
In Huntington disease, cellular toxicity is particularly caused by toxic protein fragments generated from the mutant huntingtin (HTT) protein. By modifying the HTT protein, we aim to reduce... Show moreIn Huntington disease, cellular toxicity is particularly caused by toxic protein fragments generated from the mutant huntingtin (HTT) protein. By modifying the HTT protein, we aim to reduce proteolytic cleavage and ameliorate the consequences of mutant HTT without lowering total HTT levels. To that end, we use an antisense oligonucleotide (AON) that targets HTT pre-mRNA and induces partial skipping of exon 12, which contains the critical caspase-6 cleavage site. Here, we show that AON-treatment can partially restore the phenotype of YAC128 mice, a mouse model expressing the full-length human HTT gene including 128 CAG-repeats. Wild-type and YAC128 mice were treated intracerebroventricularly with AON12.1, scrambled AON or vehicle starting at 6 months of age and followed up to 12 months of age, when MRI was performed and mice were sacrificed. AON12.1 treatment induced around 40% exon skip and protein modification. The phenotype on body weight and activity, but not rotarod, was restored by AON treatment. Genes differentially expressed in YAC128 striatum changed toward wild-type levels and striatal volume was preserved upon AON12.1 treatment. However, scrambled AON also showed a restorative effect on gene expression and appeared to generally increase brain volume. Show less
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive skeletal muscle disorder that mainly affects the muscles of the face, shoulders and upper arms. Skeletal muscle wasting in FSHD is... Show moreFacioscapulohumeral muscular dystrophy (FSHD) is a progressive skeletal muscle disorder that mainly affects the muscles of the face, shoulders and upper arms. Skeletal muscle wasting in FSHD is caused by the failure to epigenetically repress the transcription factor DUX4 that is typically expressed during early development. DUX4 expression in skeletal muscle induces several myotoxic cascades that ultimately lead to the death of skeletal muscles cells. At the moment there is no molecular therapy that can delay or stop disease progression. The work described in this thesis mainly aims to gain more insight in the different FSHD mouse models and the in vivo testing of new therapies in FSHD mice. We describe the generation of one new mouse model and the characterization of two other FSHD mouse models. In addition, we tested a RNA therapy that blocks the DUX4 transcript in vivo. We show that this therapy could reduce DUX4 and DUX4 target genes in FSHD mice. In addition, the therapy alleviated the severity of skeletal muscle pathology. With the data described in this thesis we hope to accelerate the development and testing of new therapies for a disease that cannot be treated until this day. Show less
The aim of this thesis was to work towards pre-clinical proof-of-concept for NOTCH3 cysteine corrective exon skipping as a rational therapeutic approach for CADASIL. To address all aspects required... Show moreThe aim of this thesis was to work towards pre-clinical proof-of-concept for NOTCH3 cysteine corrective exon skipping as a rational therapeutic approach for CADASIL. To address all aspects required for therapeutic development, the work performed for this thesis included not only in vitro testing of NOTCH3 exon skipping in CADASIL patient derived vascular smooth muscle cells and studies into the function of the cysteine corrected proteins, but also the generation of a relevant humanized in vivo model, pre-clinical biomarker development, and studies defining prevalence, spectrum and characteristics of NOTCH3 mutations worldwide. Show less
Rheumatoid arthritis (RA) is a chronic inflammatory joint disease leading to destruction of cartilage and bone. The inflammation in the joints is mainly caused by inflammatory cytokines that are... Show moreRheumatoid arthritis (RA) is a chronic inflammatory joint disease leading to destruction of cartilage and bone. The inflammation in the joints is mainly caused by inflammatory cytokines that are over-produced by various types of immune cells. Artritis is an autoimmune disease that is characterized by the presence of autoantibodies. These autoantibodies form immune complexes (IC) which are other important players in joint inflammation because they activate various immune cells by binding to Fc receptors (FcR). Binding and activation of FcRs initiates intracellular signaling that triggers activation and release of various inflammatory mediators. In this thesis we describe a variety of aspects of arthritis research that has been performed to get a better understanding of the underlying molecular and cellular disease mechanisms and to develop novel therapeutic strategies. Show less
