Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood

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. [Display omitted] •Peptide-MHC tetramers are displayed on nanoparticles to enhance T cell capture•Fluorescent barcodes enable multiplex capture of antigen-specific T cells•Neoantigen-specific T cell numbers track tumor regression in a melanoma patient•Neoantigen-specific T cell populations in the blood mirror those in the tumor Peng et al. report a sensitive method to detect tumor-associated neoantigen-specific T cells. Neoantigens and fluorescent DNA barcodes, presented on nanoparticle scaffolds, permit multiplex capture and analysis of specific T cell populations from blood or tumor. Neoantigen-specific T cell numbers track tumor volume in a melanoma patient responding to immunotherapy.