Pinpointing the tumor-specific T-cells via TCR clusters

Adoptive T-cell transfer is a promising approach to cancer immunotherapy. It’s efficiency essentially depends on the extent of tumor-specific T-cell enrichment within the graft that can be estimated via activation with identifiable neoantigens, tumor-associated antigens (TAAs), or living or lyzed tumor cells. However, corresponding approaches remain laborious, time-consuming, and functionally limited, hampering clinical development. We believe that our approach to the rapid assessment of tumor-specific TCRs enrichment should fuel the T-cell therapy development. Here we demonstrate that homology cluster analysis of T-cell receptor (TCR) repertoires efficiently identifies tumor-reactive TCRs, allowing to: 1) detect their presence among tumor-infiltrating lymphocytes (TILs); 2) optimize TIL culturing conditions, with IL-2low/IL-21/anti-PD-1 combination showing increased efficiency; 3) investigate surface marker-based enrichment for tumor-targeting T-cells in freshly isolated TILs (enrichment сonfirmed for CD4+/PD-1+/CD39+ and CD8+/PD-1+/CD39+ subsets), or re-stimulated TILs (informs on enrichment in 4-1BB-sorted cells). The datasets represented here display pre-processed TCR-beta repertoires of tumor-infiltrating lymphocytes from metastasized lymph nodes of melanoma patients. cDNA libraries were generated using the Human RNA TCR Multiplex kit (MiLaboratories). We aimed to achieve coverage of 20 paired-end reads per cell for sorted and cultivated TIL populations and approximately 2*10^6 reads per tumor sample fragment. Sequencing was performed using Illumina NextSeq platform (2 х 150 bp read length). Raw sequencing data fastq data was processed with MiXCR software (MiLaboratories). TCR repertoires were extracted using VDJtools v. 1.2.1. Cloneset tables are in VDJtools software format: tab-delimited text files.