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

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 condition specific cell-colocalization and communication tool named NicheSphere, we show that Spp1⁺ macrophages form core communication hubs with osteoCAR cells, fibroblasts, and megakaryocytes. This repository contains physically interacting cells datasets related to these results and the code used to produce them. Final data files are in the "final_data" folder: adata_singlets_final.h5ad Singlets data with final cell type names in the metadata "annotation" column (processing done in Python in PIC_data.ipynb) adata_singlets_final_imp.h5ad (MAGIC) Imputated singlets data with final cell type names in the metadata "annotation" column (processing done in Python in PIC_data.ipynb) adata_doublets_final.h5ad Doublets data with final doublet cluster annotation in in the metadata "max_pair" column (processing done in Python in PIC_data.ipynb) adata_doublets_final_imp.h5ad (MAGIC) Imputated doublets data with final doublet cluster annotation in the metadata "max_pair" column (processing done in Python in PIC_data.ipynb) Phenotype (TPO or EV) is indicated in the metadata "stage" columns for these datasets. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Other intermediate data files which were used in the scripts can be found in the folders "rds" and "h5ad" and are described in the README files in each of these folders. Analysis code is in the "code" folder and resulting data files and images are located in folders "res_data" and "figures" respectively. Database related files are in the "csv" folder, as well as files related to doublets annotation (BayesPrism deconvolution results).