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Transcription Factors and CD4 T Cells Seeking Identity: Masters, Minions, Setters and Spikers.
Abstract
Naïve T cells differentiate and become distinct subsets in response to changes in the cytokine milieu. Such specialization arises due to a complex and dynamic utilization of cis-regulatory enhancer elements. In this brief essay, we review recent findings on the relative contributions of sensors of the cytokine milieu, especially the STAT family transcription factors, 'master regulators', and other transcription factors in the enhancer architecture of T cells. These findings provide new insights into how signal transduction impinges upon the genome. This article is protected by copyright. All rights reserved.
... Naive CD4+ T cells (Th0) are activated when they recognize an antigen in a secondary lymphoid organ. Depending on the cytokine milieu and other signals in their micro-environment, CD4+ T cells attain different cell fates [2,[4][5][6][7] . Nonetheless , we still do not have a complete understanding of the dynamic mechanisms underlying CD4+ T cell differentiation and plasticity [5]. ...
... iTreg and Tfh cells can independently develop into other CD4+ T cell types, and they can be derived from Th1, Th2 or Th17 cells [28][29][30]. The differentiation and plasticity of CD4+ T cells depends on the interactions among the cytokines produced by other immune cells, epithelial cells, adipocytes, or by the CD4+ T cells themselves; the transduction of those signals and the regulation of this signaling by suppressors of cytokine signalling (SOCS) proteins; the set of transcription factors expressed inside the cells; epigenetic regulation; certain metabolites; and also microRNAs [4,6,[31][32][33]. Given the Fig 1.Differentiation and plasticity of CD4+ T cell types. ...
... In the proposed regulatory network, the nodes represent the regulatory components of the network and the links the interactions among them (S1 Table and S1 Fig).Given the complexity of the network, we simplified the model by removing intermediate components along a network path (S1 File) following a method proposed in [44] and checked the consistency of the reduced network using GINsim [45]. The predicted cell phenotypes arising from the steady states of the network are consistent with the available experimental data [2,[4][5][6][7] . The model assumes that all interactions are synchronous , that all cytokine receptors are present, and that the TCR and its cofactors are activated (being unable to model unactivated and anergic CD4+ T cells). ...
CD4+ T cells orchestrate the adaptive immune response in vertebrates. While both experimental and modeling work has been conducted to understand the molecular genetic mechanisms involved in CD4+ T cell responses and fate attainment, the dynamic role of intrinsic (produced by CD4+ T lymphocytes) versus extrinsic (produced by other cells) components remains unclear, and the mechanistic and dynamic understanding of the plastic responses of these cells remains incomplete. In this work, we studied a regulatory network for the core transcription factors involved in CD4+ T cell-fate attainment. We first show that this core is not sufficient to recover common CD4+ T phenotypes. We thus postulate a minimal Boolean regulatory network model derived from a larger and more comprehensive network that is based on experimental data. The minimal network integrates transcriptional regulation, signaling pathways and the micro-environment. This network model recovers reported configurations of most of the characterized cell types (Th0, Th1, Th2, Th17, Tfh, Th9, iTreg, and Foxp3-independent T regulatory cells). This transcriptional-signaling regulatory network is robust and recovers mutant configurations that have been reported experimentally. Additionally, this model recovers many of the plasticity patterns documented for different T CD4+ cell types, as summarized in a cell-fate map. We tested the effects of various micro-environments and transient perturbations on such transitions among CD4+ T cell types. Interestingly, most cell-fate transitions were induced by transient activations, with the opposite behavior associated with transient inhibitions. Finally, we used a novel methodology was used to establish that T-bet, TGF-β and suppressors of cytokine signaling proteins are keys to recovering observed CD4+ T cell plastic responses. In conclusion, the observed CD4+ T cell-types and transition patterns emerge from the feedback between the intrinsic or intracellular regulatory core and the micro-environment. We discuss the broader use of this approach for other plastic systems and possible therapeutic interventions.
... They achieve their impact not only through direct regulation of effector genes but also through positive and negative cross-regulation of collaborating and antagonistic factors, respectively, in a gene regulatory network. EBF1 and Pax5 are powerful regulators of B-cell development, Th-POK (Zbtb7b) is a powerful regulator of CD4 + T cell development, whereas for effector subtype specialization of CD4 + T cells, T-bet, GATA-3, RORγt and Foxp3 are the signature regulators of Th1, Th2, Th17, and Treg cells, respectively (rev. in [9,[24][25][26]). ...
... However, at the mechanistic level, EBF1 and Pax5 work collaboratively with other transcription factors such as E2A, which is not B-cell specific. The same requirement for combinatoriality tempers the roles of all "master regulator" candidates [9,24,25]. This is particularly true for the CD4 + T cell subset regulatory factors, GATA-3, T-bet, RORγt, and Foxp3. ...
... However, functional cooperativity can also emerge at cisregulatory elements where transcription factors bind separately in time. For example, one factor can bind initially as a "pioneer" and await the advent of others that eventually complete the quorum for enhancer or promoter activity [22,24,48,56,57]. Thus, without a needed partner, a factor may be unable to make a particular cis-regulatory element work even when it does bind. ...
T cell development from multipotent progenitors to specialized effector subsets of mature T cells is guided by the iterative action of transcription factors. At each stage, transcription factors interact not only with an existing landscape of histone modifications and nucleosome packing, but also with other bound factors, while they modify the landscape for later-arriving factors in ways that fundamentally affect the control of gene expression. This review covers insights from genome-wide analyses of transcription factor binding and resulting chromatin conformation changes that reveal roles of cytokine signaling in effector T cell programming, the ways in which one factor can completely transform the impacts of previously bound factors, and the ways in which the baseline chromatin landscape is established during early T cell lineage commitment.
... (3) the epigenetic regulation of immune cell memory [109,110]; (4) the epigenetic molecular study of CD4 T-cells [111][112][113][114][115][116][117][118][119][120]; (5) super enhancers [117,121,122]; (6) the function of noncoding RNAs (ncRNAs) [123,124]; and (7) the epigenetic repression or imprinting (DNA methylation) on the human endogenous retroviruses (HERVs) [98,125,126]. ...
... Such a primed cell enhancer allows CD4 T-cells to rapidly differentiate into effector cells upon encounter with the HIV. The antigen specific differentiation of immune cells by primed enhancers or promoters is dubbed the poised ones, and is well studied in the immunology [110][111][112][113][114][115][116][117][118]121,122]. ...
The duel between humans and viruses is unending. In this review, we examine the HIV RNA in the form of un-translated terminal region (UTR), the viral DNA in the form of long terminal repeat (LTR), and the immunity of human DNA in a format of epigenetic regulation. We explore the ways in which the human immune responses to invading pathogenic viral nucleic acids can inhibit HIV infection, exemplified by a chromatin vaccine (cVaccine) to elicit the immunity of our genome—epigenetic immunity towards a cure.
