NicheSphere reveals SPP1+ myeloid cells as central hubs of fibrotic remodeling in myeloproliferative neoplasms

Bone marrow fibrosis in myeloproliferative neoplasms arises through reciprocal interactions between mutant hematopoietic cells and fibrosis-associated stromal populations. 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 Spp1+ macrophages as central cellular communication hubs within a "Fibrosis Interacting core" comprising osteoCAR cells, fibroblasts, megakaryocytes, and additional hematopoietic populations. NicheSphere distinguished macrophage-vascular compartments enriched in inflammatory signaling from this Fibrosis Interacting core characterized by TGFB, NF-kB, and extracellular-matrix programs. CODEX imaging confirmed increased proximity of SPP1+ immune cells, activated stromal cells, and megakaryocytes. Genetic deletion of SPP1 demonstrated complementary contributions of stromal- and hematopoietic-derived Spp1 to fibrosis, inflammation, and myeloproliferative features. Human myelofibrosis single-cell analysis identified SPP1+ cells as a prominent predicted communication hub, while elevated circulating SPP1 was associated with adverse clinical outcome. Together, these findings establish SPP1-centered multicellular communication as a conserved driver of myelofibrosis and a therapeutic vulnerability of the fibrotic niche.

All code necessary to produce the analysis figures from our article is available here. Data is avilable at: https://zenodo.org/records/21900923