Single Cell Spatial Transcriptomics of the Human Bone Marrow Reveals Active Adaptive Immunity in Myelodysplastic Syndromes

Robert Stanely – Memorial Sloan Kettering Cancer Center; Beatrice Zhang – Memorial Sloan Kettering Cancer Center; Kimon Argyropoulos – Memorial Sloan Kettering Cancer Center; Brianna Gipson – Memorial Sloan Kettering Cancer Center; Kenyon Weis – Memorial Sloan Kettering Cancer Center; Alexander Lewis – Memorial Sloan Kettering Cancer Center; Zoe Katsamakis – Memorial Sloan Kettering Cancer Center; Ning Fan – Memorial Sloan Kettering Cancer Center; Catherine Snopkowski – Memorial Sloan Kettering Cancer Center; Karen Zhao – Memorial Sloan Kettering Cancer Center; Kenton Wu – Memorial Sloan Kettering Cancer Center; Yuval Elhanati – Memorial Sloan Kettering Cancer Center; Matthew Zatzman – Memorial Sloan Kettering Cancer Center; Benjamin Greenbaum – Memorial Sloan Kettering Cancer Center; Mikhail Roshal – Memorial Sloan Kettering Cancer Center; Ahmet Dogan – Memorial Sloan Kettering Cancer Center; Ronan Chaligne – Memorial Sloan Kettering Cancer Center; Umesh Bhanot – Memorial Sloan Kettering Cancer Center; Stein Eytan – Memorial Sloan Kettering Cancer Center; Marcel van den Brink – City of Hope; Omar Abdel-Wahab – Memorial Sloan Kettering Cancer Center

Abstract Text: Myelodysplastic syndromes (MDS) are malignant myeloid neoplasms defined by dysplastic growth of bone marrow populations, impaired hematopoiesis, and potential for progression to acute leukemia. While hematopoietic stem cell-intrinsic mechanisms of MDS have been rigorously analyzed, less is known about the role of the bone marrow microenvironment and adaptive immunity. To comprehensively study the human MDS microenvironment including the in situ distribution of immune populations, we built a custom targeted gene panel for spatial transcriptomic analysis of fixed, decalcified human marrow core biopsies (11 MDS, 5 controls, > 1.85x10^6 cells) paired with 5’ single-cell CITE and T cell receptor (scTCR) sequencing of 58 marrow aspirates (35 MDS patients/8 controls, >6x10^5 cells and >1.55x10^5 TCRs). Nearest neighbor analyses revealed altered cell-cell relations in the MDS marrow including increased proximity of T regulatory cells to mature B-cells and cytotoxic T-cells, evidence for large immune aggregates (clusters of B-cells, plasmacytoid dendritic cells, and T-cells) reminiscent of tertiary lymphoid structures, and enrichment of hematopoietic stem and progenitor cells within these aggregates. T-cells within immune aggregates had distinct phenotypes compared to those outside in MDS but not controls, including abundant memory T-cells with stemlike features (TCF7+). scTCR identified dominant GZMB+ memory CD8 clones in MDS compared to controls and we discovered the in situ marrow distribution of dominant TCRs via creation of clone-specific probes for paired TCR-alpha/-beta sequences. Taken together, this study reveals the distinct T-cell architecture of the MDS bone marrow microenvironment and supports a role for active T-cell immunity in the MDS marrow.