... Similar studies providing a comparative epigenetic landscape for CD4 + Th cell subsets, generated by in vitro polarization and directly ex vivo from a range of disease states, reveal dynamic changes in DNA and histone modifications as Th cells differentiate and have recently been reviewed (Tripathi and Lahesmaa 2014;Bonelli et al., 2014;Vahedi et al., 2013). Notably, the presence of H3K4me3 and H3K27me3 modifications that indicate a potential for both activation and repression at key regulatory sites of LDTF in differentiated Th cells provides insight into the substantial plasticity observed between distinct Th cell subsets ( Figure 1A). ...
... Notably, the presence of H3K4me3 and H3K27me3 modifications that indicate a potential for both activation and repression at key regulatory sites of LDTF in differentiated Th cells provides insight into the substantial plasticity observed between distinct Th cell subsets ( Figure 1A). Observations that many of the Th cell subset-distinct enhancer landscapes established in response to external stimuli such as cytokines are regulated by STAT family TFs and not LDTFs emphasize that differentiation is regulated not only by expression of key TFs but also by accessibility of regulatory elements for which the landscape may be remodeled in response to triggering of environmental sensors (Bonelli et al., 2014;Tripathi and Lahesmaa, 2014;Vahedi et al., 2013). ...
Recognition of pathogens by innate and adaptive immune cells instructs rapid alterations of cellular processes to promote effective resolution of infection. To accommodate increased bioenergetic and biosynthetic demands, metabolic pathways are harnessed to maximize proliferation and effector molecule production. In parallel, activation initiates context-specific gene-expression programs that drive effector functions and cell fates that correlate with changes in epigenetic landscapes. Many chromatin- and DNA-modifying enzymes make use of substrates and cofactors that are intermediates of metabolic pathways, providing potential cross talk between metabolism and epigenetic regulation of gene expression. In this review, we discuss recent studies of T cells and macrophages supporting a role for metabolic activity in integrating environmental signals with activation-induced gene-expression programs through modulation of the epigenome and speculate as to how this may influence context-specific macrophage and T cell responses to infection.
... Effector programs depend on an endogenous transcriptional regulatory state that sets the default gene expression preference of the cells, plus specific real-time interactions with STAT (signal transducers and activators of transcription) family factors that convey dynamic signals to the nucleus from most different kinds of cytokine receptors. STAT factors collaborate with stably expressed factors in the cells to define the set of enhancers across the genome that are available for activation at any given time (Vahedi, Kanno, Sartorelli, & O'Shea, 2013;Vahedi et al., 2012). Actual transcription of the effector genes is then triggered by signals through the T-cell receptor, which are mediated by stereotypical signal transduction factors of the NF-κB, NFAT, and AP-1 families. ...
... The sustained regulatory states that distinguish Th cells of different classes from each other between bouts of stimulation are defined by specific "lineage-determining" factors (sometimes romantically called "master regulators"). Each effector subclass is characterized by at least one of these stably expressed lineage-determining transcription factors and at least one specific type of growth factor receptor capable of mobilizing the right STATs to collaborate with the lineage-determining factors (Murphy & Stockinger, 2010;O'Shea & Paul, 2010;Oestreich & Weinmann, 2012;Vahedi et al., 2013). Thus, very broadly, the Th1 state is characterized by T-bet collaborating with STAT1 and STAT4, the Th2 state is characterized by GATA-3 collaborating with STAT6, the Th17 state by RORγt (Rorc isoform) collaborating with STAT3, the Tfh state by Bcl6 collaborating with STAT3, and the Treg state by Foxp3 supported by STAT5. ...
T-lymphocyte development branches off from other lymphoid developmental programs through its requirement for sustained environmental signals through the Notch pathway. In the thymus, Notch signaling induces a succession of T-lineage regulatory factors that collectively create the T-cell identity through distinct steps. This process involves both the staged activation of T-cell identity genes and the staged repression of progenitor-cell-inherited regulatory genes once their roles in self-renewal and population expansion are no longer needed. With the recent characterization of innate lymphoid cells (ILCs) that share transcriptional regulation programs extensively with T-cell subsets, T-cell identity can increasingly be seen as defined in modular terms, as the processes selecting and actuating effector function are potentially detachable from the processes generating and selecting clonally unique T-cell receptor structures. The developmental pathways of different classes of T cells and ILCs are distinguished by the numbers of prerequisites of gene rearrangement, selection, and antigen contact before the cells gain access to nearly common regulatory mechanisms for choosing effector function. Here, the major classes of transcription factors that interact with Notch signals during T-lineage specification are discussed in terms of their roles in these programs, the evidence for their spectra of target genes at different stages, and their cross-regulatory and cooperative actions with each other. Specific topics include Notch modulation of PU.1 and GATA-3, PU.1-Notch competition, the relationship between PU.1 and GATA-3, and the roles of E proteins, Bcl11b, and GATA-3 in guiding acquisition of T-cell identity while avoiding redirection to an ILC fate.
... Effector programs depend on an endogenous transcriptional regulatory state that sets the default gene expression preference of the cells, plus specific real-time interactions with STAT (signal transducers and activators of transcription) family factors that convey dynamic signals to the nucleus from most different kinds of cytokine receptors. STAT factors collaborate with stably expressed factors in the cells to define the set of enhancers across the genome that are available for activation at any given time (Vahedi et al., 2013;Vahedi et al., 2012). Actual transcription of the effector genes is then triggered by signals through the T-cell receptor, which are mediated by stereotypical signal transduction factors of the NF-κB, NFAT, and AP-1 families. ...
... The sustained regulatory states that distinguish Th cells of different classes from each other between bouts of stimulation are defined by specific "lineage-determining" factors (sometimes romantically called "master regulators"). Each effector subclass is characterized by at least one of these stably expressed lineage determining transcription factors and at least one specific type of growth factor receptor capable of mobilizing the right STATs to collaborate with the lineage determining factors (Murphy and Stockinger, 2010;O'Shea and Paul, 2010;Oestreich and Weinmann, 2012;Vahedi et al., 2013). Thus, very broadly, the Th1 state is characterized by T-bet collaborating with STAT1 and STAT4, the Th2 state is characterized by GATA-3 collaborating with STAT6, the Th17 state by RORγt (Rorc isoform) collaborating with STAT3, the Tfh state by Bcl6 collaborating with STAT3, and the Treg state by Foxp3 supported by STAT5. ...
