Signatures of recent activation identify a circulating T cell compartment containing tumor-specific antigen receptors with high avidity

Abstract

T cell receptor (TCR) avidity is assumed to be a major determinant of the spatiotemporal fate and protective capacity of tumor-specific T cells. However, monitoring polyclonal T cell responses with known TCR avidities in vivo over space and time remains challenging. Here, we investigated the fate and functionality of tumor neoantigen–specific T cells with TCRs of distinct avidities in a well-established, reductionist preclinical tumor model and human patients with melanoma. To this end, we used polyclonal T cell transfers with in-depth characterized TCRs together with flow cytometric phenotyping in mice inoculated with MC38 OVA tumors. Transfer of T cells from retrogenic mice harboring TCRs with high avidity resulted in best tumor protection. Unexpectedly, we found that both high- and low-avidity T cells are similarly abundant within the tumor and adopt concordant phenotypic signs of exhaustion. Outside the tumor, high-avidity TCR T cells were not generally overrepresented but, instead, selectively enriched in T cell populations with intermediate PD-1 protein expression. Single-cell sequencing of neoantigen-specific T cells from two patients with melanoma—combined with transgenic reexpression of identified TCRs by CRISPR-Cas9–mediated orthotopic TCR replacement—revealed high-functionality TCRs to be enriched in T cells with RNA signatures of recent activation. Furthermore, of 130 surface protein candidates, PD-1 surface expression was most consistently enriched in functional TCRs. Together, our findings show that tumor-reactive TCRs with high protective capacity circulating in peripheral blood are characterized by a signature of recent activation.

High-resolution profiling of neoantigen-specific T cell receptor activation signatures links moderate stimulation patterns to resilience and sustained tumor control

“…These hypotheses certainly require further comparison with additional TCRs, also from other patients. The TCRs identified in Mel15 covered an only small range of comparably overall lower functional avidity compared to another recent publication which revealed high functional avidity as surrogate marker for "high-functionality" TCRs in their setting (27). Notably, even the slight differences between the TCRs compared in our study supported the notion of stronger upregulation of activatory and inhibitory signals on T cells expressing TCRs with higher functional avidity, as described by others (27,58).…”

“…The TCRs identified in Mel15 covered an only small range of comparably overall lower functional avidity compared to another recent publication which revealed high functional avidity as surrogate marker for “high-functionality” TCRs in their setting ( 27 ). Notably, even the slight differences between the TCRs compared in our study supported the notion of stronger upregulation of activatory and inhibitory signals on T cells expressing TCRs with higher functional avidity, as described by others ( 27, 58 ). Nevertheless, the substantial differences in maintained anti-tumor reactivity upon rechallenge, despite only such minor differences in functional avidity, suggest additional complexity of individual neoTCR activation patterns potentially associated to structural compounds, binding properties or inherent signaling differences.…”

“…So far, a small number of approaches combined neoTCR identification in tumor-derived TILs across different entities with transcriptomic characterization of the whole neoTCR-population although limited focus has been put on individual TCR-clonotype properties and functional patterns (14)(15)(16)(17)(18). Few preclinical models meanwhile aimed at deciphering the impact of TCR-stimulation strength onto T cells although with, however, highly limited translational significance, so far (26,27). Despite attempts to transfer such results into patient datasets, translational assessment of different patient-neoTCRs for persistence of functionality in tumor settings with chronic antigen presence is missing (27).…”

“…Few preclinical models meanwhile aimed at deciphering the impact of TCR-stimulation strength onto T cells although with, however, highly limited translational significance, so far ( 26, 27 ). Despite attempts to transfer such results into patient datasets, translational assessment of different patient-neoTCRs for persistence of functionality in tumor settings with chronic antigen presence is missing ( 27 ).…”

Gene Signatures of T-Cell Activation Can Serve as Predictors of Functionality for SARS-CoV-2-Specific T-Cell Receptors

“…By using scRNA seq, we accessed in parallel the transcriptomic and the TCR sequence of SARS-CoV-2 CD8 + T cells. In ‘hot’ environments, meaning in situations of in vivo antigen persistence such as cancer patients or active infections, this combined information suffices for the identification of antigen-specific T cells (and corresponding TCRs) directly ex vivo by gene signatures of recent T-cell activation [ 44 , 45 ]. However, in ‘cold’ environments (absence of antigen), the information on gene expression is only long-term and might not reflect actual functionality.…”