1Department of Pathology, Harvard Medical School, Boston, Massachusetts,
USA. 2These authors contributed equally to this work. Correspondence should
be addressed to D.M. (email@example.com) or C.B. (firstname.lastname@example.org.
Published online 18 June 2009; doi:10.1038/ni.1760/
Foxp3+ regulatory T cells: differentiation,
Markus Feuerer1,2, Jonathan A Hill1,2, Diane Mathis1,2 & Christophe Benoist1,2
Regulatory T cells (Treg cells) characterized by expression of the transcription factor Foxp3 play a key role in immune homeostasis.
Rather than a monomorphic population strictly determined by Foxp3 as a ‘master regulator’, the emerging view is one of Treg cells
as a population with many levels of complexity. Several regulatory factors partake in the control of their transcriptional ‘signature’,
with Foxp3 being a key regulator but insufficient and unnecessary to specify all aspects of the lineage. Distinct subphenotypes of
Foxp3+ Treg cells are found in different anatomical locations. Some subphenotypes specifically control different facets of effector
T cell function and, perhaps surprisingly, share transcriptional control elements with the very cells they regulate. This review will
focus on these novel aspects of Treg cell diversity.
Any biological system involves negative feedback, and it is now recog-
nized that regulatory T cells (Treg cells) play key roles in the maintenance
of lymphoid homeostasis in a number of immune circumstances. These
cells maintain tolerance to self and control autoimmune deviation1,2,
prevent runaway responses to pathogens or allergens, help maintain
a balance with obligate microbial flora3, and facilitate tumors’ escape
from immune monitoring4. Although several distinct lineages may
participate in these functions, an important population was initially
identified in the mouse as CD4+CD25+ or CD4+CD45RB– and was
able to control autoimmunity elicited by thymectomy or lymphopenic
complementation5,6. A firm molecular definition for these cells came
about with the discovery that they express the forkhead–winged helix
transcription factor Foxp3 (refs. 7–10) and that deficiencies in Foxp3
underlie the lymphoproliferation and multiorgan autoimmunity of
scurfy mutant mice and human patients with immunodysregulation
polyendocrinopathy and enteropathy, X-linked (IPEX) syndrome11.
Foxp3+ Treg cells use the αβ T cell antigen receptor (TCR) for anti-
gen recognition and have a broad TCR repertoire similar in size but
largely distinct in composition relative to that of CD4+ conventional
T cells (Tconv cells)12–14. The mechanisms of action of Treg cells are
clearly pleiomorphic, and several modes and mediators of their activ-
ity that are not mutually exclusive have been described, whose relative
importance has yet to be sorted out15. Because of their fundamental
importance for immune function and because of their great potential
for therapeutic modulation, Foxp3+ Treg cells have attracted extraor-
A wide array of mice with conditional knockout of genes and mice
expressing transgenes that report Treg cell existence or function have
been constructed, and these have been the subject of intense genomic,
genetic and epigenetic investigation. More genome-wide transcriptional
profiles have been generated on Treg cells than on any other immune cell
type, which has resulted in the definition of a canonical ‘Treg signature’
that distinguishes Treg cells from Tconv cells, at least in their resting states
in lymphoid organs16–21 (Fig. 1). The Treg signature includes genes over-
expressed or repressed in Treg cells (in a proportion of 2 to 1), genes that
encode proteins with a wide range of cellular locations and functions:
cell surface receptors, signaling kinases and transcription factors. With
bioinformatic treatments that can detect fine variations, up to ~1,500
genes are found to be differentially expressed in Treg cells21, but none
or very few of these differences are absolute; instead, these variations
correspond to quantitative differences between Treg cells and Tconv cells.
Nor are they specific, as almost all transcripts overexpressed in Treg
cells can also be found in non–T cell lineages. A fraction of these Treg
signature genes have also been identified in chromatin immunoprecipi-
tation experiments with antibody to Foxp3 (refs. 22,23). However, the
overlap between differentially expressed genes and Foxp3-bound genes
is not absolute, in part because of the technical limitations of chromatin
immunoprecipitation and in part because Foxp3 does not control all
aspects of the Treg signature (discussed below).
Differentiation and specification in the thymus
Two origins have been described for Foxp3+ cells, whose numeric and
functional importance remain a matter of debate. The first is the thy-
mus, where Foxp3+ cells are generated roughly in sync with positive
selection of conventional CD4+ T cells. The second is the periphery,
where a number of triggers induce the expression of Foxp3 in Tconv
cells; we will refer to this event as ‘conversion’, avoiding the ‘natural
versus adaptive’ terminology, which could lead to the mistaken belief
that some Treg cells would be unnatural or innate (which is untrue, as
all Treg cells express rearranged antigen receptors that define adaptive
lymphocytes). We will first deal with the establishment and transcrip-
tional control of the thymus-derived population before considering the
generation and function of converted Treg cells.
nature immunology volume 10 number 7 july 2009
© 2009 Nature America, Inc. All rights reserved.
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