T-lymphocyte development branches off from other lymphoid developmental programs through its requirement for sustained environmental signals through the Notch pathway. In the thymus, Notch signaling induces a succession of T-lineage regulatory factors that collectively create the T-cell identity through distinct steps. This process involves both the staged activation of T-cell identity genes and the staged repression of progenitor-cell-inherited regulatory genes once their roles in self-renewal and population expansion are no longer needed. With the recent characterization of innate lymphoid cells (ILCs) that share transcriptional regulation programs extensively with T-cell subsets, T-cell identity can increasingly be seen as defined in modular terms, as the processes selecting and actuating effector function are potentially detachable from the processes generating and selecting clonally unique T-cell receptor structures. The developmental pathways of different classes of T cells and ILCs are distinguished by the numbers of prerequisites of gene rearrangement, selection, and antigen contact before the cells gain access to nearly common regulatory mechanisms for choosing effector function. Here, the major classes of transcription factors that interact with Notch signals during T-lineage specification are discussed in terms of their roles in these programs, the evidence for their spectra of target genes at different stages, and their cross-regulatory and cooperative actions with each other. Specific topics include Notch modulation of PU.1 and GATA-3, PU.1-Notch competition, the relationship between PU.1 and GATA-3, and the roles of E proteins, Bcl11b, and GATA-3 in guiding acquisition of T-cell identity while avoiding redirection to an ILC fate.
... Thus, the differentiation of naı¨venaı¨ve CD4 ? T-cells into T H 2 and other subsets of T helper cells is driven by their ability to sense the cytokine milieu around them and activate mainly signal transducer and activator of transcription (STAT) signaling pathways [16]. Differentiation into T H 2 cells is thus dependent on IL-2, IL-4, and antigen stimulation and subsequent STAT5 and STAT6 activation, which leads to the upregulation of the transcription factor GATA-binding protein 3 (GATA-3) [17][18][19]. ...
... Differentiation into T H 2 cells is thus dependent on IL-2, IL-4, and antigen stimulation and subsequent STAT5 and STAT6 activation, which leads to the upregulation of the transcription factor GATA-binding protein 3 (GATA-3) [17][18][19]. GATA-3 is the T H 2 master regulator that is capable of inducing and enhancing the production of the signature T H 2 cytokines IL-4, IL-5, and IL-13 from the differentiated T helper cells [15,16]. Similarly, the T-box transcription factor Tb921 (T-bet) and retinoic acid receptor-related orphan receptor ct (RORct) are the master regulators for T H 1 and T H 17 differentiation, respectively [20,21]. ...
Background:
In the respiratory mucosa, interleukin (IL)-33, has been shown to enhance T helper 2 (TH2)-type responses through the master regulatory gene GATA-3. IL-33 is upregulated in ulcerative colitis (UC), and the aim was to assess if IL-33 holds a similar key position in the shaping of the immune response in experimental colitis (piroxicam-accelerated colitis (PAC) in IL-10 (-/-) mice, dextran sodium sulfate (DSS) model) and UC.
Methods:
Colonic IL-33 expression was determined in UC (8 active UC, 8 quiescent UC, and 7 controls) and experimental colitis. Mesenteric lymph node (MesLN) T cells were isolated from PAC IL-10 (-/-) mice and stimulated with IL-33.
Results:
The colonic IL-33 expression was significantly upregulated all forms of colitis (P < 0.01) and correlated with disease severity score and inflammation (P < 0.001), and with GATA-3 expression levels (P < 0.01); no correlation with the TH1-specific T-bet expression was observed. MesLN T cells stimulated with IL-33 had increased GATA-3 expression, and showed an IL-33 dose-dependent increase in secreted TH2-type cytokines, whereas this effect was abolished by blocking IL-33 signaling. The non-TH2-type cytokine IL-17 was upregulated by IL-33 but in a T cell receptor dependent manner, as opposed to TH2-type cytokines, which required only IL-33 stimulation.
Conclusions:
The study demonstrates that intestinal IL-33 is capable of inducing GATA-3 in mucosal T cells, and suggests that IL-33 is a key mediator of pathological TH2 and non-TH2-type responses in intestinal inflammation. Blocking IL-33 signaling could be a feasible option in the treatment of UC.
... Популяция Т-хелперов (T helper, Th) включает как минимум шесть эффекторных субпопуляций Т-лимфоцитов, характеризующихся устойчивым набором секретируемых цитокинов и участвующих в активации различных звеньев иммунной системы -Th1, Th2, Th17, Th9, Th22, и фолликулярные Т-хелперы [1,2]. В противоположность эффекторным Т-хелперам, основной задачей регуляторных Т-клеток (Treg) является избирательное ограничение активности эффекторных Т-лимфоцитов (как Т-хелперов, так и цитотоксических Т-лимфоцитов), что обеспечивает контроль интенсивности иммунного ответа [3,4]. ...
Regulatory T (Treg) lymphocytes are a T helper population that controls the intensity of the immune response and maintains immune tolerance by selectively suppressing the activity of effector T lymphocytes. Treg cells are unstable and show high plasticity towards effector T helper populations, and the most common variant is Treg redifferentiation into T helpers producing interleukin-17 (IL-17 (Th17)). Although their formation has been confirmed by many studies in vivo and in vitro , Treg cells remain poorly understood in terms of their functional activity. The latter is yet fundamentally important for two major reasons. Firstly, an increase in the population of IL-17-producing Tregs has been identified for a number of diseases, raising the question of how these cells are involved in the development of pathologies. Secondly, understanding and predicting the behavior of Tregs in a pro-inflammatory environment promotes their therapeutic use. This review article analyzes the functional consequences of the redifferentiation of Treg cells into Th17.
... The immune responses to infectious agents are regulated by various cytokines [55,56]. We compared the concentration of the proinflammatory cytokines (TNF-α, IL-2, IL-12, IFN-γ) and anti-inflammatory cytokines (IL-4, IL-5, IL-10) delivered by T helper 1 (Th1) or Th2 lymphocytes, respectively, as well as the GM-CSF level. ...
Mycobacterium tuberculosis infections remain a global health problem in immunosuppressed patients. The effectiveness of BCG (Bacillus Calmette-Guérin), an anti-tuberculosis vaccine, is unsatisfactory. Finding a new vaccine candidate is a priority. We compared numerous immune markers in BCG-susceptible C57BL/6 and BCG-resistant C3H mice who had been injected with 0.9% NaCl (control) or with wild-type BCG or recombinant BCG secreting interleukin (IL)-18 (rBCG/IL-18) and in immunized mice who were immunocompromised with cyclophosphamide (CTX). The inoculation of rBCG/IL-18 in immunocompetent mice increased the percentage of bone marrow myeloblasts and promyelocytes, which were further elevated in the rBCG/IL-18/CTX-treated mice: C57BL/6 mice-3.0% and 11.4% (control) vs. 18.6% and 42.4%, respectively; C3H mice-1.1% and 7.7% (control) vs. 18.4% and 44.9%, respectively, p < 0.05. The bone marrow cells showed an increased mean fluorescence index (MFI) in the CD34 adhesion molecules: C57BL/6 mice-4.0 × 103 (control) vs. 6.2 × 103; C3H mice-4.0 × 103 (control) vs. 8.0 × 103, p < 0.05. Even in the CTX-treated mice, the rBCG/IL-18 mobilized macrophages for phagocytosis, C57BL/6 mice-4% (control) vs. 8%; C3H mice-2% (control) vs. 6%, and in immunocompetent mice, C57BL/6 induced the spleen homing of effector memory CD4+ and CD8+ T cells (TEM), 15% (control) vs. 28% and 8% (control) vs. 22%, respectively, p < 0.05. In conclusion, rBCG/IL-18 effectively induced selected immune determinants that were maintained even in immunocompromised mice.
