Precision genome editing with tandem autologous transplantation as a therapy for multiple severe immune-mediated diseases

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Autologous haemopoietic stem cell transplantation (ASCT) is emerging as an important therapy for patients with severe immune-meditated diseases (IMDs). Recent studies have shown that it is safe and effective for treating severe IMDs such as multiple sclerosis (MS) and scleroderma. This involves collecting bone marrow derived stem cells from a patient and then eliciting severe but transient immunosuppression using a combination of chemotherapy and therapeutic antibodies. This eradicates a large portion of the immune system including the autoreactive cells. Bone marrow derived stem cells are then reinfused and the immune system is reconstituted afresh with minimal long-term side effects. European Bone Marrow Transplant registry data show that more than 2500 patients have had autologous transplants for IMDs. Only one death has occurred since 2005 following autologous transplantation for MS. ASCT is superior to all other therapies in MS for inducing long-term remissions and it is the only treatment that has been found to reduce disability. In scleroderma, ASCT results in a very marked improvement in survival (86% v 51% at 6 years). Although ASCT can halt disease progression for many patients, 30-50% eventually re-develop their original IMD and 5-10% develop a different IMD. There is therefore significant scope to improve this therapeutic strategy. In recent years there has been a revolution in molecular biology due to programmable nucleases such as CRISPR-Cas9 because they allow us to make precise changes to the sequence of the genome. They are likely to become hugely important therapeutic tools within the next decade. We are using this technology to modify the genome sequence in bone marrow derived stem cells for curing inherited disorders of blood cell production and the immune system. The next step is to use this approach to treat acquired disorders of the immune system such as IMDs. Large-scale genetic analyses have revealed a target gene that is broadly protective across 20 different IMDs including multiple sclerosis (MS), scleroderma, rheumatoid arthritis and Crohn's disease. For these diseases there is around a 10- fold risk reduction; meaning that 9 in 10 patients would not have developed the disease had they had two copies of the protective variant. The protective variant does not result in increased risk for malignancy and does not lead to immunodeficiency. We will develop a strategy that allows us to change the genetic sequence of bone marrow-derived stem cells to mimic the protective genetic variants identified by large-scale genetic studies. These edited cells could then be used to repopulate the immune system with genetically modified cells with a stem cell transplant. This approach would potentially eradicate the harmful immune cells and significantly and permanently reduce the chance of relapse. This is a completely novel approach for treating IMDs and it is potentially applicable to a broad range of different diseases. Through our editing strategy we will change the DNA sequence that defines the structure of the protein, to mimic the naturally occurring protective variants, which attenuate its function. This protein plays a critical role in immune cell activation and it will cleanly and precisely decrease the immune response. The editing strategy will be tested in an IMD mouse model, which mimics the pathology of MS, to determine if the edit protects against IMD development. We will also define what proportion of edited cells required for the protective effect by performing transplants in mice using mixtures of edited and normal cells.