Description

The complexity of promiscuous gene expression in medullary thymic epithelial cells

J. Baran-Gale¹, F. Dhalia², C. Ponting¹, G Hollander^2,3

¹MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, United Kingdom;

²Developmental Immunology, Weatherall Institute of Molecular Medicine and Department of Paediatrics, University of Oxford, United Kingdom; ³Paediatric Immunology, Department of Biomedicine and University Children’s Hospital Basel, University of Basel, Switzerland

In the medulla of the thymus, medullary thymic epithelial cells (mTECs) present antigens to passing thymocytes in a process known as negative selection, whereby thymocytes that strongly react to the presented antigen are eliminated. In order to prevent self-reactive thymocytes from leaving the thymus, mTECS must collectively express most genes in order to present the majority of self-antigens that the thymocytes are likely to encounter. This process, known as promiscuous gene expression (PGE), is partially regulated by the autoimmune regulator (Aire). While we know that Aire controls the expression of a large number of tissue-restricted genes and enhances the expression of others, it remains unclear whether mTECs transition from expressing one group of promiscuously expressed genes to another or if the small networks of co-expressed genes observed is due to stochastic events.

To investigate patterns of co-expression, we sequenced individual mTECs that are unselected or physically sorted for Gp2, a pancreatic protein that is promiscuously expressed in mTEC in an Aire-enhanced fashion. Using the 10x Chromium single cell 3'- protocol, we prepared single cell libraries using the mTECs of three F1 mice that were FACS sorted to isolate Gp2-positive mTECs, and unselected mTECs are from F1, and parental strains of mice (N=2 each). These data allow us to identify genes co-expressed following the Aire-enhanced expression of Gp2, and to identify patterns of allelic co-expression in mTECs. Indeed, we find that the gene-expression profile of Gp2-postitive cells can be distinguished from unselected mTECs and that Aire transcript is less abundant in the Gp2-postive cells relative to unselected. Additionally, we find a slight preference towards the preferential detection of the maternal allele in the libraries from the F1 animals. In this poster, we catalog the complexity of co-expression patterns in single mTECs at the level of both genes and alleles.