Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer

Abstract

Anti-PD-1 treatment has shown unprecedented clinical success in the treatment of non-small-cell lung cancer (NSCLC), but the underlying mechanisms remain incompletely understood. Here, we performed temporal single-cell RNA and paired T-cell receptor sequencing on 47 tumor biopsies from 36 patients with NSCLC following PD-1-based therapies. We observed increased levels of precursor exhausted T (Texp) cells in responsive tumors after treatment, characterized by low expression of coinhibitory molecules and high expression of GZMK. By contrast, nonresponsive tumors failed to accumulate Texp cells. Our data suggested that Texp cells were unlikely to be derived from the reinvigoration of terminally exhausted cells; instead, they were accumulated by (1) local expansion and (2) replenishment by peripheral T cells with both new and pre-existing clonotypes, a phenomenon we named clonal revival. Our study provides insights into mechanisms underlying PD-1-based therapies, implicating clonal revival and expansion of Texp cells as steps to improve NSCLC treatment.

TCR-sequencing in cancer and autoimmunity: barcodes and beyond

“…(B) Work has shown that PD-1 pathway inhibitors can act on T cells in the tumor-dLN in mice [61,62] and immunological changes that have functional and prognostic significance can be detected in the peripheral blood of humans [40,67,[134][135][136]. An important mechanism of protection following PD-1 pathway blockade is recruitment of new, potentially less dysfunctional T cell clones from the periphery into the tumor [30,36,[38][39][40]67]. However, studies in mice and humans suggest that PD-1 inhibitors also likely act on T cells in the tumor as well [56][57][58][59].…”

“…Using the TCR as a barcode in cancer The TCR has been used as a barcode to identify CD8 + T cells in peripheral blood that share TCRs with CD8 + tumor-infiltrating lymphocytes (TILs) in tumors (referred to as 'tumor matching'), as shown in mice with MC38 colon adenocarcinoma [27], as well as in patients with advanced melanoma and non-small cell lung cancer (NSCLC) [27][28][29][30]. The TCR has also been valuable for studying the dynamics of individual CD8 + T cell clones, including clone-by-clone comparisons of transcriptional states across tissues and inferring lineage relationships between populations of CD8 + T cells in mouse [including MC38, B16-F10, CT26, and a genetically engineered mouse model (GEMM) of lung adenocarcinoma caused by oncogenic Kras and loss of p53] and human tumors [including melanoma, NSCLC, colorectal cancer (CRC)] [27][28][29][30][31][32][33][34][35][36][37][38]. A recent study in humans used paired scRNA seq and scTCR seq to analyze CD4 + T cells and CD8 + T cells across 21 cancer types (including melanoma and breast, gastric, pancreatic, kidney, and esophageal cancers) from 316 patients; the study identified two major developmental trajectories that contributed to T cell exhaustion across multiple tumor types, based on transcriptional information [32].…”

“…A recent study in humans used paired scRNA seq and scTCR seq to analyze CD4 + T cells and CD8 + T cells across 21 cancer types (including melanoma and breast, gastric, pancreatic, kidney, and esophageal cancers) from 316 patients; the study identified two major developmental trajectories that contributed to T cell exhaustion across multiple tumor types, based on transcriptional information [32]. Additionally, scTCR seq has been useful to inform mechanisms of response following PD-1-based immunotherapy in cancer patients [30,[36][37][38][39][40][41], as later discussed. While these studies have shown that scTCR seq data can be promising for focused analyses on T cell populations of interest, there are limitations to this method (Boxes 1-3).…”

“…Additional studies showed that the presence of clonal replacement correlated with improved clinical antitumor response [36,39,40,67]. However, work in patients with NSCLC has led to the proposal of an additional mechanism for protective immune responses following PD-1 blockade, termed clonal revival [30]. With clonal revival, new, less dysfunctional CD8 + T cell clones populate the tumor (from the periphery, local expansion within the tumor, or both), replenishing the more terminally exhausted pre-existing pool of CD8 + TILs.…”

“…With clonal revival, new, less dysfunctional CD8 + T cell clones populate the tumor (from the periphery, local expansion within the tumor, or both), replenishing the more terminally exhausted pre-existing pool of CD8 + TILs. However, these clones can either have novel TCRs to the tumor following PD-1 blockade (like clonal replacement), or TCRs matching to preexisting clones in the tumor [30]. Collectively, while all of these studies support a model where the antitumor immune response boosted by PD-1 blockade is largely generated beyond the tumor [30,[36][37][38][39][40]67] (Figure 2), whether most protective responses following PD-1 blockade are due to truly novel clones that were absent from the tumor before blockade or to both novel…”