Human and Mouse Transcriptome Profiling Identifies Cross-Species Homology in Pulmonary and Lymph Node Mononuclear Phagocytes

Cell Rep. 2020 Nov 3;33(5):108337. doi: 10.1016/j.celrep.2020.108337.


The mononuclear phagocyte (MP) system consists of macrophages, monocytes, and dendritic cells (DCs). MP subtypes play distinct functional roles in steady-state and inflammatory conditions. Although murine MPs are well characterized, their pulmonary and lymph node (LN) human homologs remain poorly understood. To address this gap, we have created a gene expression compendium across 24 distinct human and murine lung and LN MPs, along with human blood and murine spleen MPs, to serve as validation datasets. In-depth RNA sequencing identifies corresponding human-mouse MP subtypes and determines marker genes shared and divergent across species. Unexpectedly, only 13%-23% of the top 1,000 marker genes (i.e., genes not shared across species-specific MP subtypes) overlap in corresponding human-mouse MP counterparts. Lastly, CD88 in both species helps distinguish monocytes/macrophages from DCs. Our cross-species expression compendium serves as a resource for future translational studies to investigate beforehand whether pursuing specific MP subtypes or genes will prove fruitful.

Keywords: dendritic cells; human; lung; macrophages; monocytes; mononuclear phagocytes; pulmonary.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Animals
  • Antigens, CD1 / metabolism
  • Biomarkers / metabolism
  • Cell Lineage
  • Cell Membrane / metabolism
  • Dendritic Cells / metabolism
  • Female
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Humans
  • Lung / cytology*
  • Lymph Nodes / cytology*
  • Macrophages / metabolism
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Monocytes / metabolism
  • Phagocytes / metabolism*
  • RNA / isolation & purification
  • Species Specificity


  • Antigens, CD1
  • Biomarkers
  • RNA