Base edited T cell therapy against T-ALL (TvT)

Over the past few years it's become possible to use a patient's own immune cells to fight certain types of blood cancer. Generally, white blood cells called T cells are collected and taken to a special clean room, where they are modified using a disabled virus. This adds extra DNA code that programs he cells to fight leukaemia. We have previously shown that it's possible to use additional steps to allow T cells to be used from donors without any matching. These steps originally used molecular scissors called TALENs, and in 2015 we successfully treated two infants in the UK and then started clinical trials in children and adults, which were recently published. At GOS, we are now using a next version of the strategy after making ready-made CAR T cells using new versions of the scissors called CRISPR to snip two genes in T cells that allow them to used without matching.

In this new application, we want to extend the approach to used donor T cells other blood cancers, including T cell leukaemia. Up to now, this hasn't been possible because T cells armed to fight other T cells have been difficult to grow because they end up fighting each other. In recent experiments we have used genome-editing to remove markings on T cells so they become invisible and are not targeted during the engineering steps. Rather than cutting DNA, we have used an even newer version of CRISPR that changes a single letter (or base) to tell cells to stop showing their markings, also to allow them to be used without matching.

A clinical trial is proposed to treat 10 children from a cross the UK over a two year period, as part of planned bone marrow transplantation (BMT). If T cells can be used to eliminate measurable leukaemia, the chances of it coming back after BMT are very much reduced. Careful tracking of side effects and anti-cancer activity will be provided, especially in the first 4 weeks after treatment, but will continue for a year to make sure the treatment is both safe and effective.

Novel strategies against T-ALL using chimeric antigen receptor (CAR) T cells are problematic because of issues such as fratricide of healthy T cells and the need to reconstitute protective T cell immunity. Suitable antigens for targeting T cell malignancies include CD3, TCR, CD5 and CD7. The latter has recently exhibited promise in trials where T cells were disrupted for CD7 to allow expression of anti-CD7 CAR (CAR7). Strategies for disruption include protein based inhibition of CD7, and genomic disruption using CRISPR/Cas9.
We have developed a next generation base-editing approach which uses CRISPR guided cytidine deamination to create premature stop codons or splice site disruption through highly precise C>T base conversions. The technology has translated remarkably well to a GMP phase, and we are funded by Wellcome Trust (WT) to generate banks of 'universal' healthy donor T cells for Phase 1 trials in paediatric Acute Myeloid Leukaemia. Base-edited (BE) CAR T cells targeting either CD33, CD123 or CD7 are being generated, and the latter could have immediate impact against T-ALL. Our preclinical 'TvT' modelling has found BE-CAR7 cells are highly effective in vitro and in humanised models of T cell leukaemia. BE-CAR7 T cells express CAR7, but are devoid of CD7, endogenous TCRab (thus non-alloreactive) and CD52 (evade serotherapy). The application of base-editing rather than existing Cas9 which causes DNA breaks, has notable advantages in terms of eliminating translocations that otherwise arise during multiplexed genome editing.We propose an accelerated route to therapy for children with r/r T-ALL by drawing on BE-CAR7 cell banks with permission of WT. A TvT Phase 1 trial will aim to secure remission ahead of programmed allo-SCT and will generate important safety data. Children with r/r T-ALL will undergo lymphodepletion and receive a single dose of BE-CAR7 and if remission is secured within 28 days, will proceed to bone marrow transplantation and 12m follow-up.