The dimensions of human and murine CD8 T lymphocyte diversity

The adaptive immune system generates and maintains a pool of CD8+ T cells with an almost limitless specificity with the purpose of maintaining homeostasis. Upon antigen encounter, CD8+ T cells undergo functional diversification and give rise to daughter cells. The daughter cells adopt one of many distinct states along a functional gradient from stem-like towards highly cytotoxic. After antigen clearance, a small fraction of antigen-experienced CD8+ T cells survives and constitutes a long-lived memory population that conveys long-term protection. The likelihood of a T cell acquiring or possessing the ability to maintain a long-term presence is related to the functional characteristics of that T cell during the active response phase. This thesis aims to unravel the biological dimensions underlying CD8+ T cell diversity and fate determination.

Recent developments in high dimensional proteome and transcriptome analysis revealed that antigen- experienced T cells form a continuum of functional states. This continuum is in contrast with the established subsetting into discrete subpopulations. We identified the chemokine receptor CX3CR1 as a graded, cross-species, pan T cell differentiation marker. CX3CR1 can be used to, in a convenient and simple manner, capture a principal component of T cell diversity. Furthermore, the CX3CR1 expression levels reflected similar functional states across species, enabling cross-species comparison of T cell properties. The enhanced insight into differentiation revealed that CX3CR1high CD8+ T cells uniquely patrol the luminal arteriolar surface. These CD8+ T cells scan the arteriolar surface for antigen, which supported their long-term survival. Finally, we unraveled T cell activation and proliferation as principal aspects of the T cell diversity in addition to differentiation. From this data, we constructed transcriptomic- and protein-based scores to provide a precise yet practical tool to identify and isolate differentiation and phase-specific CD8+ T cells.

In this thesis, we moved beyond binary classification of CD8+ T cell states and identified transcriptomic and functional gradients of CD8+ T cell diversity. These axes of diversity precisely described the position of individual CD8+ T cells within the T cell heterogeneity found in the effector and memory phase. By leveraging these axes, we identified markers and marker panels that easily, practically and precisely characterized CD8+ T cells.

List of scientific papers

I. Graded expression of the chemokine receptor CX3CR1 marks differentiation states of human and murine T cells and enables cross-species interpretation. Anthonie J. Zwijnenburg, Jyoti Pokharel, Renate Vernaitė, Wenning Zheng, Elena Hoffer, Iman Shryki, Natalia Ramirez Comet, Marcus Ehrström, Sara Gredmark-Russ, Liv Eidsmo and Carmen Gerlach. Immunity. 2023 Augus 8;56:1955-1974.e10.
https://doi.org/10.1016/j.immuni.2023.06.025

II. The cellular microenvironment regulates CX3CR1 expression on CD8+ T cells and the maintenance of CX3CR1+ CD8+ T cells. Jyoti Pokharel*, Iman Shryki*, Anthonie J. Zwijnenburg, Ioana Sandu, Laura Krumm, Christina Bekiari, Rebecka Heinbäck, Victor Avramov, Josefin Lysell, Liv Eidsmo, Helena Erlandsson Harris and Carmen Gerlach. European Journal of Immunology. 2023 October;10:e2350658. *Equal contribution.
https://doi.org/10.1002/eji.202350658

III. Microvascular immune surveillance by CX3CR1hi effector and memory CD8+ T cells. Olga Barreiro*, Scott M. Loughhead*, Paris Pallis, Anthonie J. Zwijnenburg, Jasper van den Ende, Rodrigo González, Mahmoud Eljably, Victor Collado, Carly Ziegler, Bishan Bhattarai, Nir Yosef, Alex Shalek, Carmen Gerlach and Ulrich H. von Andrian. *Equal contribution. [Manuscript]

IV. CD8+ T cell differentiation and activation represent distinct axes of diversification. Anthonie J. Zwijnenburg*, Adam Gayoso*, Natalia Ramirez Comet, Maria-Nefeli Christakopoulou, Nir Yosef°, Aaron Streets° and Carmen Gerlach°. *Equal contribution, °Equal contribution. [Manuscript]