Stanley, R. F.; Zhang, B. D.; Argyropoulos, K. V.; Zhang, P.; Maron, M.; Gipson, B.; Park, C.; Weis, K.; Lewis, A. M.; Katsamakis, Z.; Wishnack, C.; Cuibus, M. A.; Fan, N.; Zhao, K.; Wu, K.; Snopkowski, C.; Weinreb, J.; Biswas, J.; Zatzman, M. J.; Aleynick, N.; Boiocchi, L.; Lim, M. S.; Tamari, R.; Peled, J.; Shah, G.; Moorman, A.; Elhanati, Y.; Rosiek, E.; Roshal, M.; Dogan, A.; Bhanot, U. K.; Stein, E. M.; Samorodnitsky, S.; Chaligne, R.; van den Brink, M. R. M.; Martis, S.; Greenbaum, B. D.; Abdel-Wahab, O.; DeWolf, S.

Myelodysplastic syndromes (MDS) are clonal hematopoietic malignancies characterized by ineffective hematopoiesis, dysplastic morphology, and risk of progression to acute myeloid leukemia. While genomic alterations intrinsic to malignant MDS disease-initiating cells have been well-characterized, molecular assessment of the bone marrow in situ has been limited. Here we present single cell spatial assessment of gene expression, T cell receptors, as well as MDS-defining mutations and RNA isoforms within fixed, decalcified human bone marrow core biopsies (41 MDS, 15 controls) paired with single cell immunogenomic analysis of bone marrow aspirates (35 MDS, 6 controls). Bone marrow spatial analyses of >7.47x106 cells identified hematopoietic and non-hematopoietic populations not readily captured in dissociated tissue. We developed computational methods to compare ecological niche structures, revealing enriched hematopoietic niches and reorganization of T cell immunity in MDS patient bone marrow. In situ genotyping of mutant cells revealed increased TGF{beta} expression in malignant megakaryocytes suppressing local T cell cytotoxicity. By contrast, TGF{beta} signaling was disrupted in mutant cells due to aberrant splicing of multiple TGF{beta} signaling components. This study provides a spatially resolved landscape of human MDS bone marrow and uncovers mechanisms by which malignant cells simultaneously promote intrinsic clonal persistence while rewiring the microenvironment for immune escape.