Nano and biomolecular engineered technologies for neoantigen-specific T cell capture and characterization - Project summary
Much of cancer immunotherapy is focused on engineering or activating tumor-antigen specific CD8+ T cells and,
to a lesser extent, CD4+ T cells. In particular, neoantigen-specific T cells are attractive because they can kill
cancer cells with high specificity. 1 A general approach starts with identifying T cells that recognize neoantigens
broadly expressed within the tumor, isolating the T cells and determining their T cell receptor (TCR) sequences.
These TCRs can then be transfected into patient T cells, perhaps with additional genetic engineering2 to promote
more durable anti-tumor effects, and expanded into an infusion product for patient treatment. 3 In fact, this
approach has recently entered the clinic, with one trial (NCT03970382) drawing from inventions from an NCI-
funded CCNE U54 grant led by the PI of this proposal. 4,5 However, there are still a number of fundamental and
technological challenges associated with advancing neoantigen-specific TCR-engineered therapies. First, the
discovery of neoantigen-specific TCRs relies on guidance from algorithms, such as NET MHCpan 4.1, to predict
antigen/MHC presentation (based upon binding and other considerations), and many neoantigens arising from
truncal mutations, such as mutant KRAS or mutant TP53, are predicted as unlikely, yet have been reported as
clinically effective targets. 6,7,8 Second, neoantigen-specific CD4+ T cells and their class II restricted neoantigens,
while identified as important for immunotherapy-induced anti-tumor responses, 9,10 remain a largely untapped
therapeutic resource, with prediction algorithms 11,12 for Class II antigen/MHC binding less developed. A third
challenge is that analysis of a patient blood for neoantigen-specific T cells typically requires upwards of 20M
peripheral blood mononuclear cells (PBMCs), and so isn't particularly efficient. Here we propose 3 specific Aims
designed to address these outstanding issues. At the heart of the technology solutions are combinations of
engineered nanoparticles (NPs) and biomolecular engineered constructs designed for efficient and selective
capture, analysis, and validation of truncal neoantigen-specific CD4+ and CD8+ T cell populations. Significant
preliminary data is presented for all 3 Aims, some of which uses COVID-19 patient data generated by our work
during the current pandemic. 13,14 The result of this work will be a powerful toolset designed for a minimally-biased
search for CD4+ and CD8+ T cell populations against truncal neoantigens (independent of patient HLA
haplotype), a toolset designed for the rapid validation and characterization of those neoantigen-specific T cell
clonotypes, and a public data base of Class I and Class II truncal neoantigens and T cell receptor genes specific
to those neoantigens.
