Glycogen storage disease III (GSD III) is a rare (1:100,000) autosomal recessive disorder that results from the deficiency of the glycogen debranching enzyme (GDE). The major cause of morbidity is associated with the muscle accumulation of glycogen, which leads to progressive myopathy. A dietary treatment with frequent meals high in carbohydrates, slows the progression of the pathology that is however inevitable. There is no cure for GSD III, the recent development of a mouse model lacking GDE activity, which recapitulates the human condition, represents a unique opportunity to develop and test novel therapies for the disease. Here, we propose to perform a proof-of-concept study of an adeno-associated virus (AAV) vector-mediated gene therapy for the treatment of GSD III. AAV gene therapy has been successfully used for the correction of several genetic diseases in animal models and humans. One of the main limitations of AAV vectors is that they cannot package vector genomes significantly larger than 5kb. Due to the length of the sequence of the GDE enzyme (4596 bp), we engineered a dual-vector system with a recombinogenic sequence to drive reconstitution of the full-length GDE sequence. In alternative to this strategy, we engineered also a truncated GDE that can fit in a single AAV. Because GSD III is both a liver and muscle diseases, and because the liver is involved in glycogen metabolism and, ultimately, in the supply of glucose to the muscle, we will test two main therapeutic strategies to treat GSD III, consisting of constitutive or liver-specific expression of the transgene. The rescue of the GDE enzyme deficiency will be carried out in vivo in a GDE KO mouse, and in vitro in human iPS cells-derived hepatocytes and myocites. We will generate fibroblast-derived iPS cells from GSD III patients and the pluripotent cells will be successively differentiated in hepatocytes and myocites.

Severe combined immunodeficiency (SCID) is a devastating rare disorder of immune system development. Affected infants are born without functional immune systems and die within the first year of life unless effective treatment is given. Treatment options are limited to allogeneic haematopoietic stem cell transplantation and autologous stem cell gene therapy. Over the last 15 years, gene therapy for two forms of SCID (SCID-X1 and ADA SCID) has shown significant safety and efficacy in correcting the immunodeficiency and allowing children to live normal lives. Proof of concept of gene therapy for 3 other SCID forms has also been shown by members of the proposed SCIDNET consortium and is ready for translation into clinical trials. We are therefore in a position whereby, over the next 4 years, we can offer gene therapy as a curative option for over 80% of all forms of SCID in Europe. Importantly for 1 of these conditions (ADA SCID) we will undertake clinical trials that will lead to marketing authorisation of the gene therapy product as a licensed medicine. In addition, we will investigate the future technologies that will improve the safety and efficacy of gene therapy for SCID. Our proposal addresses an unmet clinical need in SCID, which is classified as a rare disease according to EU criteria (EC regulation No. 141/2000). The proposal also addresses the need to develop an innovative treatment such as gene therapy from early clinical trials though to a licensed medicinal product through involvement with regulatory agencies and is in keeping with the ambitions of the IRDiRC. The lead ADA SCID programme has Orphan Drug Designation and clinical trial design is assisted by engagement with the European medicines Agency. The ADA SCID trial will act as a paradigm for the development of the technologies and processes that will allow gene therapy for not only SCID, but also other bone marrow disorders, to become authorised genetic medicines in the future.

Duchenne muscular dystrophy is an X-linked recessive muscle-wasting disease, characterized by progressive weakening of skeletal, respiratory, and cardiac muscle followed by necrosis and fibrosis. DMD affects ~1:3,500 live male births and is associated with delayed motor milestones. DMD occurs as a result of mutations within the DMD gene that lead to premature termination of translation. The most frequent type of mutations are exonic deletions and duplications that induce a frame-shift in the protein-coding sequence. To date no effective treatment exist for this disorder. Duplications account for ~5–10% of all reported mutations in DMD in the Leiden database, although the incidence may be higher. Despite the limited number in DMD, duplications are widespread in almost all diseases and are generally neglected by therapeutic approaches. New molecular tools, now represented by genome-editing technologies that use synthetic nucleases in order to introduce targeted alterations at specific sites in the genome, hold great promises for revolutionizing the gene therapy arena. According to these premises, we propose a novel strategy based on the CRISPR/Cas9 system to repair tandem duplications by removing the mutation: compared to the exon deletions approach which uses two gRNA targeting two unique regions defining the sequence to be deleted, our approach will employ only one gRNA against a unique intronic sequence within the tandem duplication. This strategy will exploit the characteristic of tandem duplication (two identical contiguous sequences) and will result in the deletion or inversion of the mutation restoring the dystrophin expression. As a model we chose the exon 2 duplication which is the most frequent one in the DMD gene, but the same approach would be applicable to all tandem duplications. This study will pave the way for the development of therapies against duplications also in pathologies in which the exon skipping approach is not feasible.

Liver-directed gene therapy has undergone significant development in the last two decades. Recombinant adeno-associated vectors (AAV) are the vectors of choice for liver gene transfer and have recently achieved remarkable successes in clinical trials. However, there are still large groups of patients who have limited access to therapy. The major hurdles toward expanding the indication of AAV-mediated liver gene therapy are: i) transient AAV-mediated expression in proliferating hepatocytes, i.e. newborn or regenerating livers, due to dilution of episomal AAV genome in proliferating cells; ii) dose-dependent hepatotoxicity and immune response against AAVs; and iii) pre-existing immunity to AAV capsids, which currently preclude its systemic delivery in about 50% of individuals. AAVolution gathers renowned European experts in the field of AAV vectorology, gene therapy, genome editing and immunology, with the ambitious goal to develop and implement innovative therapeutic tools to effectively address these challenges. To this aim AAVolution proposes: i) to seek novel small Cas nucleases for in vivo AAV-mediated genome editing ii)to develop self-replicating episomal AAVs to avoid transgene dilution in proliferating livers; iii) to generate synthetic AAVs characterized by enhanced potency and reduced toxicity, by screening of novel AAV capsid libraries; iv) and to develop improved technologies to overcome pre-existing immunity to AAVs by transiently reducing the levels of circulating anti-AAV neutralizing antibodies. AAVolution will significantly expand the toolkit for AAV-mediated liver gene therapy, developing novel and improved molecular instruments to address the most relevant hurdles toward safer and more effective therapies, and provide access to treatment to patients that are currently excluded from clinical trials. Moreover, these novel tools will constitute an innovative platform with a potential for broad expansion of disease indications beyond the rare diseases.