NicheSphere reveals Spp1⁺ macrophages as central hubs coordinating fibrotic remodeling in myeloproliferative neoplasms

Abstract Bone marrow fibrosis in myeloproliferative neoplasms arises from interactions between mutant hematopoietic clones and fibrosis-driving stromal cells. We identify Spp1⁺ macrophages as central “communication hubs” integrating inflammatory and fibrotic programs via spatial proximity, ECM signaling, and cytokine activation. Using dual lineage-tracing, single-cell and multiplet RNA-sequencing, and a novel computational method for cell-colocalization and communication analysis named NicheSphere, we show that Spp1⁺ macrophages form core communication hubs with osteoCAR cells, fibroblasts, and megakaryocytes. NicheSphere uncovered two distinct niches: macrophage-enriched compartments driving WNT, JAK-STAT, and TNFα cytokine signaling, and a fibrosis-interacting core enriched in TGF-β and ECM glycoproteins. Genetic ablation revealed cooperative roles of stromal and hematopoietic Spp1 in sustaining fibrosis and inflammation. Mechanistically, SPP1 promoted integrin-mediated adhesion, IL-1β secretion, and stromal activation, while IL-1 cytokines induced Spp1 and collagen expression. Loss of Spp1 in hematopoietic progenitors reduced inflammation and restored macrophage function, establishing SPP1⁺ macrophages as therapeutic targets in progressive bone marrow fibrosis.