Single-cell RNAseq and TCRseq on site-matched biopsies from patients with basal or squamous cell carcinoma before and after anti-PD-1 treatment revealed that post-treatment clonally expanded TILs were enriched in tumor-specific, exhausted CD8+ T cells, many of which exhibited TCR clonotypes that were not detected in the tumors prior to treatment and appeared to represent new antigen specificities. These results suggest that pre-existing exhausted TILs have limited capacity for reinvigoration and are replaced by newly recruited cells which themselves become exhausted.
Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of patients with cancer(1). However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear(2-4). Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Tracking T cell receptor clones and transcriptional phenotypes revealed coupling of tumor recognition, clonal expansion and T cell dysfunction marked by clonal expansion of CD8(+)CD39(+) T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, the expansion of T cell clones did not derive from pre-existing tumor-infiltrating T lymphocytes; instead, the expanded clones consisted of novel clonotypes that had not previously been observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8(+) T cells and evident in patients with basal or squamous cell carcinoma. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.
Author Info: (1) Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. (2) Center for Personal Dynamic Regulomes, Stanford University School of Medic
Author Info: (1) Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. (2) Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. satpathy@stanford.edu. Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. satpathy@stanford.edu. Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. satpathy@stanford.edu. (3) Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. (4) Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. (5) iRepertoire Inc, Huntsville, AL, USA. (6) Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. (7) Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (8) Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA. (9) Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA. (10) Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA. (11) Stanford Biobank, Stanford University School of Medicine, Palo Alto, CA, USA. (12) Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. (13) Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. (14) Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. (15) Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA. alschang@stanford.edu. (16) Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu. Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. howchang@stanford.edu. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu. Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA. howchang@stanford.edu. Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. howchang@stanford.edu.
