Single-cell RNAseq of HA-specific CD8 T cells isolated from the hypothalamus and the spleen of mice expressing the model antigen HA in orexinergic neurons

We previously generated the Orex-HA mouse model in which orexin-producing neurons residing in the hypothalamus selectively expressed a model self-antigen, namely hemagglutinin (HA) from the H1N1 influenza virus. In this model the adoptive transfer of in vitro activated HA-specific CD8 T cells leads to the specific loss of orexinergic neurons located in the hypothalamus. To assess the phenotype and investigate the pathogenic mechanisms and the potential tissue-resident properties of autoreactive (HA-specific) CD8 T cells infiltrating the hypothalamus of Orex-HA mice , we performed a single-cell transcriptomic analysis (scRNA-seq) of HA-specific CD8+ T cells isolated from the hypothalamus and the spleen at day 30 after T cell transfer in Orex-HA mice.