Next-generation insights into regulatory T cells: expression profiling and FoxP3 occupancy in Human

Abstract

Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4+ Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the Treg gene signature. Its ablation leads to severe immune deficiencies in human and mice. Recent developments in sequencing technologies have revolutionized the possibilities to gain insights into transcription factor binding by ChiP-seq and into transcriptome analysis by mRNA-seq. We combine FoxP3 ChiP-seq and mRNA-seq in order to understand the transcriptional differences between primary human CD4+ T helper and regulatory T-cells, as well as to study the role of FoxP3 in generating those differences. We show, that mRNA-seq allows analyzing the transcriptomal landscape of T-cells including the expression of specific splice variants at much greater depth than previous approaches, whereas 50% of transcriptional regulation events have not been described before by using diverse array technologies. We discovered splicing patterns like the expression of a kinase-dead isoform of IRAK1 upon T-cell activation. The immunoproteasome is up-regulated in both Treg and CD4+ Th cells upon activation, whereas the ‘standard’ proteasome is up-regulated in Tregs only upon activation.

Constitutive Activation of MEK1 Promotes Treg Cell Instability in Vivo

“…They found that the expression of the DUSP6 and DUSP4 phosphatases, which selectively inactivate ERK kinases, is up-regulated in Treg cells (23). Consistent with this, CD3/CD28-mediated activation of the MEK-ERK pathway is largely impaired in regulatory T-cell lines from human cord blood (39).…”

“…Stable Foxp3 expression in the progeny of Treg cells is ensured by a positive feedback loop comprising the CNS2 (also known as TSDR) region in the Foxp3 gene locus, the Cbf␤-Runx1 transcription factor, and Foxp3 itself, in which CNS2, Cbf␤-Runx1, and Foxp3 bind to each other to form a transcription complex (7,(21)(22)(23)(24). Treg cells lacking CNS2, Cbf␤, or Runx1 gradually lose or down-regulate Foxp3 expression, indicating that defects in this positive feedback loop promote Treg cell instability (21,22).…”

Primary Human Leukocyte Subsets Differentially Express Vaccinia Virus Receptors Enriched in Lipid Rafts

“…Using these criteria, a list of putative VV receptors was made according to mass spectrometry or transcriptome sequencing (RNA-seq) data available from previous studies ( Table 1). These proteins were selected based on their presence in monocyte DRMs (28), the upregulation on CD14 high CD16 Ϫ monocytes versus CD14 low CD16 ϩ monocytes (29), and the upregulation on activated T cells versus naive T cells (30).…”

Interindividual variation in human T regulatory cells

“…We have recently shown that several of these TFs make up, together with FOXP3, a genetic switch that locks in the Treg phenotype (13). The transcriptome of Treg cells has been less extensively studied in humans although early studies indicate that several of the more prominent members of the mouse Treg signature are also differentially expressed in human Treg cells (18)(19)(20).…”