RNA-seq comparison of YT-Indy based reconsituted cytotoxic T cells and primary activated CD8+ T cells

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.