... These findings together with the early upregulation of TCF-1 in T cell development and the ability of this protein to reprogram the gene expression profile of fibroblasts may describe TCF-1 as a "pioneer" transcription factor (140). Nonetheless, we propose that the epigenetic complexities and the requirement for combinatoriality among transcription factors suggest that even 'master regulators' or 'pioneer factors' may require additional events to fully enact the program of cell lineage that they initiate (141)(142)(143). Here, we found that TCF-1 was endowed with an unprecedented ability to target chromatin regions with repressive marks and in this manner, is more potent than the previously characterized pioneer factors in other developmental settings which are often impeded by heterochromatin (130,144). ...
An important role of cellular differentiation is to establish distinct and durable cell subsets that serve different functions over the course of an immune response. Here, I investigate the problem of cellular differentiation by considering 1) how epigenetic repression is overcome to establish unique preimmune lymphocyte identity and 2) the durability of intraclonal and interclonal diversification resulting from an immune response. The epigenetic states of hematopoietic cells contain cell-type specific accessible chromatin structures which are developmentally constructed from repressive, compacted chromatin. However, these structures feature binding sites for lineage-specific transcription factors, suggesting these factors play a role in their generation. I used measurements of chromatin accessibility in sequential stages of T cell development from bone-marrow derived progenitors alongside alternative lymphocyte lineages to identify the central role that TCF-1 plays in creating T-cell specific chromatin during differentiation. Genetic deficiency of TCF-1 reduced the accessible T cell chromatin state and the T cell gene program, whereas the ectopic expression of TCF-1 in fibroblasts caused T cell chromatin to become accessible and T cell genes to be expressed. These findings demonstrate that TCF-1 can overcome repressive chromatin to establish a naïve T cell identity distinct from other lymphocyte lineages. Despite our improved understanding of preimmune lymphocyte differentiation, much less is known about the course of lymphocyte differentiation beyond the naïve stage. During immune responses, some activated B lymphocytes express the transcription factor T-bet, but the clonal relationship to their T-bet- counterparts and the durability of the T-bet+ phenotype is unclear. I found that T-bet+ B cells are generated early after influenza infection and develop into a persistent memory pool. Immune repertoire profiling of influenza hemagglutinin-specific T-bet+ and T-bet- memory B cells demonstrates that most clones are unique to their respective subset, but lineage tree analysis of the remaining shared clones shows that T-bet+ clones can stably bifurcate from T-bet- cells. Further, genetic fate-mapping indicates that T-bet expression in B cells is stable. Together, these and other findings suggest that T-bet+ B cells are a distinct and durable memory subset and uniquely contribute to the anti-viral humoral response.
... Les lymphocytes Th2 se développent quand la stimulation des lymphocytes T CD4 + naïfs se fait en présence d'IL-4. Les Th2 produisent de l'IL-4, IL-5, IL-6, IL-10 et IL-13, et expriment le facteur de transcription GATA3 (Vahedi et al., 2013a(Vahedi et al., , 2013bZheng and Flavell, 1997;Zhu et al., 2010). Les lymphocytes Th2 expriment à leur surface le récepteur de chimiokine CCR4 dont la chimiokine correspondante est MDC (macrophage-derived chemokine) (Bonecchi et al., 1998). ...
Environ, 60 % des personnes atteintes d’un cancer auront au moins une séance de radiothérapie au cours de la prise en charge thérapeutique de leur maladie. Les doses de radiothérapie sont limitées en raison du risque important de fibrose séquellaire des tissus sains. Les rayonnements ionisants (RI) peuvent induire différents types de mort cellulaire y compris l'apoptose et la sénescence. Les cellules sénescentes ont une sensibilité réduite à l'apoptose et un phénotype sécrétoire inflammatoire. De plus, les RI peuvent induire la production d’espèces réactives de l’oxygène (ERO) qui provoquent des lésions de l'ADN dans les tissus non ciblés, et des effets systémiques associés à l'inflammation. Différentes équipes ont proposé des tests prédictifs de la radiosensibilité individuelle des patients basés sur l’évaluation du taux d'apoptose radio-induite des lymphocytes T CD4+/CD8+ (LT). Cependant, l’impact des différences de sensibilité à l’apoptose/sénescence des sous-populations de LT sur le taux d’apoptose n’a pas été étudié. Notre hypothèse est que la sensibilité à l’apoptose/sénescence radio-induite des LT circulants est associée à la sur/sous-représentation de sous-populations particulières de LT CD4+ dont les fonctions sont en rapport avec la survenue de fibrose. Nos résultats chez le donneur sain montrent que les LT CCR6+Th17 pro-fibrogéniques sont moins sensibles à l’apoptose et plus sensibles à la sénescence que les LT CCR6negTh et les Treg. Cette sénescence peut être préjudiciable car les lymphocytes CCR6+Th17 situés dans les tissus irradiés peuvent sécréter de l'IL-8 et du VEGF-A. La modulation des voies ERO/MAPK ou mTOR pourrait être une cible potentielle pour la prévention de la radiotoxicité induite par les CCR6+Th17 sénescents. Enfin, le ratio de cellules circulantes H2A.J+CCR6+Th17 sénescentes / CCR6+Treg pourrait être utilisé comme marqueur potentiel de la radiosensibilité individuelle.
... Antigen engagement of the T-cell receptor (TCR) drives the differentiation of CD4 + T cells that orchestrate an appropriate immune response [5]. Similar to B cells, CD4 + T-cell fate choices are dictated by distinctive gene programs and transcriptional regulators [6]. CD4 + T-follicular helper (Tfh) cells, dependent on the TF Bcl6, provide help to B cells in the form of survival, activation, and regulatory signals during the process of affinity maturation [7-9]. ...
Control of diverse pathogens requires an adaptive antibody response, dependent on cellular division of labor to allocate antigen-dependent B- and CD4⁺ T-cell fates that collaborate to control the quantity and quality of antibody. This is orchestrated by the dynamic action of key transcriptional regulators mediating gene expression programs in response to pathogen-specific environmental inputs. We describe a conserved, likely ancient, gene regulatory network that intriguingly operates contemporaneously in B and CD4⁺ T cells to control their cell fate dynamics and thus, the character of the antibody response. The remarkable output of this network derives from graded expression, designated by antigen receptor signal strength, of a pivotal transcription factor that regulates alternate cell fate choices.
