Periodic Reporting for period 2 - SCIMAP (Roads to memory: Studying the regulation of lymphocyte stemness by fate mapping of single T and NK cells)
Berichtszeitraum: 2022-09-01 bis 2024-02-29
After the immune system has fought off an acute infection, it enters a state of “immunological memory”, which can be maintained over long periods of time and is critical to protect the host against re-infection. However, if initial pathogen clearance fails, the immune system shifts gears and, instead of developing classical immunological memory, enters a state of “immune exhaustion” characterized by limited functionality. Adopting this state prevents excessive immunopathology but also limits the immune system’s capacity for clearance of chronic infections and cancers. It is still incompletely understood, how immunological memory and immune exhaustion are induced and maintained. Effectively modulating these processes is, however, of key importance for developing improved vaccination approaches and immunotherapeutic strategies. Therefore, our project SCIMAP aims to answer: 1) Which immune cell subsets are of critical importance for maintaining immunological memory and exhausted immune responses. 2) Along which pathways do these subsets develop and how does this developmental history influence their functionality? And, 3) which basic cellular processes, such as asymmetric cell division or cell cycle speed, are critically involved in determining their long-term fate? By answering these fundamental questions, we hope to identify new strategies for the isolation, induction and modulation of optimal immune cells for vaccination and immunotherapy.
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.
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.
As indicated above, our project SCIMAP has already provided critical new insight into the cellular and molecular regulation of CD8+ T and Natural Killer cell responses to acute and chronic infections. Throughout the second half of the project, we now aim to increase our understanding of memory and exhausted CD4+ T cell responses in the same infection settings. Moreover, we will embark on an in-depth investigation of the stem-like basis of NK cell memory and explore the early T cell fate decisions and cellular properties leading towards immunological memory directly or via an effector T cell intermediate. Taken together, by identifying stem-like immune cell subsets and deciphering their molecular regulation, SCIMAP has already provided fundamentally new and translationally relevant immunological insight and has a high potential of enabling further transformative discoveries in the context of vaccination and immunotherapy until the end of the project.