Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.

The promiscuous nature of T-cell receptors (TCRs) is fundamental for our ability to recognize a large range of pathogens; however, this feature makes it challenging to understand and control Tcell recognition 1. Existing technologies provide limited information about the key requirements for T-cell recognition and the ability of TCRs to cross-recognize structurally related elements 2,3. Herein we present a proof-of-concept of a novel 'one-pot' strategy to establish the patterns that govern TCR recognition of peptide-major histocompatibility complex (pMHC). We determine the affinity-based hierarchy of TCR interactions with MHC loaded with peptide variants, and apply this knowledge to understand the recognition motif, here termed the TCR fingerprint. The TCR fingerprints of 16 different TCRs were identified and used to predict and validate crossrecognized peptides from the human proteome. The identified fingerprints differed amongst TCRs recognizing the same epitope, demonstrating the value of this strategy for understanding T-cell interactions and assessing potential cross-recognition prior to selection of TCRs for clinical development.

No abstract

BackgroundClinical efficacy of immune checkpoint blocking (ICB) therapy critically relies on the killing of melanoma cells by CD8+ T cells, becoming activated upon recognition of tumor antigens presented by HLA class I (HLA-I) surface molecules. Patient-derived melanoma cells can escape from cytotoxic T cell effector functions by loss of HLA-I surface expression due to the silencing of HLA-I antigen processing and presentation machinery (APM) genes.Material and MethodsSeeking for a strategy to restore HLA-I expression, we transfected melanoma cells obtained from distinct patient metastasis with synthetic short double stranded RNA (3pRNA), an activating ligand of the cytosolic innate pattern recognition receptor RIG-I. 3pRNA-transfected melanoma cells were analyzed for HLA-I surface expression by FACS analysis and gene expression of HLA-I APM components by qPCR. In vivo 3pRNA-transfected tumors were analyzed for HLA-I expression by immunohistochemistry staining. Furthermore, T cell activation after coincubation with 3pRNA-transfected melanoma cells was determined by IFNγ-ELISpot assay. The effect of combined 3pRNA and blocking anti-PD-1 antibody treatment on T cell activation was measured by intracellular cytokine staining and FACS analysis.ResultsActivation of RIG-I by 3pRNA increased the expression of HLA-I APM components and strongly enhanced recognition of melanoma cells by autologous CD8+ T cells. Based on these findings, we asked whether the combination of 3pRNA and blocking anti-PD-1 antibodies could improve anti-melanoma T cell responses in an anti-PD-1 non-responder patient model. Indeed, T cell activation by 3pRNA-transfected melanoma cells was significantly increased in the presence of anti-PD-1 antibodies. In line with the enhancement of anti-tumor T cell responses, we found an association of elevated RIG-I mRNA levels with prolonged patient survival in TCGA melanoma samples.ConclusionsIn summary, this study demonstrates a beneficial effect of RIG-I activation on antigen presentation and T cell recognition of melanoma cells. Improved T cell responses by combined 3pRNA and anti-PD-1 treatment suggests that combinational therapy could be a strategy to overcome T cell resistance in melanoma.Disclosure InformationB. Thier: None. L. Such: None. M. Schwamborn: None. A. Sucker: None. C. Coch: None. D. Schadendorf: None. K. Griewank: None. M. Trilling: None. F. Zhao: None. A. Paschen: None.