Defect drives primary resistance to CAR-T cell therapy

Cancer cells have inherent properties that can cause primary resistance to CAR‑T cell therapy, according to US researchers.

Researchers at the Abramson Cancer Center of the University of Pennsylvania say they are the first to show that natural cancer features can influence response to CAR‑T cells, and that cancer cells can drive the development of CAR‑T cell dysfunction.

Co-senior author Dr Marco Ruella from the Perelman School of Medicine at the University of Pennsylvania, said: “Most theories have centred around a defect in the T cells, but what we've shown here is that the problem originates in an important death signalling pathway in the cancer cell itself, which prevents the T cell from doing its job.”

Writing in Cancer Discovery, the research team describe how they performed a genome-wide CRISPR/Cas9-based screen in an acute lymphoblastic leukaemia (ALL) cell line known as Nalm6 to identify pathways associated with CAR‑T cell resistance.

Cells were edited for loss of function of single genes and combined with CAR-T cells for 24 hours to identify the pathway driving the primary resistance.

They discovered that in ALL cells resisting CAR-T attack, there was depletion of genes involved in activating the cell death pathway, FADD, BID, CASP8 and TNFRSF10B, and enrichment of genes required for resisting the cell death pathway, CFLAR, TRAF2 and BIRC2.

The effect was even more significant when it was tested in animal models, which led them to study the effect of the cancer on the T cells trying to kill it. It was at this point they found that prolonged survival of cancer cells led to T cell dysfunction.

They then explored the clinical relevance of these findings using paediatric patient samples from previous CAR-T trials. They discovered that the previously identified signalling pathways in cancer cells were directly associated with responses to CAR-T therapy in the patients from two clinical trials. This suggested that death receptor signalling is a key regulator of primary resistance to CAR-T cell therapy in ALL.

Co-first author Dr Nathan Singh, who led the work while he was a post-doctoral researcher at the Center for Cellular Immunotherapies, said: “We now know that resistance occurs in two phases: the cancer cells’ initial resistance to death, followed by the cancer’s ability to impair T cell function. Together, this leads to CAR-T cell failure that allows the disease to progress.”

Researchers say these findings suggest the use of healthy donor T cells for CAR-T manufacturing may face the same barriers as cells used from the patient.

Source: Singh N, Lee YG, Shestova O, Ravikumar P, Hayer KE, Hong SJ, Lu XM, Pajarillo R, Agarwal S, Kuramitsu S, Orlando EJ, Mueller KT, Good CR, Berger SL, Shalem O, Weitzman MD, Frey NV, Maude SL, Grupp SA, June CH, Gill S, Ruella M (2020) “Impaired death receptor signaling in leukemia causes antigen-independent resistance by inducing CAR-T cell dysfunction”, Cancer Discovery, doi: 10.1158/2159-8290.CD-19-0813