TCR engineered T cell therapies for hematologic malignancies

Division Of Basic Sciences - Nci

Investigators

Abstract

Activity 1: TCR class I and II epitope discovery for myeloid malignancies (AML/MDS/MPN): The objective of this activity is to discover epitopes that can be targeted with T cell receptors. The project is pursued in collaboration with Dr. Josh Elias (Stanford/Chan Zuckerberg Biohub). Recurrent somatic mutations or chromosomal breakpoints shared across patients with frequencies of at least 2% in a given disease category were curated using the publicly accessible COSMIC database. A total of 47 such genetic abnormalities were chosen, and expression vectors for tandem minigenes (as described by Tran E et al. Science 2014) encoding these genetic abnormalities were manufactured. Then a panel of artificial antigen presenting cells expressing tandem minigene with one or two HLA class I or II alleles were engineered. A total of sixty cell lines were established, which cover 12 most frequent HLA class I and II alleles in the US population. These artificial cell lines were lysed, peptide-MHCs were pulled down, and the lysates are currently being analyzed by mass spectrometry by Dr. Elias' team. The initial assay identified multiple new epitopes derive from PRAME restricted by HLA-A*02:01, HLA-B*08:01, HLA-C*07:02, HLA-B*07:02, an BCR-ABL1 fusion onco-protein-derived epitope restricted by HLA-B*08:01, and several TMG-encoded neoantigen-derived epitopes. Top candidate epitopes identified in this project will be used for TCR discovery using reverse immunology approaches. ------Activity 2: Pre-clinical development of HLA-A*02:01-restricted CD22TCR: We have discovered T cell receptor that recognizes HLA-A*02:01-restricted epitope of CD22, which is an antigen expressed broadly by mature B-cell malignancies and a portion of acute lymphoblastic leukemia. The CD22TCR demonstrates promising pre-clinical anti-leukemia/lymphoma activity against multiple cell lines in both CD22- and HLA-A2-restricted manner. Furthermore, the CD22TCR does not demonstrate severe cross-reactivity that would cause off-target toxicities on normal tissues. The CD22 TCR is patented (International Patent Application No. PCT/US2022/016561 filed February 16, 2022). Extensive pre-clinical safety evaluation was completed, which confirmed that the CD22 TCR-T cells do not cross-react with peptides derived from other human proteins. In NSG xenograft models, CD22 TCR-T cells mediated anti-leukemia/lymphoma cytotoxicity at clinically relevant cell doses. Leukemia clearance by CD22 TCR-T cells was not associated with systemic cytokine elevation. In contrast, CD22 CAR-T was not able to control leukemia at its clinically relevant dose. The CD22 CAR-T cells at higher cell dose (500-fold higher than the dose feasible/safe in humans) cleared leukemia, but the treatment was associated with systemic proinflammatory cytokine elevation reminiscent of cytokine release syndrome. These data support that the CD22 TCR-T cells is an active and potentially safer alternative cell-based treatment for B-cell malignancies and the data warrant clinical translation of the TCR. Through the NCI DCTD NExT Program, we are currently in the process of GMP-grade vector manufacturing, which will be used in the early-phase clinical trial of the CD22 TCR-T cells. ------Activity 3: Establishment of TCR cross-reactivity screening strategy: Using a panel of murine TCRs recognizing HLA-A*02:01-restricted epitope of CD20, we established a method of prospectively identifying the cross-reactivity that could cause prohibitive toxicities if translated into clinic. The method was patented (Patent Application No. 63/481,757 filed January 26, 2023) and published (Ishii K et al., Science Advances. 2023, In Press). ------Activity 4: Discovery of TCRs against HLA class I-restricted epitopes of brachyury and PRAME: Using in vitro stimulation of human PBMCs, we have isolated multiple TCRs against HLA class I-restricted epitopes of brachyury and PRAME. We are currently vetting the antigens and these TCRs for further clinical translation. ------Activity 5: Development of technologies to safely enhance the potency of TCR-T cell therapies: In this activity, we are evaluating various methods of improving the therapeutic potency of TCR-engineered T-cell therapies developed in activity #2 and #4. Methods being developed and evaluated include 1) Augmentation of CD8 co-receptor expression and modulation of CD8 intracellular sequences, and 2) modulation of CD22 TCR signaling by introducing CD3z mutation (collaboration with Dr. Paul Love, NICHD, NIH).