Bulk RNAseq of OT-1 T cells in OVA-pregnant and OVA-grafted mice

Purpose: The molecular circuits which govern CD8 T cell fate after alloimmunization by transplantation or pregnancy are unknown. The goals of this study are to perform whole transcriptome profiling (RNA-seq) of antigen-experienced CD8 T cells in parous and grafted mice to determine whether these cells become memory or exhausted T cells. Methods: mRNA profiles of OT-1 T cells recovered fom naive,OVA-skin grafted and OVA-parous mice were generated by bulk RNA-sequencing. OT-1 cells were FACS sorted from 10 individual mice per each of the three groups and then pooled together into three replicate samples per group. The sequence reads that passed quality filters were analyzed after aligning (STAR) with EdgeR. Results: Comparison of OT-1 T cells from OVA-grafted and OVA-parous mice revealed 400 differentially expressed genes. Conclusions: Skin grafting promotes the differentiation of canonical memory CD8 T cells whereas pregnancy promotes the differentiation of exhausted CD8 T cells with diminished recall capacity. OVA-specific OT-1 T cells were adoptively transferred into congenic naïve mice. Mice received either no OVA exposure (Naïve), a skin graft from an Act-mOVA mouse (gOVA), or were mated with an Act-mOVA male (pOVA). Thirty days after antigen exposure, OT-1 T cells were sorted from the spleen, pooled, and bulk RNA-sequencing was performed.