CRISPR-engineered T cells treat patients with refractory cancer

Date: 13th February 2020

The gene-editing field is waiting with hope as the first wave of CRISPR-trials start to release patient data. Now the latest results from patients receiving CRISPR-edited T cells are emerging in the plight to fight resistant cancers.

In September last year we saw an attempt to use CRISPR genome-edited donor cells to treat a HIV patient with blood cancer for the first time. The gene edits were made to the CCR5 gene, which encodes the major HIV co-receptor that allows viral entry into the host cells, however, the results of the study were mixed.

On the positive side: successful transplantation and long-term engraftment of CRISPR-edited haematopoietic and progenitor stem cell (HSPCs) was seen and the CRISPR-edited cells persisted in the patient’s blood for the duration of a 19 month period. Furthermore, no off-target effects were observed. However, the efficiency of editing events was low, and the treatment ultimately failed to reduce HIV levels.

Then in November, came the release of patient data following clinical trials from CRISPR Therapeutics and Vertex Pharmaceuticals. Similarly, this trial used CRISPR-edited HSPCs, this time for the treatment of transfusion-dependent β thalassemia (TDT), and sickle cell disease (SCD). In this case the cells were engineered to produce high levels of foetal haemoglobin (HbF) in red blood cells.

The emerging feeling from this data was a little more encouraging and both patients showed engraftment of cells, and their symptoms were alleviated such that one was transfusion independent (TDT) and the other was vaso-occlusive crises free (SCD).

Now scientists from the University of Pennsylvania and Stanford University School of Medicine, have reported a first-in-human phase I clinical trial to test the safety and feasibility of multiplex CRISPR-Cas9 editing to engineer T cells in three patients with refractory (unresponsive) cancer.

• T cells were transduced with a lentiviral vector to express a synthetic, cancer-specific T cell receptor (TCR) transgene which recognised the immunogenic NY-ESO-1 tumour antigen.
• Mispairing of the therapeutic TCR alpha and beta chains with endogenous alpha and beta chains on the T cells has previously been shown to reduce therapeutic TCR cell surface expression and potentially generate self-reactive TCRs – the team therefore used CRISPR-cas9 to delete the endogenous alpha and beta TCR domain genes TRACand TRBC in theNY-ESO-1 TCR-expressing engineered T cells.
• Previous work has demonstrated that a PD-1 (Programmed cell death) protein on T cells plays a negative regulatory role in antigen responses and leads to T cell exhaustion – to avoid this the team also removed of a third gene encoding PD-1 (PDCD1).
• 3 patients with advanced, refractory cancer were given infusions of the CRISPR-Cas9 engineered T cells – this was a mixed population in which the cells contained different number and combinations of edits.
• The treatment was not toxic and was tolerated well by all the patients.
• There was a high-level of engraftment and long-term persistence of the infused CRISPR-Cas9 engineered T cells up to 9 months.
• Engraftment efficiencies varied - sustained persistence of TRAC and PDCD1 edits were seen at around 5-10% in the circulating blood, but TRBC edited cells were only detected at low levels and transiently.
• Whilst most mutations were determined to be on target, there were off-target mutations also identified.
• The frequency of gene-edited cells was quite stable between day 10 and 4 months post-infusion. Furthermore, approximately 40% of the peripheral blood circulating T cells in one of the patients at 4 months after infusion were mutated at any one of the targeted genes sites.
• The clinical observations showed mixed results - The best clinical responses were stable disease in two patients i.e. the tumours didn’t progress or regress. The other showed ~50% decrease in a large abdominal mass that was sustained for four months however, other lesions did progress.
• However, as of December 2019, all patients had progressed: two were receiving other therapies whilst the third died from progressive myeloma.

Conclusion and future directions

This is the first trial of its type – a phase I human pilot study that has used multiplexed CRISPR-Cas9 gene editing and with it the team has opened the door of possibility. With 20% of the TCR transgenic T cells in circulation 4 months post infusion persisting to contain di-genic and tri-genic edits this type of therapy could provide advantages over current chimeric antigen receptor (CAR) T cell therapy. It also provides a lower baseline toxicity profile, high-level of engraftment and long-term persistence of the infused CRISPR-Cas9 engineered T cells.

From a safety perspective, there is still a way to go before this multiplexed approach will be ready for widespread use, and the presence of off-targets edits still remains a challenge, even if they occur at a low level. However, with the return of first patient data from several CRISPR-trials we are starting to build a picture of the potential CRISPRs have to offer. CRISPR-edited cells (HSPCs and T cells) appear to engraft well, are able to persist long-term, and show low adverse effects. Their success in treating disease is still a question, and results remain mixed however, it should be said that in this study the patients enrolled on the trial were resistant to other treatments.

With the recent discovery of a new type of T-cells with a T-cell receptor which recognises and kills most human cancer types, the question arises as to whether this ‘universal’ cure for cancer could be further enhanced by similar CRISPR-edits.

For more information please see the press release from Stanford Medicine

Stadtmauer, E. A., J. A. Fraietta, M. M. Davis, A. D. Cohen, K. L. Weber, E. Lancaster, P. A. Mangan, I. Kulikovskaya, M. Gupta, F. Chen, L. Tian, V. E. Gonzalez, J. Xu, I.-y. Jung, J. J. Melenhorst, G. Plesa, J. Shea, T. Matlawski, A. Cervini, A. L. Gaymon, S. Desjardins, A. Lamontagne, J. Salas-Mckee, A. Fesnak, D. L. Siegel, B. L. Levine, J. K. Jadlowsky, R. M. Young, A. Chew, W.-T. Hwang, E. O. Hexner, B. M. Carreno, C. L. Nobles, F. D. Bushman, K. R. Parker, Y. Qi, A. T. Satpathy, H. Y. Chang, Y. Zhao, S. F. Lacey and C. H. June (2020). “CRISPR-engineered T cells in patients with refractory cancer.” Science: eaba7365.

https://doi.org/10.1126/science.aba7365