... PU.1 binding shifts the disposition of other factors in the cell across the genome, even when their own expression levels and total numbers of binding sites remain essentially unchanged (80). The positive regulatory significance of these kinds of shifts is well established; many factors recruit others to collaborate with them in functional complexes at active enhancers [e.g., reviews by (17,(109)(110)(111)], and PU.1 is known to establish preferential binding sites for multiple other transcription factors in myeloid cells. However, in this case the positive impact is coupled with a negative regulatory consequence, via action at a distance (Figure 7). ...
PU.1 is an ETS-family transcription factor that plays a broad range of roles in hematopoiesis. A direct regulator of myeloid, dendritic-cell, and B cell functional programs, and a well-known antagonist of terminal erythroid cell differentiation, it is also expressed in the earliest stages of T-cell development of each cohort of intrathymic pro-T cells. Its expression in this context appears to give T-cell precursors initial, transient access to myeloid and dendritic cell developmental competence and therefore to represent a source of antagonism or delay of T-cell lineage commitment. However, it has remained uncertain until recently why T-cell development is also intensely dependent upon PU.1. Here, we review recent work that sheds light on the molecular biology of PU.1 action across the genome in pro-T cells and identifies the genes that depend on PU.1 for their correct regulation. This work indicates modes of chromatin engagement, pioneering, and cofactor recruitment (“coregulator theft”) by PU.1 as well as gene network interactions that not only affect specific target genes but also have system-wide regulatory consequences, amplifying the impact of PU.1 beyond its own direct binding targets. The genes directly regulated by PU.1 also suggest a far-reaching transformation of cell biology and signaling potential between the early stages of T-cell development when PU.1 is expressed and when it is silenced. These cell-biological functions can be important to distinguish fetal from adult T-cell development and have the potential to illuminate aspects of thymic function that have so far remained the most mysterious.
... The lack of immediate response to a TF's binding can have different causes (Ghisletti et al. 2010;Smale 2010;Rothenberg 2013;Vahedi et al. 2013), of course. Thus, it is possible that some of the unassigned TF occupancies could play a role in the timing events discussed next. ...
Gene regulatory networks account for the ability of the genome to program development in complex multi-cellular organisms. Such networks are based on principles of gene regulation by combinations of transcription factors that bind to specific cis-regulatory DNA sites to activate transcription. These cis-regulatory regions mediate logic processing at each network node, enabling progressive increases in organismal complexity with development. Gene regulatory network explanations of development have been shown to account for patterning and cell type diversification in fly and sea urchin embryonic systems, where networks are characterized by fast coupling between transcriptional inputs and changes in target gene transcription rates, and crucial cis-regulatory elements are concentrated relatively close to the protein coding sequences of the target genes, thus facilitating their identification. Stem cell-based development in post-embryonic mammalian systems also depends on gene networks, but differs from the fly and sea urchin systems. First, the number of regulatory elements per gene and the distances between regulatory elements and the genes they control are considerably larger, forcing searches via genome-wide transcription factor binding surveys rather than functional assays. Second, the intrinsic timing of network state transitions can be slowed considerably by the need to undo stem-cell chromatin configurations, which presumably add stability to stem-cell states but retard responses to transcription factor changes during differentiation. The dispersed, partially redundant cis-regulatory systems controlling gene expression and the slow state transition kinetics in these systems already reveal new insights and opportunities to extend understanding of the repertoire of gene networks and regulatory system logic.
... H3K27me3, in particular, is a conventionally "repressive" histone modification (9,14) that plays a role in CD4 T cell differentiation (15,16). However, its dynamics during CD4 T cell activation and early differentiation has not been explored, and its role in early differentiation is still poorly characterized. ...
The changes to the epigenetic landscape in response to Ag during CD4 T cell activation have not been well characterized. Although CD4 T cell subsets have been mapped globally for numerous epigenetic marks, little has been done to study their dynamics early after activation. We have studied changes to promoter H3K27me3 during activation of human naive and memory CD4 T cells. Our results show that these changes occur relatively early (1 d) after activation of naive and memory cells and that demethylation is the predominant change to H3K27me3 at this time point, reinforcing high expression of target genes. Additionally, inhibition of the H3K27 demethylase JMJD3 in naive CD4 T cells demonstrates how critically important molecules required for T cell differentiation, such as JAK2 and IL12RB2, are regulated by H3K27me3. Our results show that H3K27me3 is a dynamic and important epigenetic modification during CD4 T cell activation and that JMJD3-driven H3K27 demethylation is critical for CD4 T cell function.
... based on production of specific cytokines whose expression is regulated by different transcription factors 58 . However, the phenotype of many of these T cell lineages is not always stable, as T cells that appear to belong to one lineage can convert to a cytokine expression profile associated with a different lineage depending on the environment that the T cell encounters [59][60][61] . ...
Cytokines provide cells with the ability to communicate with one another and orchestrate complex multicellular behaviour. There is an emerging understanding of the role that cytokines play in normal homeostatic tissue function and how dysregulation of these cytokine networks is associated with pathological conditions. The central nervous system (CNS), where few blood-borne immune cells circulate, seems to be particularly vulnerable to dysregulated cytokine networks. In degenerative diseases, such as proteopathies, CNS-resident cells are the predominant producers of pro-inflammatory cytokines. By contrast, in classical neuroinflammatory diseases, such as multiple sclerosis and encephalitides, pro-inflammatory cytokines are mainly produced by tissue-invading leukocytes. Whereas the effect of dysregulated cytokine networks in proteopathies is controversial, cytokines delivered to the CNS by invading immune cells are in general detrimental to the tissue. Here, we summarize recent observations on the impact of dysregulated cytokine networks in neuroinflammation.
... Immune cells are surrounded by a chemical milieu in vivo, 8 which induces and directs immune cell differentiation. 5 Many cell types, including immune cells, secrete cytokines into the extracellular matrix (ECM). ...
Immune cells react to a wide range of environments, both chemical and physical. While the former has been extensively studied, there is growing evidence that physical and in particular mechanical forces also affect immune cell behaviour and development. In order to elicit a response that affects immune cell behaviour or development, environmental signals must often reach the nucleus. Chemical and mechanical signals can initiate signal transduction pathways, but mechanical forces may also have a more direct route to the nucleus, altering nuclear shape via mechanotransduction. The three-dimensional organisation of DNA allows for the possibility that altering nuclear shape directly remodels chromatin, redistributing critical regulatory elements and proteins, and resulting in wide-scale gene expression changes. As such, integrating mechanotransduction and genome architecture into the immunology toolkit will improve our understanding of immune development and disease.
