Spatial multi-omics reveals targetable immunosuppressive macrophage T-cell interactions in human AML bone marrow
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
Summary The immunosuppressive bone marrow microenvironment is an important contributor to the limited success of immunotherapy in acute myeloid leukemia (AML), but the cellular interactions underlying AML immune evasion are incompletely understood. We therefore generated a single-cell spatial transcriptomic and proteomic atlas using 148 bone biopsies from 113 individuals comprising pediatric and adult AML at diagnosis and non-leukemic controls. We observed an expansion of regulatory T cells (Tregs) in AML, with stronger colocalization between Tregs and macrophages compared to non-leukemic bone marrow. Distinct cellular neighborhoods were enriched for myeloid progenitor-like cells together with macrophages and T cells, which correlated with higher macrophage and T cell immune checkpoint expression. Moreover, these neighborhoods were associated with specific AML subtypes, especially KMT2A -rearranged and RUNX1 :: RUNX1T1 AML. These spatial patterns were validated by identification of malignant cells via in situ fusion detection in RUNX1 :: RUNX1T1 cases. Functional experiments revealed that macrophages and AML cells not only actively recruit Tregs, but also promote naïve T cell differentiation into Tregs. Spatially informed ligand-receptor analysis predicted the involvement of the Galectin-9 – CD44/TIM-3 axis in this immunosuppressive crosstalk, which was supported by in vitro inhibition of CD44 and/or TIM-3 preventing macrophage- and AML-induced Treg differentiation. Collectively, this comprehensive spatial map of the AML bone marrow identified tripartite crosstalk between AML, macrophages, and T cells mediated by the Galectin-9 – CD44/TIM-3 axis as a key component of the immunosuppressive microenvironment. Targeting Galectin-9 – CD44/TIM-3 interactions may be a promising strategy to overcome immune evasion and enhance immunotherapeutic success in AML. Highlights Spatial transcriptomic and proteomic atlas of pediatric and adult acute myeloid leukemia (AML) bone marrow Increased colocalization of macrophages and regulatory T cells (Tregs) in AML Macrophages and AML cells induce differentiation of naïve T cells to Tregs in vitro , which can be prevented by inhibition of CD44 or TIM-3 Abstract Figure
Authors 24
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Princess Máxima Center · Erasmus MC - Sophia Children’s Hospital
Affiliation as printed
Department of Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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Princess Máxima Center · Erasmus MC - Sophia Children’s Hospital
Affiliation as printed
Department of Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Princess Máxima Center · Erasmus MC - Sophia Children’s Hospital
Affiliation as printed
Department of Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Princess Máxima Center · Erasmus MC - Sophia Children’s Hospital
Affiliation as printed
Department of Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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University Medical Center Utrecht · Princess Máxima Center
Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
University Medical Center Utrecht, Utrecht, The Netherlands
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Humboldt-Universität zu Berlin · Berlin Institute of Health at Charité - Universitätsmedizin Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Humboldt-Universität Berlin and Freie Universität Berlin, Germany
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German Cancer Research Center · Humboldt-Universität zu Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
Institute of Pathology, Charité Universitätsmedizin Berlin, corporate member of Humboldt-Universität Berlin and Freie Universität Berlin, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
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University Medical Center Utrecht · Princess Máxima Center
Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
University Medical Center Utrecht, Utrecht, The Netherlands
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Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Hendrik Veelken Aachen Department of Hematology, Leiden University Medical Center Leiden Center for Computational Oncology
Leiden University Medical Center
Affiliation as printed
Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
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Humboldt-Universität zu Berlin · Berlin Institute of Health at Charité - Universitätsmedizin Berlin · Freie Universität Berlin · Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
Department of Hematology, Oncology, and Tumor Immunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
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Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Erik van den Akker Aachen Department of Molecular Epidemiology and Leiden Computational Biology Center
Leiden University Medical Center · Delft University of Technology
Affiliation as printed
Delft Bioinformatics Lab, TU Delft, Delft, The Netherlands
Department of Molecular Epidemiology and Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
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Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Princess Máxima Center · Erasmus MC - Sophia Children’s Hospital
Affiliation as printed
Department of Pediatric Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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Olaf Heidenreich corresponding
University Medical Center Utrecht · Princess Máxima Center
Affiliation as printed
Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
University Medical Center Utrecht, Utrecht, The Netherlands
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