Resistant to CAR-T therapies? It's the cancer, not your immune system — study
Safety concerns and manufacturing shortcomings aside, existing CAR-T therapies — Novartis’ Kymriah and Gilead’s Yescarta — simply don’t work in 10% to 20% of patients with B cell malignancies. What factors underpin this resistance to CAR-T therapy? The main culprit could be the cancer cells themselves, according to a team of researchers at Penn.
CAR-T therapies are engineered to work in this way: Cells are extracted from the patient and then manipulated in a lab where chimeric antigen receptors are added to direct the patient’s own T cells to snuff out specific cancer cells once re-infused back into the patient. But in a fraction of patients, the armed immune attack does not obliterate the disease. By targeting CD19, a marker present on almost all B cells, CAR-T therapies have shown remarkable potency and durability in a number of blood cancers, including acute lymphoblastic leukemia (ALL).
Research so far suggests that resistance to CAR-T therapies is related to the loss of CD19. When CD19 disappears from leukemic cells, they become invisible to CAR-T therapies, noted the study’s co-senior author Marco Ruella, an assistant professor of hematology-oncology at the University of Pennsylvania, in an interview with Endpoints News.
“That explains maybe half of the relapses in leukemia and maybe a third in lymphoma — so there is still a vast majority of patients where we simply don’t know what’s going on,” he said.
Another factor driving resistance was dysfunctional T cells, he added. “What we are hypothesizing here is that there can be a third mechanism…that even in the presence of CD19 those leukemic cells are unable to die when they are triggered by CAR-T.”
“The constant presence of the leukemic cells that basically cannot die — they’re sort of highlanders — causes dysfunction in the T-cells. To start with — the CAR-T (cells) are okay — but then they keep trying to kill leukemic cells that intrinsically cannot die, and then, over time, they become dysfunctional.”
The findings were published on Thursday in Cancer Discovery, a journal of the American Association for Cancer Research.
In the Penn study, researchers performed a genome-wide CRISPR/Cas9-based screen of an ALL cell line to isolate pathways associated with 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. The in vitro data showed that in the ALL cells that resisted the CAR-T attack, there was a shortage of genes involved in activating the cell death pathway and a spike in genes necessary for evading the cell death pathway.
Instead of interrogating samples from patients that have failed to benefit from CAR-T therapies, the plan was to model a genome-wide resistance mechanism and then confirm it in patients. Many patients are now being treated with CAR-Ts, but still, the numbers are limited — so this approach was used to discover aberrations that the limited number of patient samples would not be powered to identify, Ruella said.
“We started with an unbiased genome-wide approach to study resistance and we saw that the new CRISPR/Cas9 genome knockout libraries were perfect because they would allow you to explore knockouts in the whole genome and interrogate it for resistance to CAR-T.”
The findings were amplified in animal models. The researchers then tried to make sense of the results by using pediatric patient samples from previous CAR-T trials by analyzing the genes in leukemia cells and in T cells — pre- and post-infusion — from responders and non-responders. The data were stark: previously identified signaling pathways in cancer cells were directly associated with responses to CAR therapy, suggesting that death receptor signaling is a key regulator of primary resistance to CAR T cell therapy in ALL, the authors concluded.
“This mechanism appears to rely on two phases: an initial resistance to death receptor-driven killing, followed by an antigen-driven, progressive impairment in CAR-T cell function. Together this leads to CAR T cell failure that perpetuates disease progression,” they wrote.
The uptake of Kymriah was plagued by manufacturing problems, and despite Novartis’ attempt to expand its capacity, sales continue to disappoint commercially, giving Yescarta an edge in the market. Meanwhile, big side effects — notably life-threatening episodes of cytokine release syndrome and neurotoxicity — as well as the therapies’ expensive price tags have also limited their use. Other drug developers have taken note of these constraints and are developing off-the-shelf CAR-T therapies, designed to smoothen manufacturing complexities by using healthy donor cells.
But the team at Penn cautioned that the practice may not necessarily help the subset of patients whose cancer cells carry this proportion of unfavorable genes.
“A possible implication of our observations is that the use of healthy donor (i.e. allogeneic donor or “universal” donor) T cells as a substrate for CAR T cell manufacturing may face the same barriers as autologous products,” the authors wrote. “Understanding how intrinsic and acquired T cell dysfunction cooperate to cause therapeutic failure will be critical to the design of the next generation of cellular therapies.”