... Also of interest are epigenetic and epigenomic changes that may relate to T1D immunopathology and responses to therapy. Epigenetic changes (DNA methylation and histone modifications) affect T cell lineage commitment, progression from naïve to effector and memory compartments, and switching between activated and hypo-functional phenotypes [71,72]. Treg stability and function depends on expression of the FoxP3 gene, which is demethylated in a region known as the TSDR (Treg-specific demethylated region) [73]. ...
During the past one to two decades, substantial progress has been made in our understanding of the immunopathology of type 1 diabetes (T1D) and the potential for immune interventions that can alter the natural history of the disease. This progress has resulted from the use of standardized study designs, endpoints, and, to a certain extent, mechanistic analyses in intervention trials in the setting of new-onset T1D. To date, most of these trials have involved single-agent interventions but, increasingly, future trials will test therapeutic combinations that are based on a compelling scientific rationale and testable mechanistic hypotheses. These increasingly complex trials will benefit from novel trial designs (such as factorial or adaptive designs), enhanced clinical endpoints that more directly assess islet pathology (such as β-cell death assays and islet or pancreatic imaging), improved responder analyses, and sophisticated mechanistic assays that provide deep phenotyping of lymphocyte subsets, gene expression profiling, in vitro T cell functional assessments, and antigen-specific responses. With this developing armamentarium of enhanced trial designs, endpoints, and clinical and mechanistic response analyses, we can expect substantial progress in better understanding the breakdown in immunologic tolerance in T1D and how to restore it to achieve significant and long-lasting preservation of islet function.
... Nevertheless, recently a new concept emerged for the specification of Th-cell identity which takes regulatory elements of the genome into consideration. Enhancers are extragenic DNA sequences that mediate the combinatorial recruitment of transcription factors to "enhance" transcription of cognate target genes [18]. They are the accessible part of a cell's genome and are hypersensitive to digestion by DNaseI. ...
T helper (Th) cells are important mediators of adaptive immunity and involved in various diseases. During the past decade, the Th family has expanded from including Th1 and Th2 cells to also encompass Th9, Th17, Th22 and Treg cells; the original classification using the expression of signature cytokines is still the gold standard for definition of subset affiliation. However, the identification of Th cells that do not fit into these tight conceptual boundaries has tumbled the field into an identity crisis. This review gives an overview on different Th-cell classification approaches, their advantages and drawbacks. In addition, this review highlights the functional properties of distinct Th subsets and their effector cytokines in tissues and disease-specific settings with a special focus on inflammatory skin diseases.This article is protected by copyright. All rights reserved
... For example, of nearly 2,000 predicted conventional DNA-binding transcription factors in the murine genome (Gray et al., 2004), fewer than 15 have validated roles in effector CD8 + T cell differentiation (Kaech and Cui, 2012;Pipkin and Rao, 2009). The same limitations probably hold for Tfh cell differentiation and other CD4 + T cell differentiation pathways (Crotty, 2012;Oestreich and Weinmann, 2012;Vahedi et al., 2013). Thus, a functional genetic approach in which inhibition of a large number of genes individually, in separate cells in parallel, during T cell differentiation has the potential to rapidly identify factors comprising the genetic networks underlying T cell function. ...
Classical genetic approaches to examine the requirements of genes for T cell differentiation during infection are time consuming. Here we developed a pooled approach to screen 30-100+ genes individually in separate antigen-specific T cells during infection using short hairpin RNAs in a microRNA context (shRNAmir). Independent screens using T cell receptor (TCR)-transgenic CD4(+) and CD8(+) T cells responding to lymphocytic choriomeningitis virus (LCMV) identified multiple genes that regulated development of follicular helper (Tfh) and T helper 1 (Th1) cells, and short-lived effector and memory precursor cytotoxic T lymphocytes (CTLs). Both screens revealed roles for the positive transcription elongation factor (P-TEFb) component Cyclin T1 (Ccnt1). Inhibiting expression of Cyclin T1, or its catalytic partner Cdk9, impaired development of Th1 cells and protective short-lived effector CTL and enhanced Tfh cell and memory precursor CTL formation in vivo. This pooled shRNA screening approach should have utility in numerous immunological studies.
... Although this may reflect an inherent functional instability or flexibility in the Th1/17 cells, their cytokine profiles were relatively stable during in vitro activation and expansion in the absence of added polarizing cytokines, suggesting that they are not innately less stable that those of Th1 or Th17 cells. Alternatively, recent epigenetic data have demonstrated that the "enhancer landscape" available to T-bet and RORgt is dictated by TCR-and cytokine-dependent activation of AP-1 and STAT transcription factors (28). Thus, heterogeneity in availability of specific promoter/enhancer elements to T-bet and RORgt caused by differences in TCR/cytokine signals the cells have been exposed to during differentiation may underlie the various patterns of cytokine secretion present in the Th1/17 cell population. ...
In humans, Th1/17 cells, identified by coexpression of the chemokine receptors CCR6 and CXCR3, are proposed to be highly pathogenic in several autoimmune disorders due in part to their expression of the proinflammatory cytokines IL-17, IFN-γ, and GM-CSF. However, their developmental requirements, relationship with "classic" Th17 and Th1 cells and physiological role in normal immune responses are not well understood. In this study, we examined CCR6(+)CXCR3(+) Th1/17 cells from healthy individuals and found that ex vivo these cells produced the effector cytokines IL-17, IL-22, and IFN-γ in all possible combinations and were highly responsive to both IL-12 and IL-23. Moreover, although the Ag specificity of CCR6(+)CXCR3(+) Th1/17 cells showed substantial overlap with that of Th1 and Th17 cells, this population was enriched in cells recognizing certain extracellular bacteria and expressing the intestinal homing receptor integrin β7. Finally, we identified IL-1β as a key cytokine that renders Th17 cells sensitive to IL-12, and both cytokines together potently induced the differentiation of cells that produce IL-17, IFN-γ, and GM-CSF. Therefore, interfering with IL-1β and IL-12 signaling in Th17 cells during inflammation may be a promising therapeutic approach to reduce their differentiation into "pathogenic" CCR6(+)CXCR3(+) Th1/17 cells in patients with autoimmune diseases.
... Hence, TCRinduced pioneering factors [such as nuclear factor of activated T cells (NFAT) and activator protein 1 (AP1)] and environment-sensing STAT factors cooperate to shape the global enhancer landscapes, whereas master transcription factors exploit them and focus on controlling chromatin remodelling and gene expression of a small number of signature genes for their respective subsets. [43][44][45] STAT5 is critical for cytokine-mediated T-cell proliferation and survival. 46 It is activated by a variety of cytokines, including IL-2, IL-7 and thymic stromal lymphopoietin. ...
