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 5

CBFB-MYH11/B*40:01–specific T cells control AML in vivo in a PDX murine model.

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CBFB-MYH11/B*40:01–specific T cells control AML in vivo in a PDX murine ...
(A) Experiment overview: Newborn, preconditioned MISTRG mice were injected intrahepatically with 1 × 106 PBMCs (OKT3-pretreated to prevent xenogeneic graft-versus-host disease) from HLA-B*40:01+ patients with active CBFB-MYH11+ AML. After 12 weeks of AML engraftment, mice received 10 × 106 CD8+ T cells i.v., either D2.C24 clone (high-avidity, CBFB-MYH11/B*40:01–specific) or a control clone (specific for a candidate neoantigen epitope, IPRAHNRLV, presented by HLA-B*07:02, for which this AML was genotypically negative), then were monitored by weekly PB sampling. (B) Primary AML PBMCs (AML1, 81% blasts) before OKT3 treatment and injection into mice were stained for myeloid markers using AML tracking in mice. (C) Representative flow plots of mice PB pretreatment (left) and 7 days after injection (right) with either CBFB-MYH11/B40:01–specific (red box) or control (blue box) T cell clones. (D) Summary of PB disease burden by flow cytometry after CBFB-MYH11/B40:01–specific (red circles) or control (blue squares) T cell treatment. Statistics were calculated using repeated-measures 2-way ANOVA. (E) Human CBFB-MYH11 type A transcript expression, normalized to murine CD45 (Ptprc) as 2–ΔCq, was assessed before and 7 days after administration of CBFB-MYH11/B40:01–specific or control T cells. (F–H) AML burden in terminal bone marrow as percentage (F) or absolute number (G) of human CD33+ cells, and relative CBFB-MYH11 type A transcript expression (H). (I) Correlation between marrow disease burden as measured by flow cytometry and real-time qPCR was determined by calculation of Pearson correlation coefficient. For all groups and time points, n = 5, except for control T cell–treated mice on day 7 (n = 4) owing to poor RNA yield from 1 sample. Except where noted, statistics were calculated using unpaired 2-tailed parametric t tests. Mean and SD are shown.