Adoptive Transfer of T Cells Genetically Engineered to Express T-Cell Receptors Targeting Neoantigens Arising from p53 and Ras Hotspot Mutations in Hematologic Malignancies
Authors: Cappell Kathryn M , Kim Sanghyun P , Levin Noam , Lam Norris , Amatya Christina , Cutmore Lauren C , Beyer Rachel , Rosenberg Steven A , Kochenderfer James N 
Published: December 2023

The tumor suppressor gene p53 and the oncogenes NRAS and KRAS (shortened to Ras) are frequently mutated in many difficult-to-treat hematologic malignancies including myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and relapsed multiple myeloma. Driver mutations in p53 and Ras are associated with treatment-refractory malignancies. There are no Food and Drug Administration (FDA)-approved therapies specifically targeting hematologic malignancies with p53 or Ras mutations. Some missense mutations in p53 and Ras lead to immunogenic peptides (neoepitopes) that are presented by human leukocyte antigens (HLA). Members of our group have identified T-cell receptors (TCRs) targeting some of these neoepitopes and used T cells expressing these TCRs as treatments for epithelial tumors (Levin et al. Clin Cancer Res, 2021 and Kim et al. Cancer Immunol Res, 2022). Adoptively transferred T cells expressing some of these TCRs have caused objective responses of advanced epithelial cancers in patients. Here, we report preclinical experiments with T cells genetically engineered to target neoantigens arising from p53 and Ras mutations in hematologic malignancies.

p53 mutations occur in approximately 5-10% of de novo AML, 25-50% of treatment-related or complex-karyotype MDS/AML, 5-10% of multiple myeloma, and 25% of plasma cell leukemia. Mutations in Ras occur in 15-20% of AML and 20% of multiple myeloma.

Our TCR panel targets neoepitopes arising from 2 of the 5 most common p53 mutation sites and 2 of the 3 most common Ras mutation sites . The human leukocyte antigen (HLA) restriction of these TCRs is shown along with the HLA frequencies ( Table 1).

In all experiments, human donor peripheral blood mononuclear cells were activated in culture with an anti-CD3 antibody. Two days later, T cells were transduced with a gamma-retroviral vector encoding a neoepitope-specific TCR. Presence of mutations in target cell lines was confirmed by DNA sequencing. Cell lines which did not naturally express the appropriate HLA were transduced with a gamma-retroviral construct encoding the HLA.

We assessed the general specificity of TCRs for each targeted neoepitope. For each neoepitope-specific TCR, T cells expressing the TCR were cultured overnight with target cell lines expressing the neoepitope plus the HLA targeted by that TCR. We cultured T cells from the same cultures with 12 to 16 negative-control target cell lines that lacked the appropriate mutation and/or HLA. Negative control cell lines were from a variety of human tissues. Enzyme-linked immunosorbent assays (ELISA) performed on the culture supernatants showed that IFN-gamma release was much higher when T cells expressing a neoepitope-specific TCR were cultured with target cells having both the targeted mutation and the appropriate HLA (Table 1). We conducted another set of experiments to evaluate the neoepitope-specificity of the TCRs. For each neoepitope, COS7 cells with the appropriate HLA were transfected with plasmids encoding either wild-type or mutant versions of p53 or Ras differing from wild-type by 1 amino acid. The COS7 cells were cultured with T cells expressing the appropriate TCR. IFN-gamma was released in a neoepitope-specific manner. Higher levels of T-cell degranulation and interleukin-2 release occurred when T cells expressing neoepitope-specific TCRs were cultured with target cells having the targeted mutation and HLA versus target cells lacking the appropriate mutation and/or HLA.

We evaluated efficacy of the T53-R175H-A2 TCR in vivo. Immunocompromised NOD-scid common gamma-chain-deficient mice received intravenous injections of the KMS26-luciferase multiple myeloma cell line, which naturally expresses HLA-A*02:01 and the p53 R175H mutation. One week later when all mice had detectable tumor burdens, mice received either 10 million R175H-targeted T cells, T cells expressing an irrelevant TCR, or untransduced T cells. All groups received 3 doses of interleukin-2. Mice treated with R175H-targeted T cells cleared the tumor while mice in all other groups had progressive tumor growth (Figure 1). In vivo studies of additional TCRs are in progress.

In conclusion, we have demonstrated activity of neoantigen-targeted T cells against hematologic malignancies in preclinical models. We plan to evaluate adoptively transferred autologous T cells targeting p53 and Ras mutations in an upcoming clinical trial.