Nature Immunology
6, 10 - 12 (2005)
doi:10.1038/ni0105-10
Sliding doors in the immune responseFederica Sallusto1
& Steven L Reiner21 Federica Sallusto is at the Institute for Research in Biomedicine, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland. federica.sallusto@irb.unisi.ch 2 Steven L. Reiner is at the Abramson Family Cancer Research Institute of the University of Pennsylvania, Philadelphia, Pennsylvania, USA. sreiner@maie.med.upenn.edu When confronted with a pathogen, the immune system must develop the appropriate type of immune response. Recent work provides new insight into how regulated gene activation and silencing occurs in helper T cells.A naive helper T cell is initially ignorant of whether it will help defend its host against a tiny intracellular protozoan or a large intestinal helminth. When confronted by a pathogen, it rapidly abandons its indecisiveness and begins to generate either a polarized population of daughter cells that secrete large amounts of interferon- (IFN-) but not interleukin 4 (IL-4) or a population of daughter cells that secrete large amounts of IL-4, IL-5 and IL-13 but not IFN-. This important cellular decision-making process is determined by cytokines and other cues that the pathogen elicits from cells of the innate immune system, and it results in a restricted, heritable pattern of gene expression in daughter T cells.
The mechanisms that control and maintain differentiation of effector T cells have been investigated for close to 20 years. A quartet of recent papers in Nature Immunology1,
2,
3,
4 are now helping to shed light on some of its enduring mysteries. Together, these studies do more than serve up heaping portions of mechanistic detail about regulated gene expression. Their insights are likely to spark innovative strategies for changing the class of an immune response, before or after it has begun.
In recent years, it has become increasingly appreciated that covalent modifications of DNA and histones, as well as the three-dimensional structure of chromatin fibers and chromosomes, can influence eukaryotic gene activity5. This regulation is likely to occur both in normal development and homeostasis and in pathological situations, such as the silencing of tumor suppressor genes that might lead to cancerous transformation. As a result of the efforts of numerous laboratories in the past few years, there is an emerging view that the spectacle of regulated gene activity in helper T cell differentiation is, indeed, intimately linked to the way in which lineage-specific loci are marked, packaged and positioned6,
7. Yet how the genome is filed and arranged, and how a specific arrangement could be seamlessly propagated during cell division, which T cells must often do, has remained enigmatic.
In naive T cells, the genes encoding the effector cytokines, IFN- for TH1 cells and the trio of IL-4, IL-5, and IL-13 for TH2 cells, exist in a restrictive chromatin configuration that is not completely silent but rather poised for some rapid, albeit submaximal, activity upon antigen stimulation6,
7. Ifng seems to be remodeled owing to lineage-restricted transcription factors such as T-bet and Hlx. Il4, the most studied of the TH2 cytokine cluster, also seems to be regulated at the level of chromatin, by factors such as GATA-3. How each selected cytokine gene is remodeled in an active way, and how the forbidden cytokine gene (Ifng in TH2 cells and Il4 in TH1 cells) is made more silent in the transition from naive to mature effector cells, are not fully understood.
The new papers on this subject point to several important details of the ways in which activity of the TH2 cytokine genes are (i) established (ii) maintained or (iii) silenced (Fig. 1). An analysis of the long-range intrachromosomal interactions of the TH2 cytokine cluster reveals that the promoters are closely apposed to an important cis-acting sequence, the TH2 cytokine locus control region (LCR)2 (Fig. 1). The looping depends on the LCR4, which, curiously, is not within the gene body encoding either of the three cytokines, but rather in the interspersed Rad50 gene. The looping is also regulated by STAT6 and GATA-3 (ref. 2). This chromatin looping provides a satisfying explanation for how cytokines within the TH2 cluster can be coordinately regulated, despite one of the three being at a great distance from the others (more than 100 kb apart). Remarkably the poised chromatin state of TH2 cytokine genes is similar in naive, TH1, and TH2 cells. Thus, the decision to transcribe these cytokines seems to depend on additional lineage-specific factors, post-translational modifications of histones, and local chromatin decondensation (Fig. 1).
