Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy

Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells(1-14). The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies(15-17) to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8(+) T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.

Automated summary

We isolated neoantigen-specific T cells from blood and tumors of melanoma patients using newly developed technologies. Multiple T cell clones with different neoTCR sequences recognized a limited number of mutations in samples from patients with clinical responses. These recurring neoTCR clonotypes were detected in blood and tumors over time. Patients with no response also showed neoantigen-specific T cell responses, but with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstructing neoTCRs in donor T cells demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines.