A study using single-cell RNA sequencing (scRNA-seq) identified a transitional profibrotic macrophage in bleomycin-induced lung fibrosis. The macrophage, characterized by CX3CR1+ and SiglecF+ markers, localized to the fibrotic niche and exhibited a profibrotic effect in vivo. These macrophages were found to be associated with fibrosis in human idiopathic pulmonary fibrosis patients. The study used a computational tool, SingleR, to annotate and cluster macrophages based on reference transcriptomes, revealing a transitional gene expression profile between monocyte-derived and alveolar macrophages. These transitional macrophages were shown to drive fibroblast proliferation through the secretion of PDGF-AA, a key factor in fibrosis. The study also demonstrated that ablation of these macrophages prevented lung fibrosis, highlighting their critical role in the fibrotic response. The findings suggest that these transitional macrophages are essential for fibrogenesis and provide new insights into myeloid-mesenchymal crosstalk in response to injury. The study underscores the importance of reference-based annotation in understanding macrophage heterogeneity and their functional roles in disease.A study using single-cell RNA sequencing (scRNA-seq) identified a transitional profibrotic macrophage in bleomycin-induced lung fibrosis. The macrophage, characterized by CX3CR1+ and SiglecF+ markers, localized to the fibrotic niche and exhibited a profibrotic effect in vivo. These macrophages were found to be associated with fibrosis in human idiopathic pulmonary fibrosis patients. The study used a computational tool, SingleR, to annotate and cluster macrophages based on reference transcriptomes, revealing a transitional gene expression profile between monocyte-derived and alveolar macrophages. These transitional macrophages were shown to drive fibroblast proliferation through the secretion of PDGF-AA, a key factor in fibrosis. The study also demonstrated that ablation of these macrophages prevented lung fibrosis, highlighting their critical role in the fibrotic response. The findings suggest that these transitional macrophages are essential for fibrogenesis and provide new insights into myeloid-mesenchymal crosstalk in response to injury. The study underscores the importance of reference-based annotation in understanding macrophage heterogeneity and their functional roles in disease.