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

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’ comprising osteoCAR cells, fibroblasts, megakaryocytes and additional hematopoietic populations, in which Spp1⁺ myeloid cells occupied a central communication position.

NicheSphere distinguished macrophage–vascular compartments enriched in inflammatory signaling from this “Fibrosis interacting core” characterized by TGF-β, NF-κB, and extracellular-matrix programs. CODEX imaging confirmed increased proximity of SPP1⁺ immune cells, activated stromal cells, and megakaryocytes. Genetic deletion of Spp1 demonstrated complementary functional contributions from stromal and hematopoietic compartments, supporting Spp1 as a multicellular mediator of fibrosis, inflammation and myeloproliferative features rather than a macrophage-restricted effector..