Transcriptome profiling of human FoxP3+ regulatory T cells

Hum Immunol. 2016 Feb;77(2):201-13. doi: 10.1016/j.humimm.2015.12.004. Epub 2015 Dec 10.


The major goal of this study was to perform an in depth characterization of the "gene signature" of human FoxP3(+) T regulatory cells (Tregs). Highly purified Tregs and T conventional cells (Tconvs) from multiple healthy donors (HD), either freshly explanted or activated in vitro, were analyzed via RNA sequencing (RNA-seq) and gene expression changes validated using the nCounter system. Additionally, we analyzed microRNA (miRNA) expression using TaqMan low-density arrays. Our results confirm previous studies demonstrating selective gene expression of FoxP3, IKZF2, and CTLA4 in Tregs. Notably, a number of yet uncharacterized genes (RTKN2, LAYN, UTS2, CSF2RB, TRIB1, F5, CECAM4, CD70, ENC1 and NKG7) were identified and validated as being differentially expressed in human Tregs. We further characterize the functional roles of RTKN2 and LAYN by analyzing their roles in vitro human Treg suppression assays by knocking them down in Tregs and overexpressing them in Tconvs. In order to facilitate a better understanding of the human Treg gene expression signature, we have generated from our results a hypothetical interactome of genes and miRNAs in Tregs and Tconvs.

Keywords: Differentially expressed; FoxP3; Gene signature; LAYN; MiR-146a; MiR-146b; MiR-21; MiRNA; PNA; RNA sequencing; RTKN2; Suppressive cells; nCounter analysis.

Publication types

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

MeSH terms

  • Cells, Cultured
  • Forkhead Transcription Factors / metabolism
  • Gene Regulatory Networks
  • Humans
  • Immune Tolerance / genetics*
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Lectins, C-Type / genetics
  • Lectins, C-Type / metabolism
  • MicroRNAs / genetics
  • RNA, Small Interfering / genetics
  • T-Lymphocyte Subsets / immunology*
  • T-Lymphocytes, Regulatory / immunology*
  • Transcriptome*


  • FOXP3 protein, human
  • Forkhead Transcription Factors
  • Intracellular Signaling Peptides and Proteins
  • LAYN protein, human
  • Lectins, C-Type
  • MicroRNAs
  • RNA, Small Interfering
  • RTKN2 protein, human