All Memory Lymphocytes Share a Common Differentiation Program.
Authors: Haining W. Nicholas , Ebert Benjamin , Subramanian Aravind , Wherry E. John , Evans John , Mak Raymond , Rivoli Stephen , Angelosanto Jill , Pretz Jennfer , Kaech Susan , Ahmed Rafi , Nadler Lee M. , Golub Todd R. 
Published: April 2020

Although memory lymphocytes in CD4, CD8 and B cell lineages are characterized by a strikingly diverse array of functions and phenotypes, they share common properties of longevity, lowered response threshold and the ability to self-renew. The development of these memory functions is essential for immunity to pathogens and tumors, but it is not known how diverse lineages acquire these same properties. We therefore studied the transcriptional profile of memory differentiation to determine whether the development of memory in disparate lineages involves a common differentiation program. To identify a core signature of memory differentiation, we used cross-species genomic analysis to identify genes differentially expressed by both human and murine memory CD8 T cells compared to their naive precursors. We identified 220 genes significantly increased in human memory-phenotype cells, and found this signature to be highly conserved in two different TCR transgenic murine models of memory differentiation (P&lt;0.001). Our analysis thus revealed an evolutionarily conserved transcriptional signature of CD memory differentiation. Several of the genes in this signature are known to be required for CD8 memory development, while others are novel markers of memory differentiation. We validated the signature at the protein and functional level, and demonstrated that it is highly enriched in the gene expression profiles of human CD8 T cells specific for CMV, influenza and EBV, suggesting that diverse viral pathogens can induce a similar differentiation program. We next tested whether this conserved signature is necessary for memory cells to be fully functional. To address this question, we studied memory differentiation in TCR transgenic T cells responding acute or chronic LCMV infection. Adult mice resolve an acute LCMV infection and then exhibit long-term CD8 T cell memory. In contrast, chronic LCMV infection results in exhausted CD8 cells that fail to demonstrate the properties of memory cells. Hierarchical clustering of the memory signature genes showed marked differences between functional memory cells and virally-exhausted T cells. Thus the signature of memory differentiation is disrupted in CD8 cells that fail to manifest the properties of memory. Finally, we tested the conserved CD8 memory signature in gene expression profiles of human memory CD4 and memory B cells compared to their naïve precursors. We found that the CD8 memory signature was highly enriched not only in CD4 memory (P&lt;0.001) but also in B cell memory (P&lt;0.001). Thus a single transcriptional signature is a general feature of memory differentiation in CD8, CD4 and B cells, and disruption of this signature is associated with defective T cell memory. Analysis of the regulation of this transcriptional program may help identify the mechanisms governing memory differentiation. Our data represent a novel approach to predicting the function of antigen-specific memory cells in vivo, and suggest that drugs which target this single differentiation program could profoundly influence the formation of immunologic memory.