Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution

Cell Rep. 2018 Oct 23;25(4):871-883. doi: 10.1016/j.celrep.2018.09.006.


Perturbations in the transcriptional programs specifying epidermal differentiation cause diverse skin pathologies ranging from impaired barrier function to inflammatory skin disease. However, the global scope and organization of this complex cellular program remain undefined. Here we report single-cell RNA sequencing profiles of 92,889 human epidermal cells from 9 normal and 3 inflamed skin samples. Transcriptomics-derived keratinocyte subpopulations reflect classic epidermal strata but also sharply compartmentalize epithelial functions such as cell-cell communication, inflammation, and WNT pathway modulation. In keratinocytes, ∼12% of assessed transcript expression varies in coordinate patterns, revealing undescribed gene expression programs governing epidermal homeostasis. We also identify molecular fingerprints of inflammatory skin states, including S100 activation in the interfollicular epidermis of normal scalp, enrichment of a CD1C+CD301A+ myeloid dendritic cell population in psoriatic epidermis, and IL1βhiCCL3hiCD14+ monocyte-derived macrophages enriched in foreskin. This compendium of RNA profiles provides a critical step toward elucidating epidermal diseases of development, differentiation, and inflammation.

Keywords: epidermis; keratinocyte; single-cell RNA-seq; skin.

Publication types

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

MeSH terms

  • Amphiregulin / pharmacology
  • Biomarkers / metabolism
  • Cell Aggregation / genetics
  • Cell Communication
  • Cell Differentiation
  • Cell Proliferation
  • Epidermis / metabolism*
  • Epidermis / pathology*
  • Foreskin / cytology
  • Hair Follicle / metabolism
  • Humans
  • Inflammation / genetics*
  • Inflammation / immunology
  • Inflammation / pathology*
  • Keratinocytes / metabolism
  • Kinetics
  • Male
  • Psoriasis / genetics
  • Psoriasis / immunology
  • Psoriasis / pathology
  • S100 Proteins / metabolism
  • Single-Cell Analysis*
  • Time Factors
  • Transcription, Genetic*
  • Transcriptome / genetics
  • Wnt Proteins / metabolism


  • Amphiregulin
  • Biomarkers
  • S100 Proteins
  • Wnt Proteins