Background During thymic development, cytotoxic T cells that can bind to and attack self antigens undergo negative selection thus preventing damage to the self tissues. The sparse medullar thymic epithelial cells (mTECs) present in the thymus are responsible for presenting self antigens to T cells so that they can trigger apoptosis or differentiation into non-cytotoxic lineages if they bind too strongly.

Materials and Methods Understanding gene expression in mTECs is essential for understanding the shape of the human T cell receptor repertoire, which is key for current and emerging cancer immunotherapies. Recent availability of human thymus single cell RNAseq (scRNAseq) data provides an extremely high-resolution view into the pattern of expression within this critical cell type. To determine which epitopes have had to opportunity to be presented during T cell negative selection, we analyzed the human thymus scRNAseq dataset to establish which genes are expressed in mTECs and therefore subject to central tolerance.

Results The coverage of the whole transcriptome of a particular cell is generally sparse. It is therefore difficult to understand basic features of individual cells or cell types such as how many genes are expressed. We used cell- and read-level subsampling to estimate whether a sufficient number of cells and reads had been captured to support categorizing a gene as non-expressed in mTECs. We also examined the expression of the genes not expressed in mTECs in other healthy tissues, and found their expression was almost exclusively restricted to the testis (an immune-privileged site) and the liver (a site of peripheral tolerance)

Conclusions Altogether, these analyses establish a strategy for determining if a data set has sufficient depth to estimate the total number of genes expressed and secondly define a key list of genes that are not expressed during central tolerization of T cells, which represent a compelling list of possible cancer immunotherapy targets.

Disclosure Information L. Blumenberg: A. Employment (full or part-time); Significant; Regeneron Pharmaceuticals. G. Atwal: A. Employment (full or part-time); Significant; Regeneron Pharmaceuticals. A. Dhanik: A. Employment (full or part-time); Significant; Regeneron Pharmaceuticals.