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Abstract

Chronic lymphocytic leukemia (CLL) is a lymphoid neoplasm characterized by an accumulation of mature B lymphocytes in blood and peripheral lymphoid organs which highly depend on a tumor-supportive microenvironment. Altered T-cell distribution and function have since long been observed in the CLL microenvironment, but the exact pathological role of the different T-cell subsets remains uncertain. In the present work, the spectrum of CLL-associated T-cell phenotypes were investigated by using leading-edge single-cell technologies. Mass cytometry analyses of lymph nodes (LN), peripheral blood and bone marrow of CLL patients together with reactive lymph nodes (rLNs) of donors without cancer identified the CLL LN as a distinct niche, where CD8+ effector memory T-cells with an exhausted phenotype accumulate. Single-cell transcriptome and TCR-clonality analyses of LN T-cells further revealed a clonal expansion restricted to effector memory CD8+ T-cells, and enabled the characterization of the specific cross-talk between CLL cells and T- cell subsets. Besides, the single-cell transcriptome of T-cells from the Eμ-TCL1 mouse model of CLL was examined and shown to be similar to that of T-cells from CLL patients. Since genome-wide association studies have identified that a single-nucleotide polymorphism affecting the T-cell master regulator EOMES is associated with CLL development, the role of this transcription factor in the disease was investigated. Epigenetic and single-cell RNA sequencing analyses revealed that EOMES is not expressed in CLL cells but in T-cells, and that its levels are highest in exhausted CD8+ T-cells. Interestingly, Eomes deficiency in CD8+ T-cells prevented their expansion and led to a decreased leukemia control in the TCL1 mouse model, providing a novel layer of evidence for an anti-tumor role of CD8+ T-cells in CLL. Furthermore, mass cytometry and single-cell RNA-sequencing analyses revealed an increase of T regulatory type 1 (TR1) CD4+ T-cells in CLL LNs compared to rLNs. Such accumulation was likewise confirmed in spleen of Eμ-TCL1 mice using flow cytometry. Strikingly, TR1 cells failed to expand from Eomes-deficient CD4+ T-cells adoptively transferred in leukemic mice, and consequently were less capable of controlling leukemia development. Moreover, TR1 cell-mediated CLL control required IL-10 receptor signaling, as Il10rb-/- CD4+ T- cells showed impaired anti-leukemia activity. Taken together, the data generated herein comprehensively and deeply characterize the composition and phenotype of the T-cell compartment of CLL patients in comparison to individuals without cancer, and significantly improve our understanding of the function of distinct T-cell subsets in CLL.