The Role of Gene Editing Within CAR T-Cell Therapy Development - Interview with Professor Waseem Qasim

Trials that involve the use of CRISPR, base editing, and other gene-editing techniques to improve CAR T-cell therapies, including one currently recruiting in the UK, are focusing on paediatric patients with relapsed or refractory B-cell acute lymphoblastic leukemia, with the potential to expand to other indications in the future. Professor Waseem Qasim tells us here about his group’s work within this area and where the field stands as a whole.

- What makes T cells an attractive target for gene-edited therapies?

There’s a longstanding experience with T cells from the bone marrow transplant setting. And you can collect them reasonably easily from peripheral blood, and you can take them to a clean room and do things them — engineer them, manipulate them, characterise them, you can freeze them, and thaw them and give them back, so that makes them attractive.

When we come to gene editing, we now need to do other things including electroporation steps to get, for example, CRISPR reagents into the cells, or the RNPs [ribonucleoproteins] and guides. And they tolerate that reasonably well — I mean, they don’t like it, they get upset, and some will die through that process, but you can recover them, you can expand them, and then you can freeze them back down again.

TALEN-Edited CAR T-cells

- Where does your group stand on the various trials using edited T cells? You started with TALENs [transcription-activator-like effector nucleases] a few years ago, correct?

It’s still very early days. Yes, in London we have done the first TALEN-edited CAR T-cells, and that we reported back in 2015. That had gone remarkably quickly from laboratory development into the clinic; they had only been described a few years before that, TALENs, and the ability to then manipulate them and use them for a useful purpose was fairly rapid.

We did learn quite a lot, and are still learning, from those original trials about what it takes to engineer T cells that are otherwise allogeneic, meaning not matched to a particular recipient, and how difficult it is to actually overcome the barriers we all have to HLA immunity. We did two things to those cells: we removed the T cell receptor, and instead of removing Class 1 or Class 2 MHC, we removed something called CD52, which was the antigen that would otherwise render them susceptible to alemtuzumab, one of the conditioning antibodies.

[With these phase I trials], if things are looking like they’re going to work, we’re expecting companies to pick them up or take them on for development, and that’s exactly what happened with the TALEN version.

[Ed. note: alemtuzumab, a monoclonal antibody used to treat chronic lymphocytic leukemia and some other malignancies, targets B and T lymphocytes expressing CD52, so T cells engineered to lack CD52 would have a survival advantage in the presence of the drug, thus enriching the TCR-free cells' activity.]

From TALENS to CRISPR

- And from there you fairly quickly moved on to CRISPR?

As soon as the TALEN study had opened, we realised that the CRISPR platform was going to be more flexible from an academic point of view, and set off making a CRISPR version of T cells that are edited for those same sites, TCR and CD52. And that’s taken us about three years, and it’s now ready, and we’ve manufactured enough cells to service the Phase I study. The study is open in the UK but it has been held up with the COVID issues obviously, but it is open now and we’ll start recruiting children in the same situation [with relapsed/refractory B-cell acute lymphoblastic leukaemia]. The study is aiming to treat 10 children in a Phase I setting. At the moment we’re only open for children, but we’ll see if that changes.

- What are the challenges or obstacles inherent to using this approach?

Generally, with the use of CAR T-cells, from the beginning, there have been worries about the cytokine storm, the neurotoxicity, so the infrastructure around managing all those side effects has to be in place in the hospital setting. In the UK, the NHS has been quite good to make sure it’s being offered in centers that can offer all of that.

As the experience builds up, it’s becoming more familiar, so the side effects and the profiles are being understood. From the point of view of these versions, the allogeneic versions that we’re trying to make universal, I think we have a good understanding now that the barrier actually is quite high. Overcoming GVHD [graft-versus-host disease] I think has turned out to be more straightforward — you remove the T cell receptor and GVHD risk goes down. Overcoming the host’s ability to reject is more of a challenge.

There’s no free lunch, there’s always something in the formula that needs to be accounted for.

- So even though the gene-editing approach allows CAR T-cell therapy to move away from a “bespoke” treatment tailored to each patient separately and toward an off-the-shelf option, there are still aspects that are very patient-specific?

In reality I don’t think these issues are insurmountable, they will be overcome, because the same issues are there if you have an autologous product — you still need to be given some degree of lymphodepletion, you still have to tolerate the cytokine issues and the neurotoxicity and everything.

And the ability to do it off-the-shelf, I think, could change the dynamic of how we do it and when we do it, whether it’s brought earlier into the hierarchy of treatments, as the experience builds up. We are just at the outset here, it’s very early days, and the numbers need to build up for the experience to be understood across the different patient groups.

Broad Indications for Gene-Edited T Cells

- So far you’ve focused on paediatric patients with B-cell malignancies. What other settings do you anticipate might make it to clinical trials in the near future using gene-edited T cells?

We’ve got patients with unmet need around other forms of blood cancers — myeloid leukaemias in particular. These are very difficult to treat if they don’t respond to the first rounds of treatment, or if they go to transplant and they relapse it’s then very difficult to treat those patients and they almost inevitably end up in palliation, so that’s one group we’re building towards the next round of trials.

And for those, in fact, we’ll move from CRISPR to base editing, because we’re doing multiplex editing and we like using base editing there because the risk of translocations between different edited sites drops off.

And then there are the T cell malignancies themselves where we’re trying to use CAR T-cells to treat T cell cancers. Up until now that has been very difficult because of the issue of fratricide, it’s very hard to make products because they kind of fight each other and consume each other in the culture period. So we can address that with the editing steps.

Those two targets in particular are for us the next goals — AML, and T-ALL in children. We’re in a stage where we’re trying to translate those into a manufacturing phase now, so we’re probably 12 or 18 months away from trying to get trials under way in those particular settings.