Rroid2 regulates effector and memory CD8+ T cell response during infection in vivo

CD8+ T cell differentiation has been associated with changes in the expression of long noncoding RNA (lncRNAs). Yet, which and how lncRNAs regulate CD8+ T cell responses following infection in vivo remain incompletely understood. We performed deep RNA-seq to map the lncRNA expression landscape of CD8+ T cell subsets during infection and generated lncRNA knockout mouse models to evaluate the in vivo relevance of six lncRNAs. We identified the enhancer lncRNA Rroid2 to regulate effector CD8+ T cell function as well as effector-to-memory differentiation. Rroid2-deficient mice displayed increased CD44dim Foxp3+ regulatory T cells while the development of other immune cells, such as natural killer cells, was not affected. In CD8+ T cells, Rroid2 deficiency resulted in a fine-tuned downregulation of transcription factors Id2 and T-bet and impaired effector CD8+ T cell proliferation and cytotoxicity as well as memory CD8+ T cell generation and recall responses. In contrast to Id2, Rroid2 deficiency affected both KLRG1+ and KLRG1- effector CD8+ T cells. Taken together, Rroid2 represents a key regulatory layer that controls CD8+ T cell responses to pathogens. Overall design: RNA-seq analysis of MPEC OT-I cells 14 days post infection and SLEC OT-I cells 7 and 14 days post infection with LM-OVA. Following adoptive transfer of WT and Rroid2 KO OT-I cells and listeria infection, Fluorescence-activated cell sorting (FACS) of transferred OT-I cells from the spleen of infected host mice was performed. RNA was isolated and samples were analyzed with RNA-seq.