This thesis starts with a broad introduction of Duchenne muscular dystrophy (DMD) and several therapies targeting the primary underlying genetic cause or the secondary effects caused by the disease... Show moreThis thesis starts with a broad introduction of Duchenne muscular dystrophy (DMD) and several therapies targeting the primary underlying genetic cause or the secondary effects caused by the disease. DMD is caused by a genetic defect in the DMD gene encoding the dystrophin protein, which plays an important function inside muscle cells. A more detailed analysis of 2__-O-methyl phosphorothioate antisense oligonucleotide ( 2OmePS AON)-mediated exon skipping in mouse models for DMD is given. This therapy aims to correct the genetic defect at RNA level and turn the disease in a milder form. Furthermore it describes several strategies to increase the therapeutic effects of AONs by combining it with another drug. First a compound that could potentially enhance the working of the AONs itself. Secondly, two compounds that might improve the muscle quality (thereby providing more targets for the AONs) by targeting secondary effects. The results of these experiments are described and put in a broader context Show less
Nonsense mutations in the gene encoding dystrophin cause Duchenne muscular dystrophy (DMD), a lethal and debilitating neuromuscular disorder. Dystrophin is an important muscle structural protein... Show moreNonsense mutations in the gene encoding dystrophin cause Duchenne muscular dystrophy (DMD), a lethal and debilitating neuromuscular disorder. Dystrophin is an important muscle structural protein that protects muscle membrane from contraction-induced damage. Therefore, in the absence of dystrophin, the integrity of muscle fibers will be compromised and severe degeneration will take place. When the regeneration process mediated by satellite cells can no longer compensate, muscle fibers is eventually replaced by connective or fibrotic tissue, leading to the loss of muscle function. Multiple stages in DMD pathology are associated with the Transforming Growth Factor (TGF)-_ signaling pathway (Chapter 1). The TGF-_ superfamily consists of more than 30 secreted proteins including TGF-_, bone morphogenetic protein (BMP), activin/inhibins and growth and differentiation factor (GDF). These proteins regulate many biological processes, such as cell growth and differentiation, and maintain homeostasis during development and in multiple adult tissues. To elicit these diverse physiological responses, a fairly simple and yet powerful signaling pathway is utilized by the TGF-_ family members. The basic signaling engine consists of two receptor serine/threonine kinases, termed receptor types I and II, and intracellular Smad proteins. The ligand assembles a receptor complex that activates Smad proteins, which will assemble multisubunit complexes that regulate transcription. Two general steps thus actually suffice to carry the TGF-_ stimuli to target genes. How can such a simple system mediate a variety of cell-specific gene response? It is now apparent that TGF-_ signaling pathways have equally important extracellular and intracellular control mechanism. This includes myostatin (GDF-8), one of the members that is highly expressed in skeletal muscle. In addition to being a negative regulator of myoblast differentiation, myostatin also plays role in adipogenesis, skeletal muscle fibrosis and myometrial cell proliferation. Genetic mutation of myostatin leads to a remarkable increase of muscle mass, but, as myostatin is found in the circulation, effects on other tissues are somehow expected. We hypothesized that such remarkable effects of myostatin in the muscle are controlled by a unique modulatory mechanism. Indeed, we found that myostatin signaling in myogenic and non myogenic cells are conferred by different utilization of type I receptors, which are also termed activin receptor-like kinases (ALKs), and co-receptor (Chapter 2). In myogenic cells, myostatin signaling is dependent on activin receptor-like kinase-4 (ALK4), whereas ALK5 is utilized in non myogenic cells. Furthermore, we found that the ALK4-dependent myostatin signaling in muscle is largely conferred by a membrane-associated co-receptor Cripto, which is predominantly expressed in myogenic cells but absent in non muscle cells. Moreover, Cripto has different influences on TGF-_ family members that play a role in muscle, i.e. myostatin, activin and TGF-_. As such, Cripto may also be an interesting therapeutic target to