Friday, April 19, 2024
4/19/2024
Project Summary Immune checkpoint inhibitors (ICIs) provide durable clinical responses in about 20% of cancer patients, but have been largely ineffective for non-immunogenic cancers that lack intratumoral T cells. Most tumors have somatic mu- tations that encode for mutant proteins that are tumor-speci¿c and not expressed on normal cells (termed neoanti- gens). Cancers, such as melanoma, with the highest mutational burdens are more likely to respond to single agent ICIs. However, most cancers, including pancreatic ductal adenocarcinoma (PDAC), have lower mutational loads, resulting in fewer T cells in¿ltrating the tumor. Studies have previously demonstrated that an allogeneic GM-CSF- based vaccine enhances T cell in¿ltration into human pancreatic cancer. Recent work with Panc02 cells, which express around 60 neoantigens similar to human PDAC, showed that PancVAX, a neoantigen-targeted vaccine, when paired with immune modulators cleared tumors in Panc02-bearing mice. This data suggests that cancer vaccines targeting tumor neoantigens induce neoepitope-speci¿c T cells, which can be further activated by ICIs, leading to tumor rejection. Currently the impact of such treatment on T cell expression states and the underly- ing mechanism of therapeutic response remains poorly de¿ned. Comprehensive characterization of responding T cells will be critical in understanding mechanisms of response and providing rationale for combinatorial therapy. In this proposal we will test the hypothesis that when used alongside neoantigen-targeted vaccines, individual ICIs have distinct as well as synergistic modes of action and that different treatment combinations result in distinct changes in the T cell repertoire related to immunotherapy response. To address this hypothesis, I propose two speci¿c aims. Aim 1: To characterize the transcriptional changes in T cells during immunotherapy treatment. I will ¿rst investigate the effect of PancVAX, with and without addition of ICIs, on gene expression at a single-cell level in the Panc02 mouse model. Then I will determine biological processes driving differences in anti-tumor response between treatment arms. I will experimenally validate these differences using ¿ow cytometry. Aim 2: To develop trajectory building methods depicting the clonal evolution of T cells. We will apply this method to T cell receptor sequencing data from human clinical trials of PDAC treated with vaccine and ICI to identify key changes within the T cell repertoire associated with tumor regression or resistance. Successful completion of these aims will inform future combination immunotherapy approaches in PDAC patients and provide new open-source computational software to characterize T cell populations that can be applied to diverse cancer types. The skills I will acquire as I complete this research will prepare me for a career as an interdisciplinary scientist, characterizing the tumor immune landscape to inform precision immunotherapy.
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