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.
Author Info: (1) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (2) Department of Medicine, University
Author Info: (1) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (2) Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA. (3) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA. (4) Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. (5) Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. (6) Institute for Systems Biology, Seattle, WA 98109, USA. (7) Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. (8) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (9) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. (10) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (11) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (12) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA. (13) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (14) Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. (15) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA. (16) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA. (17) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA. (18) Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA. (19) Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA. (20) Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA. (21) Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. (22) Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA. (23) Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA. Electronic address: jheath@systemsbiology.org.
