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Acute lymphoblastic leukemia

Leukemia-induced dysfunctional TIM-3+CD4+ bone marrow T cells increase risk of relapse in pediatric B-precursor ALL patients

Abstract

Interaction of malignancies with tissue-specific immune cells has gained interest for prognosis and intervention of emerging immunotherapies. We analyzed bone marrow T cells (bmT) as tumor-infiltrating lymphocytes in pediatric precursor-B cell acute lymphoblastic leukemia (ALL). Based on data from 100 patients, we show that ALL is associated with late-stage CD4+ phenotype and loss of early CD8+ T cells. The inhibitory exhaustion marker TIM-3 on CD4+ bmT increased relapse risk (RFS = 94.6/70.3%) confirmed by multivariate analysis. The hazard ratio of TIM-3 expression nearly reached the hazard ratio of MRD (7.1 vs. 8.0) indicating that patients with a high frequency of TIM-3+CD4+ bone marrow T cells at initial diagnosis have a 7.1-fold increased risk to develop ALL relapse. Comparison of wild type primary T cells to CRISPR/Cas9-mediated TIM-3 knockout and TIM-3 overexpression confirmed the negative effect of TIM-3 on T cell responses against ALL. TIM-3+CD4+ bmT are increased in ALL overexpressing CD200, that leads to dysfunctional antileukemic T cell responses. In conclusion, TIM-3-mediated interaction between bmT and leukemia cells is shown as a strong risk factor for relapse in pediatric B-lineage ALL. CD200/TIM-3-signaling, rather than PD-1/PD-L1, is uncovered as a mechanism of T cell dysfunction in ALL with major implication for future immunotherapies.

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Fig. 1: Pediatric B-precursor ALL is associated with late stage bone marrow T cell differentiation.
Fig. 2: Expression of exhaustion marker TIM-3 on CD4+ bone marrow T cells is a risk factor for relapse of pediatric B-precursor ALL.
Fig. 3: Leukemia is associated with upregulation of TIM-3 on T cells leading to reduced activation and proliferation potential of T cells.
Fig. 4: ALL-induced upregulation of TIM-3 on CD4+ T cells is mediated by CD200.

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Acknowledgements

The authors thank the patients and their families for participating in the study. We thank Tanja Weißer, Nicola Habjan and Nadine Stoll for excellent technical assistance. This work was supported by the Elterninitiative Ebersberg, Elterninitiative Intern 3, Bettina Braeu Stiftung, Gesellschaft für KinderKrebsForschung e.V. and Dr. Sepp und Hanne Sturm Gedaechtnisstiftung. S.W. was supported by the Else-Kröner-Fresenius Stiftung and D.S. was supported by the German Cancer Research Center/German Cancer Consortium (DKTK).

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The concept was set up by T.F. Design and approach of experiments was done by F.B. and T.F. Diagnostic characterization and follow-up analyses were performed by M.H. and G.E. Statistics were done by M.Z. RNA sequencing was done by M.R., S.W., and C.K. V.B. provided patient and healthy donor samples. TIM-3 and CD200 experiments were done by F.B., M.L., D.S., S.W., and T.K. Bioinformatics were done by F.R.R. and S.C. Data analysis and manuscript preparation was done by F.B. and T.F. The manuscript was reviewed by all authors.

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Correspondence to Tobias Feuchtinger.

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Blaeschke, F., Willier, S., Stenger, D. et al. Leukemia-induced dysfunctional TIM-3+CD4+ bone marrow T cells increase risk of relapse in pediatric B-precursor ALL patients. Leukemia 34, 2607–2620 (2020). https://doi.org/10.1038/s41375-020-0793-1

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