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Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

Nature Medicine volume 22, pages 433–438 (2016)Cite this article

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Abstract

Detection of lymphocytes that target tumor-specific mutant neoantigens—derived from products encoded by mutated genes in the tumor—is mostly limited to tumor-resident lymphocytes1,2, but whether these lymphocytes often occur in the circulation is unclear. We recently reported that intratumoral expression of the programmed cell death 1 (PD-1) receptor can guide the identification of the patient-specific repertoire of tumor-reactive CD8+ lymphocytes that reside in the tumor3. In view of these findings, we investigated whether PD-1 expression on peripheral blood lymphocytes could be used as a biomarker to detect T cells that target neoantigens. By using a high-throughput personalized screening approach, we identified neoantigen-specific lymphocytes in the peripheral blood of three of four melanoma patients. Despite their low frequency in the circulation, we found that CD8+PD-1+, but not CD8+PD-1−, cell populations had lymphocytes that targeted 3, 3 and 1 unique, patient-specific neoantigens, respectively. We show that neoantigen-specific T cells and gene-engineered lymphocytes expressing neoantigen-specific T cell receptors (TCRs) isolated from peripheral blood recognized autologous tumors. Notably, the tumor-antigen specificities and TCR repertoires of the circulating and tumor-infiltrating CD8+PD-1+ cells appeared similar, implying that the circulating CD8+PD-1+ lymphocytes could provide a window into the tumor-resident antitumor lymphocytes. Thus, expression of PD-1 identifies a diverse and patient-specific antitumor T cell response in peripheral blood, providing a novel noninvasive strategy to develop personalized therapies using neoantigen-reactive lymphocytes or TCRs to treat cancer.

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Figure 1: Frequency of PD-1 expression on circulating and tumor-resident CD8+ lymphocytes and prospective identification of circulating neoantigen-reactive cells in melanoma patients.
Figure 2: Characterization of neoantigen-specific lymphocytes isolated from the circulating CD8+PD1+ subset of subject NCI-3998.
Figure 3: Identification of neoantigens targeted by circulating CD8+PD-1+ cells isolated from subjects NCI-3784, NCI-3903 and NCI-3713.
Figure 4: Recognition of tumors and self-antigens by TCRs or CD8+ T cells isolated from peripheral blood, and comparison of the specificity and TCR repertoire between circulating and tumor-infiltrating CD8+ T cell subsets.

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Acknowledgements

This work was supported by the Center for Cancer Research intramural research program of the NCI, US National Institutes of Health (NIH). We thank the members of the Surgery branch for helpful discussions, R. Somerville and members of the tumor-infiltrating lymphocytes (TIL) lab for technical support, and L. Liu for kindly providing the PD-1–specific AMP-514 antibody. This work used the computational resources of the NIH High-Performance Computing (HPC) Biowulf cluster (http://hpc.nih.gov).

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Authors and Affiliations

  1. Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland, USA

    Alena Gros, Maria R Parkhurst, Eric Tran, Anna Pasetto, Paul F Robbins, Sadia Ilyas, Todd D Prickett, Jared J Gartner, Jessica S Crystal, Ilana M Roberts, Kasia Trebska-McGowan, John R Wunderlich, James C Yang & Steven A Rosenberg

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  1. Alena Gros
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Contributions

A.G. designed, performed, analyzed and interpreted experiments; M.R.P. performed and analyzed experiments; E.T. and A.P. analyzed and interpreted the data; P.F.R. helped in selecting the mutant antigens screened and interpreted data; S.I. performed experiments; T.D.P. and J.S.C. provided valuable advice and reagents for subjects NCI-3713 and NCI-3903; J.J.G. performed the tumor-exome and transcriptome bioinformatics analysis; I.M.R. provided technical support; K.T.-M. provided valuable advice and reagents for subject NCI-3998; J.R.W. established tumor cell lines; J.C.Y. supervised the clinical treatment of the patients included in the study and interpreted the data; and S.A.R. supervised the clinical treatment of the patients included in the study, supervised the project, designed experiments and interpreted the data. A.G. and S.A.R. wrote the manuscript.

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Correspondence to Steven A Rosenberg.

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Gros, A., Parkhurst, M., Tran, E. et al. Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat Med 22, 433–438 (2016). https://doi.org/10.1038/nm.4051

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