Considerable progress has been made in recent years towards our understanding of the molecular mechanisms of transcriptional regulation of Th2 cell differentiation. Additional transcription factors and chromatin modifying factors were identified and shown to promote Th2 cell differentiation and inhibit differentiation into other subsets. Analyses of mice lacking several cis-regulatory elements have yielded more insight into the regulatory mechanism of Th2 cytokine genes. Gene deletion studies of several chromatin modifiers confirmed their impact on CD4 T cell differentiation. In addition, recent genome-wide analyses of transcription factor binding and chromatin status revealed unexpected roles of these factors in Th2 cell differentiation. In this review, these recent findings and their implication are summarized. This article is protected by copyright. All rights reserved.
Inflammation is the response of cells and tissues to potential harm. Though inflammation is a stereotyped process, various cells and tissues contribute to its onset and maintenance in a highly specific manner. Uncontrolled inflammation may contribute to infection, autoimmunity, allergies, or cancer. A group of regulatory events, referred to as epigenetics, govern gene expression without affecting the underlying DNA sequence. In a signal-, tissue-, and organ-specific manner, epigenetic mechanisms control the accessibility of genes to transcription factors and RNA polymerases. Epigenetics comprises the combined action of DNA methylation, histone modifications, and noncoding RNAs. Here, we discuss the contribution of epigenetic events to the regulation of inflammation, including T helper cell differentiation, DNA contraction during B- and T-cell receptor rearrangement, and epigenetic control of cytokine genes, and intrinsic factors that may alter the epigenetic landscape.
Interleukin (IL)-33, a member of the IL-1 cytokine family, is associated with autoimmune diseases including inflammatory bowel diseases (IBD). A few studies on animal models have shown that IL-33 can suppress Th1 cell response and improve Th2 cell response in mesenteric lymph nodes (MLN) and sera. However, there is little data published about the effect of IL-33 on Th17 cell in and Th1/Th2 cell in colon lamina propria. The aim of this study was to investigate the effect of IL-33 on Th17 cell in colon lamina propria of mice with dextran sulfate sodium (DSS) induced chronic colitis. We studied the influence of IL-33 on colonic tissue injury and clinical symptoms of colitis. The T cell subsets were measured by flow cytometry and the production of cytokines secreted by lamina propria lymphocytes (LPL) was measured by Enzyme-Linked Immunosorbent Assay (ELISA) and quantitative real-time PCR. We have found that rIL-33 treatment led to a significant alleviation of DSS induced chronic colitis as evidenced by 1) alleviation of weight loss, DAI, macroscopic changes and histological score; 2) down-regulating the rates and absolute cell numbers of Th17 and Th1 cell in LPL; 3) inducing secretion of lower levels of IFN-γ and IL-17A. It is therefore concluded that IL-33 may play a therapeutic role in DSS-induced chronic colitis in mice by suppressing Th17 response and switching Th1 to Th2 response.
The past two decades of research into the pathogenesis of Alzheimer disease (AD) have been driven largely by the amyloid hypothesis; the neuroinflammation that is associated with AD has been assumed to be merely a response to pathophysiological events. However, new data from preclinical and clinical studies have established that immune system-mediated actions in fact contribute to and drive AD pathogenesis. These insights have suggested both novel and well-defined potential therapeutic targets for AD, including microglia and several cytokines. In addition, as inflammation in AD primarily concerns the innate immune system - unlike in 'typical' neuroinflammatory diseases such as multiple sclerosis and encephalitides - the concept of neuroinflammation in AD may need refinement.
T cell lymphopoiesis is a complex, stepwise process in which the transcriptional program of the progenitor cells is progressively adapted in order to generate mature phenotypes. This transcriptional program in differentiated cells is also very flexible, allowing the silencing or activation of critical genes in response to extrinsic or intrinsic stimuli, or, in the case of progenitors, to developmental signals. Thus, progenitor and mature cells must maintain a balance between stability, to preserve their phenotypic identity, and plasticity, to respond and adapt to stimuli. A long-standing question is, therefore, how the transcriptional program is regulated to allow both controlled differentiation and a flexible response. Here we review the contribution of epigenetic mechanisms to transcriptional control during CD4 T cell differentiation and the ways in which these mechanisms interact with key transcription factors to ensure proper maturation and maintenance of cell identity.
Copyright © 2015. Published by Elsevier Ltd.
Although each T lymphocyte expresses a T-cell receptor (TCR) that recognizes cognate antigen and controls T-cell activation, different T cells bearing the same TCR can be functionally distinct. Each TCR is a heterodimer, and both α- and β-chains contribute to determining TCR antigen specificity. Here we present a methodology enabling integration of information about TCR specificity with information about T cell function. This method involves sequencing of TCRα and TCRβ genes, and amplifying functional genes characteristic of different T cell subsets, in single T cells. Because this approach retains information about individual TCRα-TCRβ pairs, TCRs of interest can be expressed and used in functional studies, for antigen discovery, or in therapeutic applications. We apply this approach to study the clonal ancestry and differentiation of T lymphocytes infiltrating a human colorectal carcinoma.
The transcription factor Foxp3 participates dominantly in the specification and function of Foxp3(+)CD4(+) regulatory T cells (T(reg) cells) but is neither strictly necessary nor sufficient to determine the characteristic T(reg) cell signature. Here we used computational network inference and experimental testing to assess the contribution of other transcription factors to this. Enforced expression of Helios or Xbp1 elicited distinct signatures, but Eos, IRF4, Satb1, Lef1 and GATA-1 elicited exactly the same outcome, acting in synergy with Foxp3 to activate expression of most of the T(reg) cell signature, including key transcription factors, and enhancing occupancy by Foxp3 at its genomic targets. Conversely, the T(reg) cell signature was robust after inactivation of any single cofactor. A redundant genetic switch thus 'locked in' the T(reg) cell phenotype, a model that would account for several aspects of T(reg) cell physiology, differentiation and stability.
The immune system has evolved to mount an effective defense against pathogens and to minimize deleterious immune-mediated inflammation caused by commensal microorganisms, immune responses against self and environmental antigens, and metabolic inflammatory disorders. Regulatory T (Treg) cell-mediated suppression serves as a vital mechanism of negative regulation of immune-mediated inflammation and features prominently in autoimmune and autoinflammatory disorders, allergy, acute and chronic infections, cancer, and metabolic inflammation. The discovery that Foxp3 is the transcription factor that specifies the Treg cell lineage facilitated recent progress in understanding the biology of regulatory T cells. In this review, we discuss cellular and molecular mechanisms in the differentiation and function of these cells.
