Puig-Saus et al. characterized the neoantigen-specific T cell response in patients with melanoma with or without a clinical response to anti-PD-1-based therapy using high-throughput tetramer screening and CRISPR-based TCR replacement. In patients with a response to anti-PD-1 therapy, neoantigen-specific T cell responses were polyclonal, targeted a limited number of immunodominant mutations despite higher mutational load, and were recurrently detected in the blood and tumor. Neoantigen-specific TCR T cells showed potent and specific cytotoxicity to patient-matched melanoma cell lines irrespective of clinical responses to immunotherapy.
Contributed by Shishir Pant
ABSTRACT: 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.