follow up in the future. As DMD is caused by the lack of dystrophin, one strategy is to bring back dystrophin in the dystrophic muscle. Antisense oligonucleotide (AON)-mediated exon skipping has been used to reframe the mutated DMD gene and restore dystrophin protein synthesis. It will, however, be less effective in the later stage of the disease where fibrosis is already extensive. This thesis explores the possibility of using exon skipping AONs to inhibit several components of the TGF-_ family signaling and blunt their inhibitory effects on muscle regeneration and fibrosis. In Chapter 3, we first used AONs to functionally knockdown myostatin expression. They efficiently downregulate myostatin in vitro, but induce only subtle exon skipping in vivo. Nevertheless, in a relatively straightforward manner, we were able to combine myostatin and dystrophin AONs and induce exon skipping of both genes without functional interference. This provides a conceptual foundation for a combinatorial therapeutic approach, which targets the primary genetic defect and attempts to improve muscle quality. We further sought to use AON to functionally knockdown myostatin and/or TGF-_ receptors ALK4 and/or ALK5 (Chapter 4). This strategy allowed us to target the activity of a broader spectrum of TGF-_ members, including but not limited to myostatin. Administration in dystrophic mice reduces fibrosis in the diaphragm, which is known to be the most affected muscle. Interestingly, combination of both ALK4 and ALK5 inhibition induces most pronounced effects. The beneficial response after targeting ALK4 or ALK5 separately demonstrates the involvement of TGF-_ and activin in DMD pathology. Overall, in addition to its therapeutic potential, the AON-mediated exon skipping approach also enables the dissection of the roles of TGF-_ family members in muscle regeneration and fibrosis, and potentially other aspects of DMD pathology. In summary, this thesis discusses how the inhibition of several members of the TGF-_ signaling pathway has been implicated in ameliorating DMD pathology. Furthermore, it also increases the awareness that more knowledge on how these family members actually play role in (dystrophic) muscle may still be needed. Finally, alteration of TGF-_ signaling components is involved in various diseases with multilayered pathophysiology, including but not limited to other neuromuscular disorders. Thus, the use of AONs has potential therapeutic value for other TGF-_-related disorders and is also important research tools to study the effect of modulation of TGF-_ receptor family members in the different facets of these diseases. Show less
Duchenne muscular dystrophy (DMD) is a severe, lethal neuromuscular disorder caused by reading frame disrupting mutations (mostly deletions) in the dystrophin gene. This results in the complete... Show moreDuchenne muscular dystrophy (DMD) is a severe, lethal neuromuscular disorder caused by reading frame disrupting mutations (mostly deletions) in the dystrophin gene. This results in the complete absence of dystrophin and leads to the continuous loss of muscle fibers and fibrosis. As a consequence, DMD patients are wheelchair dependent before the age of 12 and often die in the third decade of the life (or earlier) due to respiratory- or heart failure. Deletions in the dystrophin gene that keep the reading frame intact allow the generation of internally deleted, partly functional dystrophins and are associated with the milder Becker muscular dystrophy (BMD). Becker patients often remain ambulant until later in life and have near normal life expectancies. Normal dystrophin consists of an N-terminal actin-binding domain, a central rod domain (containing 24 spectrin-like repeat units and 4 hinge regions) a cysteine-rich and a C-terminal domain. Dystrophin is thought to fulfill a bridge function between the cytoskeleton and the extracellular matrix, since the actin binding domain binds to cytoskeletal actin, while the C-terminal domain is involved with the transmembranal dystrophin glycoprotein complex (DGC) that is connected to the extracellular matrix via laminin 2. In DMD patients this bridge function is completely lost, since the C-terminal bridgehead is lacking due to a truncating mutation. In BMD patients on the other hand, an internal deletion results in a shorter, but still semi-functional bridge that contains both the N-terminal and C-terminal bridgeheads. As yet there is no clinically applicable therapy for DMD patients, despite extensive research for a variety of different approaches. Currently, one of the most promising strategies is the antisense-mediated reading frame restoration. The aim of this approach is to induce specific exon skipping to convert an out of frame DMD transcript into its nearest in frame BMD-like counterpart. This would allow the generation of an internally deleted but partly functional dystrophin and should convert DMD into a milder BMD phenotype. The skipping of a specific exon can be induced by antisense oligoribonucleotides (AONs), which are small synthetic RNAs. Upon binding of the AONs to the pre-mRNA the splicing machinery does not recognize the exon as such anymore, and as a result the targeted exon is spliced out with its flanking introns (i.e. the exon is "skipped"). The broad mutation spectrum found for DMD would require the skipping of a series of exons to restore the reading frame for several patients. Fortunately, designing efficient DMD specific AONs has proven relatively easy, and we can currently induce the specific skipping of 20 different exons in human control myotube cultures after PEI-mediated AON delivery (Chapter 2). This would restore the reading frame for over 40% of all DMD patients. The broad therapeutic applicability of this technique was confirmed in myotube cultures derived from 8 different patients (Chapter 3). For each patient skipping of the specific exons could be induced on RNA level and dystrophin synthesis was restored in over 75% of treated myotubes. Time course experiments revealed that dystrophin was detectable as early as 16 hours post transfection and increasing levels were found for up to 7 days. In addition, expression of DGC proteins was restored in treated myotube cultures, further confirming the functionality of the BMD-like dystrophins. Since a significant part of DMD patients carries a mutation that requires the skipping of two exons, we also tested the feasibility of double-exon skipping in two patients (Chapter 4). After treatment with a mix of the respective AONs, double exon skipping was detected on RNA level and dystrophin synthesis was restored for over 70% of treated myotube cultures for both patients. Furthermore, when we treated control myotubes with AONs targeting exons 45 and 51 we observed multi-exon skipping of exon 45 through 51. Multi-exon skipping not only increases the applicability of this technique, it also reduces the mutation specificity, since it allows for the generation of a BMD-like deletion that covers the majority of DMD mutations. The skipping of exon 45 through 51 would already be applicable to 15% of all patients and its feasibility was confirmed in myotubes derived from a patient carrying an exon 48-50 deletion. Subsequent experiments aiming at the skipping of a larger number of exons seem to indicate that the number of exons that can be skipped is limited due to hitherto unknown processes. Thus far we have used AONs containing 2'-O-methyl RNA with a full-length phosphorothioate backbone (2OMePS), which are cytotoxic at high concentrations. For future clinical applications the optimal AON induces high levels of specific exon skipping at low levels of cytotoxicity. We thus compared the efficacy and efficiency of our most efficient exon 46 2OMePS AON to those of a morpholino, a locked nucleic acid (LNA) and a peptide nucleic acid (PNA) AON (Chapter 5). Only the LNA induced higher levels of exon skipping than 2OMePS in patient and control myotube cultures. However, when we compared the sequence specificity of these analogues we observed that LNAs appear to be much less sequence specific than 2OMePS AON. Therefore, we conclude that 2OMePS currently seem the favorable compounds to establish clinical trials. To study exon skipping in vivo we injected PEI-coupled 2OMePS AONs specific for murine exon 46 into the gastrocnemius muscle of normal mice (Chapter 6). Relatively low levels of exon 46 skipping could be detected on RNA level and persisted for over four weeks post injection. Furthermore, we have previously engineered a mouse model that contains the entire human DMD gene (2.6 Mb) integrated into the murine genome (hDMD mouse). These transgenic mice uniquely allow for the preclinical testing of human-specific AONs in vivo. We have injected AONs targeting human exons 44, 46 and 49 into the musculus. gastrocnemicus of hDMD mice, and showed that the skipping of the human exons (but not the murine exons) was indeed specifically induced. Based on pre-clinical data obtained by our group and others, we are currently setting up a clinical trial aiming at local dystrophin restoration following intramuscular injections of exon 46 and 51 specific AONs. For future application, however, we aim at systemic delivery of AONs. Therefore, we are currently investigating delivery methods that will allow systemic delivery of AONs. Show less
