Single-Cell Omics Analyses Identify the TIM-3 Ligand Galectin-9 As Novel Immunotherapy Target for Chronic Lymphocytic Leukemia

Laura Llaó Cid, John KL Wong, Marina Wierz, Yashna Paul, Tobias Roider, Iria Fernandez Botana, Susanne Gonder, Alessia Floerchinger, Dolors Colomer, Elías Campo, Sascha Dietrich, Peter Lichter, Marc Zapatka (Main author), Etienne Moussay (Main author), Jérôme Paggetti (Main author), Martina Seiffert (Main author)

Research output: Contribution to journalMeeting Abstractpeer-review


Failure of response to immunotherapy including checkpoint inhibitors or CAR-T-cell therapy in chronic lymphocytic leukemia (CLL) has been linked to dysfunctional effector T cells. Using single-cell analyses, we performed an in-depth characterization of the T-cell compartment in blood and tissue samples of CLL patients and mouse models to gain insights into the spectrum of phenotypes and transcriptional programs of T cells and the underlying mechanisms of their development.
By mass cytometry (CyTOF) using 35 antibodies, we characterized T cells in blood (n=8), bone marrow (n=3), and lymph nodes (n=21) of CLL patients, as well as reactive lymph nodes of non-tumor patients (n=13). Integrative analyses of all data sets allowed us to identify and quantify 15 clusters of CD4+ and 14 clusters of CD8+ T cells. First, our data showed that T cells in blood and bone marrow are similar, but clearly distinct from lymph node derived cells. Second, we observed an accumulation of several regulatory T-cell subsets, as well as T cells harboring an exhausted and dysfunctional phenotype in the lymph node samples, and a positively correlated abundance of these T-cell subsets. Third, an increased frequency of regulatory and exhausted T cells was detected in CLL in comparison to non-malignant lymph nodes.
We further performed single-cell RNA-sequencing generating transcriptome and T-cell receptor (TCR) data of T cells from lymph nodes of CLL patients (n=5) and spleen samples of the Eµ-TCL1 mouse model (n=3). These data confirmed the presence of several exhausted T-cell clusters in CLL lymph nodes and spleens of Eµ-TCL1 mice, and allowed for the identification and transcriptional characterization of terminally exhausted T cells and their precursor state (Figure A). By integrating single-cell TCR data, a clonal expansion mainly of the precursor exhausted T cells was observed, suggesting their reactivity for CLL cells.
Finally, we used the single-cell transcriptome data for interactome analyses and identified both known and novel ligand-receptor-interactions between CLL and different T-cell clusters with a presumable function in survival and growth support of CLL cells, but also in suppression of T cells. Among the latter, we focused on galectin-9 which is expressed by CLL cells in patients and mice, and known as ligand for the immunoregulatory receptor TIM-3. We treated mice that had developed CLL after injection of Eµ-TCL1 leukemic cells with galectin-9 blocking antibodies and showed that this treatment slowed down disease development (Figure B).
Altogether, our study provides a detailed characterization of the T-cell compartment in CLL that helps to understand T-cell exhaustion and suggests the TIM-3 ligand galectin-9 as novel target for immunotherapy in CLL.
Original languageEnglish
Pages (from-to)1805-1806
Number of pages2
Issue numberSupplement 1
Publication statusPublished - 15 Nov 2022
Event64th Annual Meeting of the American Society of Hematology - New Orleans, Louisiana, United States
Duration: 10 Dec 202213 Dec 2022


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