CBFB-MYH11 fusion neoantigen enables T cell recognition and killing of acute myeloid leukemia
Melinda A. Biernacki, Kimberly A. Foster, Kyle B. Woodward, Michael E. Coon, Carrie Cummings, Tanya M. Cunningham, Robson G. Dossa, Michelle Brault, Jamie Stokke, Tayla M. Olsen, Kelda Gardner, Elihu Estey, Soheil Meshinchi, Anthony Rongvaux, Marie Bleakley
Melinda A. Biernacki, Kimberly A. Foster, Kyle B. Woodward, Michael E. Coon, Carrie Cummings, Tanya M. Cunningham, Robson G. Dossa, Michelle Brault, Jamie Stokke, Tayla M. Olsen, Kelda Gardner, Elihu Estey, Soheil Meshinchi, Anthony Rongvaux, Marie Bleakley
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Research Article Immunology Oncology

CBFB-MYH11 fusion neoantigen enables T cell recognition and killing of acute myeloid leukemia

Abstract

Proteins created from recurrent fusion genes like CBFB-MYH11 are prevalent in acute myeloid leukemia (AML), often necessary for leukemogenesis, persistent throughout the disease course, and highly leukemia specific, making them attractive neoantigen targets for immunotherapy. A nonameric peptide derived from a prevalent CBFB-MYH11 fusion protein was found to be immunogenic in HLA-B*40:01+ donors. High-avidity CD8+ T cell clones isolated from healthy donors killed CBFB-MYH11+ HLA-B*40:01+ AML cell lines and primary human AML samples in vitro. CBFB-MYH11–specific T cells also controlled CBFB-MYH11+ HLA-B*40:01+ AML in vivo in a patient-derived murine xenograft model. High-avidity CBFB-MYH11 epitope–specific T cell receptors (TCRs) transduced into CD8+ T cells conferred antileukemic activity in vitro. Our data indicate that the CBFB-MYH11 fusion neoantigen is naturally presented on AML blasts and enables T cell recognition and killing of AML. We provide proof of principle for immunologically targeting AML-initiating fusions and demonstrate that targeting neoantigens has clinical relevance even in low–mutational frequency cancers like fusion-driven AML. This work also represents a first critical step toward the development of TCR T cell immunotherapy targeting fusion gene–driven AML.

Authors

Melinda A. Biernacki, Kimberly A. Foster, Kyle B. Woodward, Michael E. Coon, Carrie Cummings, Tanya M. Cunningham, Robson G. Dossa, Michelle Brault, Jamie Stokke, Tayla M. Olsen, Kelda Gardner, Elihu Estey, Soheil Meshinchi, Anthony Rongvaux, Marie Bleakley

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Figure 3

T cells specific for the HLA-B*40:01–restricted CBFB-MYH11 epitope kill AML cell lines.

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T cells specific for the HLA-B*40:01–restricted CBFB-MYH11 epitope kill ...
(A) Absolute cell number of viable NB-4 cells either CBFB-MYH11–transduced (TD) (solid line) or mock-TD (dashed line) after coculture with high-avidity REEMEVHEL-specific clone D2.C24 from a representative experiment. (B) Representative flow plots for experiments shown in A and C, depicting viable single cells at time points after coculture. (C) Percentage survival of NB-4 cells, either WT (left) or transduced to express the full-length CBFB-MYH11 type A fusion (right), at time points after coculture with the D2.C24 T cell clone. (D) Absolute cell number of viable ME-1 cells either HLA-B*40:01–TD (solid line) or mock-TD (dashed line) and cocultured with clone D2.C24 from a representative experiment. (E) Representative flow plots for experiments shown in D and F, depicting viable single cells at time points after coculture. (F) Percentage survival of ME-1 cells, either WT (left) or transduced to express HLA-B*40:01 (right), at time points after coculture with the D2.C24 T cell clone. Viable cell numbers were assessed at varying time points by flow cytometry and percent survival calculated as described in Supplemental Methods. For C and F, colored bars indicate mean and error bars SD for 3–10 technical replicate samples. Two-sample unpaired 2-tailed t tests were performed to compare 0 hours with each subsequent time point.