BioProject

Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. More...

Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. We have implemented a granzyme-activatable sensor of T cell cytotoxicity in a universal prototyping platform which enables facile recombinant expression of any combination of TCR-, peptide-, and class I MHC-coding sequences and direct assessment of resultant responses. This system consists of an engineered cell platform based on the immortalized natural killer cell line, YT-Indy, and the MHC-null antigen-presenting cell line, K562. These cells were engineered to furnish the YT-Indy/K562 pair with appropriate protein domains required for recombinant TCR expression and function in a non-T cell chassis, integrate a fluorescence-based target-centric early detection reporter of cytotoxic function, and deploy a set of protective genetic interventions designed to preserve antigen-presenting cells for subsequent capture and downstream characterization. As part of the development of the system, we conducted an RNA-seq study to characterize transcript expression in the base YT-Indy cell line, the genome engineered YT-rCTL version in the presence or absence of cognate antigen-presenting cells, and primary tissue derived TCR-T comparator cells in the presence or absence of cognate antigen-presenting cells. These data represent a supplement to the bioRxiv pre-print (DOI 10.1101/2023.11.20.567960) and the final published version in npj Precision Oncology (2024). An identical dataset corresponding to this entry has also been previously deposited in the Zenodo repository (DOI 10.5281/zenodo.8428843). Overall design: Files named YT-Indy denote unmodified, non-co-cultured samples of the YT-Indy base cell line. Files named with a3a-rCTL nomenclature denote YT-rCTL cell lines (YT-Indy cells transduced with all human CD3 and CD8 genes) harboring the a3a T cell receptor. Files named with a3a-TCRT nomenclature denote host effector cells are primary healthy donor cytotoxic T cells, isolated from cryopreserved healthy donor PBMC by sorting on CD8+ CD4- CD56- population, and activated by anti-CD3/28 stimulation. The additional modifier "AgExp" indicates that the corresponding effector cell format was co-cultured with antigen-bearing target cells for 12 hours prior to FACS re-isolation and immediate cryopreservation. Included here are raw paired-end 150bp Illumina reads in fastq format. Data is compressed as .gz files. These data are derived from RNA-seq conducted on polyA selected mRNA from flash-frozen cell pellets performed off-site using a commercial NGS service provider. Less...