Transcriptional comparison of ptpn2-deficient and competent effector and memory precursor cells in acute HSV infection

We compared the transcriptional profile of FACS-purified total effector, KLRG1+ effector and KLRG1- effector Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells from spleens of acutely infected mice. As expected, we found a large number of differentially expressed genes (DEG; |log2(fold-change)| >1; false discovery rate <0.05) between KLRG1– and KLRG1+ subsets of both Lck-Cre;Ptpn2fl/fl (712 DEG) and Ptpn2fl/fl (528 DEG) OT-I cells. Furthermore, we found 190 DEGs between total populations of Ptpn2-deficient and control OT-I cells. Considerably fewer genes were differentially expressed between Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells amongst the KLRG1– (93 DEG) and KLRG1+ (59 DEG) subsets. Hierarchical clustering analysis further revealed clustering of KLRG1– cells of both genotypes with total Ptpn2fl/fl OT-I cells, whereas KLRG1+ cells of both genotypes clustered with total Lck-Cre;Ptpn2fl/fl OT-I cells. Gene set enrichment analysis further showed that differential gene profiles between Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells for all subfractions (total, KLRG1+, KLRG1–) were enriched significantly for previously identified effector versus memory CD8+ T cell signature genes. Taken together, these findings indicate that after in vivo priming following HSV infection, Ptpn2 deficiency resulted in the preferential generation of OT-I cells with a transcriptional profile biased towards more terminally differentiated KLRG1+ effector cells with restricted memory potential. mRNA sequencing of FACS-purified total effector, KLRG1+ effector and KLRG1- effector Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells from spleens of acutely infected mice (day 8 after HSV skin infection).