Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

Nat Immunol. 2019 Feb;20(2):163-172. doi: 10.1038/s41590-018-0276-y. Epub 2019 Jan 14.


Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologs of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens, Differentiation, Myelomonocytic / genetics
  • Antigens, Differentiation, Myelomonocytic / immunology
  • Antigens, Differentiation, Myelomonocytic / metabolism
  • Bleomycin / immunology
  • CX3C Chemokine Receptor 1 / genetics
  • CX3C Chemokine Receptor 1 / immunology
  • CX3C Chemokine Receptor 1 / metabolism
  • Cells, Cultured
  • Disease Models, Animal
  • Female
  • Gene Expression Profiling / methods
  • Humans
  • Idiopathic Pulmonary Fibrosis / immunology*
  • Idiopathic Pulmonary Fibrosis / pathology
  • Lung / cytology
  • Lung / immunology
  • Lung / pathology*
  • Macrophage Activation*
  • Macrophages, Alveolar / immunology*
  • Macrophages, Alveolar / metabolism
  • Male
  • Mice
  • Sequence Analysis, RNA / methods
  • Sialic Acid Binding Immunoglobulin-like Lectins
  • Single-Cell Analysis / methods
  • Up-Regulation


  • Antigens, Differentiation, Myelomonocytic
  • CX3C Chemokine Receptor 1
  • CX3CR1 protein, human
  • Cx3cr1 protein, mouse
  • Sialic Acid Binding Immunoglobulin-like Lectins
  • Siglecf protein, mouse
  • Bleomycin