Innate-like functions of natural killer T cell subsets result from highly divergent gene programs

Nat Immunol. 2016 Jun;17(6):728-39. doi: 10.1038/ni.3437. Epub 2016 Apr 18.


Natural killer T cells (NKT cells) have stimulatory or inhibitory effects on the immune response that can be attributed in part to the existence of functional subsets of NKT cells. These subsets have been characterized only on the basis of the differential expression of a few transcription factors and cell-surface molecules. Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic level and epigenomic level and by single-cell RNA sequencing. Our data indicated that despite their similar antigen specificity, the functional NKT cell subsets were highly divergent populations with many gene-expression and epigenetic differences. Therefore, the thymus 'imprints' distinct gene programs on subsets of innate-like NKT cells that probably impart differences in proliferative capacity, homing, and effector functions.

Publication types

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

MeSH terms

  • Animals
  • Antigens, CD1d / metabolism
  • Cell Movement / genetics
  • Cell Proliferation / genetics
  • Cells, Cultured
  • Epigenesis, Genetic
  • Gene Expression Regulation* / immunology
  • Immunity, Innate*
  • Jumonji Domain-Containing Histone Demethylases / metabolism
  • Lymphocyte Subsets / immunology*
  • Mice
  • Mice, Inbred BALB C
  • Mice, Inbred C57BL
  • Natural Killer T-Cells / immunology*
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Thymus Gland / immunology*
  • Transcriptome


  • Antigens, CD1d
  • Cd1d1 protein, mouse
  • Jumonji Domain-Containing Histone Demethylases
  • Kdm6b protein, mouse