A novel method (pNP) of detecting, quantifying, and isolating neoantigen-specific CD8+ T cells from small amounts of patient tumor or blood utilizes magnetic nanoparticles (NPs) that present MHC tetramers loaded with neoantigen peptides (pMHC). pMHC tetramers are coupled to NPs via DNA linkers, which also serve as barcodes for multiplexed T cell profiling. pNP captured antigen-specific T cells more efficiently than multicolor flow cytometry. In patients with metastatic melanoma responding to anti-PD-1, pNP-detected neoantigen-specific T cells in tumor and in blood tracked with each other and with tumor volume, suggesting that pNP could monitor clinical response.
Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.