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Rewiring T Cells To Enhance Immunotherapy Efficacy

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Various chimeric antigen receptor (CAR) T-cell therapies, which are engineered using autologous patient T cells redirected against a specific tumor antigen, have been approved by the US Food and Drug Administration (FDA) as treatment options for blood cancers.

However, for many patients, these therapies do not result in long-lasting disease remission and there has been very limited success applying these therapies beyond blood cancers, for example, to treat solid tumors. Therefore, researchers are looking at ways of improving efficacy by identifying genes and signaling pathways that have the potential to be modified to improve treatment response.

A genetic screening approach has recently been developed that can identify genes capable of enhancing T cells’ ability to eradicate tumor cells. The research, which was led by New York University’s Dr. Neville Sanjana and published in Nature, involved profiling 12,000 different genes in various T cell subsets derived from human donors. The team identified a modifier gene called lymphotoxin beta receptor (LTBR) – which is not normally expressed in T cells – and combined it with CARs to create T cells that were better equipped at killing tumor cells.

Technology Networks had the pleasure of speaking with Sanjana to learn more about how they were able to rewire the T-cell genome using LTBR and how this triggered the expression of several other genes that potentiate the cells’ activity.

Laura Lansdowne (LL): Why do a large majority of cancer patients receiving CAR T-cell therapy fail to achieve lasting remission?

Neville Sanjana (NS): There are a few different modes of failure. Sometimes the tumor cells lose expression of the antigen (e.g., CD19 in B-cell lymphomas). But in other instances, the engineered T cells simply do not persist long-term in the patient post-treatment. A recent study found that in patients with long-lasting remission – more than a decade – the engineered T cells were found circulating even 10 years later. Our goal is to understand whether we can program T cells in specific ways to make them more persistent and keep up their surveillance long term.

LL: What approaches are typically used to engineer T cells, how does your team’s method differ and what potential benefits does it offer?

NS: The major focus with engineering T cells is adding in receptors either CARs or T-cell receptors to enable them to target tumor-specific antigens. This is what is used in current FDA-approved cell therapies for blood cancers. Our lab looked at 12,000 different human genes to see whether certain genes, when delivered together with the targeting receptors, could enhance the T cells in different ways. For example, to make them more persistent, more cytotoxic for tumor cells and better at secreting special molecules called cytokines that can activate other immune cells.

LL: Could you tell us more about the significance of the modifier gene LTBR?

NS: Sure! LTBR deeply reprograms T cells. When it is expressed, it potentiates many different aspects of T-cell function. For example, it makes T cells much more proliferative and also activates stem-cell-like factors that give the T cells a younger phenotype, prolonging their life and self-renewal capacities. They also become more resilient with LTBR. Normally, if T cells are stimulated by a cancer antigen repeatedly, they get tired. We see this tiredness in many different ways, such as by expressing genes that inhibit immune activation and encode programmed cell death protein 1 (PD-1) or cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), and by reducing their release of immune-activating cytokines like interferon-gamma or interleukin-2. With LTBR, the T cells become more resilient in the face of repeated antigen exposure, keeping high expression of key cytokines and expressing less of the inhibitory receptors.

To be honest, LTBR was a surprising discovery for us. It is a human gene, but it is normally never expressed in T cells. This highlights the beauty of our genome-scale screening approach. It would’ve been impossible to discover this kind of T-cell modifier without casting a wide net through our screen.

LL: By adding LTBR it was possible to rewire the T-cell genome, triggering the expression of many other genes that potentiate the cells’ function. Could you tell us more about these “other” genes were there any in particular that stood out?

NS: By expressing LTBR, we find hundreds of genes with altered expression. Some highly expressed genes are clearly playing roles in extending the life of T cells like TRAF1 and BIRC3, which block the programmed cell death pathway, and transcription factors like JUN and transcription factor T cell factor 1 (TCF1) that promote a youthful phenotype by enhancing self-renewal and secretion of cytokines that make T cells divide. We also see an upregulation of genes that are typically associated with so-called professional antigen-presenting cells. Certain subsets of T cells are very sensitive to antigens presented in this way and thus LTBR-engineered T cells are likely facilitating interactions with each other that encourages a more robust response.

One underappreciated aspect of the immune system is how much of what it does is communication between different cell types. LTBR makes T cells better at passing messages to each other and, by facilitating this improved communication, we get a more coordinated response and attack on tumor cells.

LL: Can you comment more broadly on the potential impact new gene editing and functional genomic technologies may have on anticancer immunotherapeutic strategies?

NS: We have certainly entered the age of genome engineering. The programmability of tools like CRISPR – and more broadly DNA synthesis methods – has made it possible to create and screen large libraries of genetic perturbations. In this way, we can quickly understand the impact of thousands of genetic perturbations on any biological phenotype. This is an incredibly powerful approach and one that my lab has capitalized on over the past few years to understand cancer drivers, find therapies for COVID-19, identify essential human genes and engineer new immunotherapies.

In particular, I am very excited by work at the intersection of functional genomics and synthetic biology. That is, can we find all genes that, like LTBR, improve desirable properties of gene or cell therapies? And, once we find these genes, can we use them as a chassis upon which to precisely engineer new and improved versions. This is an exciting challenge for future anticancer immunotherapies.

More broadly, I think these scalable methods will allow us to predict the impact of virtually any human mutation – germline or somatic – on any tissue or cell type. A key challenge will be translating these kinds of insights into precision medicine.

Reference: Legut M, Gajic Z, Guarino M, et al. A genome-scale screen for synthetic drivers of T cell proliferation. Nature. 2022;603:728–735. doi: 10.1038/s41586-022-04494-7

Dr. Neville Sanjana was speaking with Laura Elizabeth Lansdowne, Managing Editor for Technology Networks.