 | | Figure 1. Establishing and maintaining lineage-defining gene activity during T cell differentiation. | | |  | A speculative model of how the type 2 cytokines, IL-4, IL-5 and IL-13, become induced or repressed during TH2 and TH1 differentiation, respectively. In naive (blue), TH1 (red) and TH2 (green) configurations, the three distant cytokine promoters are looped into proximity of the TH2 locus control region within the lineage-nonspecific Rad50 gene. STAT6 and GATA-3 are sequence-specific activators that control induction of chromatin remodeling for the establishment of the transcriptionally permissive state of the locus. As subsequent generations of the TH2 lineage arise, maintenance of the overall permissive state seems to become independent of both inducing activators. In mature TH2 cells, GATA-3 is still required to trans-activate the Il5 and Il13 promoters, while other transcription factors, such as NFAT and c-Maf, are likely to drive the Il4 promoter. During TH1 differentiation, a sequence next to Il4 acts as a silencer that is necessary to repress Il4 expression in TH1 cells. The sequence-specific repressor acting at the silencer has not been yet identified, and it is not clear whether this repression ever becomes heritable or stably independent of the initial repressor silencer interaction. Although this cartoon depicts the type 2 cytokines, similar processes of successive epigenetic induction and silencing is thought to occur at the Ifng locus in TH1 and TH2 cells, respectively.
 Full Figure and legend (14K) |
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On the basis of its pattern of expression and on over-expression studies, it was assumed that GATA-3 had a role in establishing TH2 fate6,
7. Now, conditional gene deletion of Gata3 has, indeed, been shown to compromise induction of IL-4, IL-5 and IL-13 activity in developing TH2 cells (as well as proliferation of the TH2 lineage) both in vitro and in vivo1 (Fig. 1). Mice engineered to delete Gata3 during T cell activation in vivo cannot reject parasitic helminths or produce IL-4 and immunoglobulin E (IgE). Notably, in established TH2 cells GATA-3 seems dispensable to maintaining IL-4 activity but is essential for reiteration of IL-5 and IL-13.
A similar situation of conditional requirement for an inducing activator has been suggested to exist during TH1 differentiation, where it seems that establishment of transcriptional competence of Ifng requires T-bet activity, but maintenance of the permissive state may not8. Taken together, these studies are consistent with a model in which T-bet and GATA-3 are required to establish but not maintain permissive chromatin structure for the Ifng and Il4 loci, respectively. Why some lineage-specific genes of TH1 and TH2 cells may remain dependent on continuous expression of fate-determining transcription factors, while others do not, is currently uncertain, but this diversity in stabilization strategies may explain some of the apparent heterogeneity in the stages or subsets of memory T cells9.
In addition to induction of genes, TH1 and TH2 maturation seems to also involve silencing of the unselected potential repertoire10. Now, a conserved sequence downstream of the Il4 gene body, termed the Il4 silencer, has been implicated in controlling repression of Il4 in TH1 cells3 (Fig. 1). When this regulatory element was deleted from the germline of mice, it was discovered that developing TH1 cells misexpressed the forbidden cytokine, IL-4, in addition to expressing the selected cytokine, IFN-. Of importance, mice harboring deletion of the silencer exhibit defective resistance to an intracellular parasite, Leishmania major.
In the forbidden TH1 lineage, the locus of TH2 cytokines seems to remain in a poised, looping configuration, without obvious spread of nonpermissive chromatin around the Il4 silencer2,
3,
11 (Fig. 1). This lack of global restriction in the TH2 cytokine cluster might support a model in which Il4 is actively repressed, rather than irrevocably silenced, in the forbidden lineage. Such a model might also be consistent with the finding that TH1 cells can be reprogrammed to express IL-4 as well as IFN-12. The molecular nature of the repressor(s) targeting the Il4 silencer, however, remains to be determined. Whether the repression involves continual sequence-specific repressor-chromatin interaction, or can be propagated in a heritable way in the absence of the repressor, is still uncertain (Fig. 1).
Why have a system in place for making regulated changes in gene activity become progressively less dependent on an inducing activator or an initiating repressor? One could imagine that the clonal descendants of TH1 or TH2 cells, as they move through the body, might become spatially and temporally separated from some signal that was critical to mobilize an initial activator or repressor. A system that could lock in the activation or the silence of a gene could be a useful way of remembering the inductive milieu. By contrast, there might be some regulatory advantage to giving the clonal descendants some freedom to modify an original decision. Thus, it is likely that epigenetic mechanisms will maintain some but not all regulated changes in gene activity, thus permitting more imprinted and more flexible attributes within the same cell.
In conclusion, these studies and their extensions should provide a framework for understanding the very nature of polarity and plasticity of helper T cell fates at different stages of immunity and in different species. These papers also illustrate that helper T cell effector fate, which can be studied in vitro and in vivo, can provide a paradigm for regulated and heritable alterations of gene activity. The feasibility of investigating these issues using immunological model systems should make for exciting advances in an area that is likely to be relevant across many biological systems, physiological and pathological. Furthermore, a deeper understanding of our genomic filing systems should offer new therapeutic strategies to alter apparently fixed cell fates, in the immune system and elsewhere.
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