Discovery of frameshift-associated TCRs following personalized neoantigen vaccination in a patient with osteosarcoma

Authors

Bennett, S. N., Alley, J., Shabrang, M., Garness, J., McKinnon, K., Smith, A., Inabinett, W. B., Hoos, W. A., Thompson, M. A., Rubinsteyn, A. N., Vincent, B. G.

Abstract

Personalized antigen-directed immunotherapies, including personalized cancer vaccines, are emerging as promising therapeutic modalities for a range of cancer types. Immune monitoring can be used to evaluate the efficacy of a vaccine in stimulating the immune response pre- and post-vaccination; however, such approaches typically stop short of identifying which T cell receptors (TCRs) are functionally driving therapeutic responses. Here, we present a case report of immune monitoring and subsequent TCR discovery experiments following administration of personalized cancer vaccines in a patient with locally recurrent osteosarcoma. Whole PBMCs were stimulated with vaccine peptides (>16 AA) in vitro for 11 days, after which IFN{gamma} ELISPOT identified total T cell responses for 12 of 15 tested peptides post-vaccination. In vitro expanded samples were submitted for 10x single-cell TCR sequencing, from which 26 TCRs were chosen for generation of TCR-T cells based on clonal expansion and culture specificity. Of the generated TCR-T cells, 25 produced functional TCRs, 4 of which were specific to vaccine peptides. However, downstream testing revealed each was MHC class-II restricted. To address this, we repeated the in vitro stimulations with co-cultures of isolated CD8+ T cells with autologous dendritic cells, and cultures of whole PBMCs with anti-MHC class-II blocking antibody. These cultures yielded 10 additional TCRs, 2 of which were responsive to a vaccine peptide containing a MAP2 frameshift mutation. These findings demonstrate an effective approach for leveraging post-vaccination expanded antigen-specific T cell populations for discovery of novel T cell receptors for downstream cellular therapies.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 16 Oct 2026.

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