One of our key hypotheses is that immune cells, which are capable of maintaining immunological memory or exhausted immune responses over long-periods of time, must possess stem-cell-like qualities. This means that, upon reactivation, an individual stem-like memory or stem-like exhausted immune cell must be capable of self-renewing divisions that maintain the stem-like compartment, and, in parallel, of multipotent differentiation into a diverse offspring of shorter-lived immune effector cells, responsible for pathogen control. To test these features, we have developed single-cell-based approaches that track the fate of an individual immune cell and its offspring in vivo and in vitro over extended periods of time.
Based on these approaches, we have identified a new subset of stem-like exhausted CD8+ T cells that stands at the top of the developmental hierarchy of all exhausted CD8+ T cells responding to chronic viral infection. We found that these CD62L+ stem-like exhausted T cells depend on the transcription factor MYB and are critical for conveying the proliferative burst upon immune checkpoint blockade, which makes them a prime target for immunotherapies of chronic infection and cancer. Using a similar single-cell-based approach, we identified a hitherto unrecognized subset of Natural Killer cells that coordinates the interaction of antigen-presenting Dendritic cells and antigen-specific CD8+ T cells during the early phase of viral infection. It thereby supports the optimal induction of T cell memory and is of high potential relevance for T cell-targeted vaccination approaches. Moreover, through continuous live-cell imaging in vitro, we found that emergence of T cell memory precursors within the progeny of a single activated T cell, correlated with slower cell cycle activity of these cells, highlighting cell cycle speed as a major heritable property that is regulated in parallel to key lineage decisions of activated T cells. Finally, using new in vivo single-cell fate-mapping technologies developed within the scope of this project, we found that most CD8+ T cells, which recognize their cognate antigen with low affinity, fail to engage in clonal expansion and, instead, remain immunologically ignorant, even upon systemic infection with the antigen-expressing pathogen.
