NicheSphere reveals an Spp1-centered multicellular niche in myeloproliferative neoplasm-associated fibrosis

Bone marrow fibrosis in myeloproliferative neoplasms arises through reciprocal interactions between mutant hematopoietic cells and fibrosis-associated stromal populations. Here, using dual lineage tracing, single-cell and multiplet RNA sequencing, spatial proteomics, and NicheSphere, a framework integrating condition-specific co-localization with ligand-receptor inference, we identified an Spp1-centered multicellular “fibrosis-interacting core.” NicheSphere distinguished macrophage-vascular compartments from the “fibrosis-interacting core.” CODEX imaging confirmed increased proximity of SPP1+ immune cells, activated stromal cells, and megakaryocytes. Genetic deletion of Spp1 in mice demonstrated complementary functional contributions from stromal and hematopoietic compartments, supporting Spp1 as a multicellular mediator of fibrosis, inflammation, and myeloproliferative features. Human myelofibrosis single-cell analysis identified SPP1+ cells as prominent communication hubs, while elevated circulating SPP1 was associated with adverse clinical outcome. Together, these findings define SPP1-centered multicellular communication as a conserved feature of the fibrotic niche and identify SPP1-associated signaling as a potential therapeutic vulnerability in myelofibrosis.