Signal transducer and activator of transcription (STAT) proteins are well known for their essential roles in transmitting cytokine-mediated signals and specifying T helper (T(H)) cell differentiation. Recent technological advances have revealed that STAT proteins have broad and complex roles in gene regulation and epigenetic control, including important roles as functional repressors. However, the challenge of how to link signal transduction, nucleosome biology and gene regulation remains. The relevance of tackling this problem is highlighted by genome-wide association studies that link cytokine signalling and STATs to various autoimmune or immune deficiency disorders. Defining exactly how extrinsic signals control the specification and plasticity of T(H) cells will provide important insights and perhaps therapeutic opportunities in these diseases.
The binding of transcription factors to specific DNA target sequences is the fundamental basis of gene regulatory networks. Chromatin immunoprecipitation combined with DNA tiling arrays or high-throughput sequencing (ChIP-chip and ChIP-seq, respectively) has been used in many recent studies that detail the binding sites of various transcription factors. Surprisingly, data from a variety of model organisms and tissues have demonstrated that transcription factors vary greatly in their number of genomic binding sites, and that binding events can significantly exceed the number of known or possible direct gene targets. Thus, current understanding of transcription factor function must expand to encompass what role, if any, binding might have outside of direct transcriptional target regulation. In this review, we discuss the biological significance of genome-wide binding of transcription factors and present models that can account for this phenomenon.
Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.
Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene expression programs through epigenetic modification of the genome. These regulatory events at enhancers contribute to the specific gene expression programs that determine cell state and the potential for differentiation into new cell types. Although enhancer elements are known to be associated with certain histone modifications and transcription factors, the relationship of these modifications to gene expression and developmental state has not been clearly defined. Here we interrogate the epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse. We find that histone H3K27ac distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone. This indicates that the amount of actively used enhancers is lower than previously anticipated. Furthermore, poised enhancer networks provide clues to unrealized developmental programs. Finally, we show that enhancers are reset during nuclear reprogramming.
Transcriptional regulation of gene expression plays a significant role in establishing the diversity of human cell types and biological functions from a common set of genes. The components of regulatory control in the human genome include cis-acting elements that act across immense genomic distances to influence the spatial and temporal distribution of gene expression. Here we review the established categories of distant-acting regulatory elements, discussing the classical and contemporary evidence of their regulatory potential and clinical importance. Current efforts to identify regulatory sequences throughout the genome and elucidate their biological significance depend heavily on advances in sequence conservation-based analyses and on increasingly large-scale efforts applying transgenic technologies in model organisms. We discuss the advantages and limitations of sequence conservation as a predictor of regulatory function and present complementary emerging technologies now being applied to annotate regulatory elements in vertebrate genomes.
The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene, the relative roles of these regulatory elements in this process are not clear. We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators in the human genome. Here we use the same approach to identify these elements in multiple cell types and investigate their roles in cell-type-specific gene expression. We observed that the chromatin state at promoters and CTCF-binding at insulators is largely invariant across diverse cell types. In contrast, enhancers are marked with highly cell-type-specific histone modification patterns, strongly correlate to cell-type-specific gene expression programs on a global scale, and are functionally active in a cell-type-specific manner. Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.
According to current models, once the cell has reached terminal differentiation, the enhancer repertoire is completely established and maintained by cooperatively acting lineage-specific transcription factors (TFs). TFs activated by extracellular stimuli operate within this predetermined repertoire, landing close to where master regulators are constitutively bound. Here, we describe latent enhancers, defined as regions of the genome that in terminally differentiated cells are unbound by TFs and lack the histone marks characteristic of enhancers but acquire these features in response to stimulation. Macrophage stimulation caused sequential binding of stimulus-activated and lineage-determining TFs to these regions, enabling deposition of enhancer marks. Once unveiled, many of these enhancers did not return to a latent state when stimulation ceased; instead, they persisted and mediated a faster and stronger response upon restimulation. We suggest that stimulus-specific expansion of the cis-regulatory repertoire provides an epigenomic memory of the exposure to environmental agents.
Signaling pathways are intimately involved in cellular differentiation, allowing cells to respond to their environment by regulating gene expression. Although enhancers are recognized as key elements that regulate selective gene expression, the interplay between signaling pathways and actively used enhancer elements is not clear. Here, we use CD4(+) T cells as a model of differentiation, mapping the activity of cell-type-specific enhancer elements in T helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the activation of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. Transcriptome analysis further supports a functional role for enhancers regulated by STATs. Importantly, expression of lineage-defining master regulators in STAT-deficient cells fails to fully recover the chromatin signature of STAT-dependent enhancers. Thus, these findings point to a critical role of STATs as environmental sensors in dynamically molding the specialized enhancer architecture of differentiating cells.
Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively bound BATF and IRF4 contribute to initial chromatin accessibility and, with STAT3, initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple data sets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease.
Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis. It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape. Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to preaccessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers lacking in Foxp3(-) CD4(+) cells became accessible upon T cell receptor activation prior to Foxp3 expression, and only a small subset associated with several functionally important genes were exclusively Treg cell specific. Thus, in a late cellular differentiation process, Foxp3 defines Treg cell functionality in an "opportunistic" manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.
Interleukin-27 (IL-27) is a key immunosuppressive cytokine that counters T helper 17 (Th17) cell-mediated pathology. To identify mechanisms by which IL-27 might exert its immunosuppressive effect, we analyzed genes in T cells rapidly induced by IL-27. We found that IL-27 priming of naive T cells upregulated expression of programmed death ligand 1 (PD-L1) in a signal transducer and activator of transcription 1 (STAT1)-dependent manner. When cocultured with naive CD4(+) T cells, IL-27-primed T cells inhibited the differentiation of Th17 cells in trans through a PD-1-PD-L1 interaction. In vivo, coadministration of naive TCR transgenic T cells (2D2 T cells) with IL-27-primed T cells expressing PD-L1 inhibited the development of Th17 cells and protected from severe autoimmune encephalomyelitis. Thus, these data identify a suppressive activity of IL-27, by which CD4(+) T cells can restrict differentiation of Th17 cells in trans.
Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the expression of the E-protein antagonist Id2. Hematopoietic progenitors that express Id2 are multipotent and readily differentiate upon withdrawal of Id2 expression into committed B lineage cells, thus indicating a causative role for E2A (Tcf3) in promoting the B cell fate. Genome-wide analyses revealed that a substantial fraction of lymphoid and myeloid enhancers are premarked by the poised or active enhancer mark H3K4me1 in multipotent progenitors. Thus, in hematopoietic progenitors, multilineage priming of enhancer elements precedes commitment to the lymphoid or myeloid cell lineages.
Ligand-dependent transcription by the nuclear receptor glucocorticoid receptor (GR) is mediated by interactions with coregulators. The role of these interactions in determining selective binding of GR to regulatory elements remains unclear. Recent findings indicate that a large fraction of genomic GR binding coincides with chromatin that is accessible prior to hormone treatment, suggesting that receptor binding is dictated by proteins that maintain chromatin in an open state. Combining DNaseI accessibility and chromatin immunoprecipitation with high-throughput sequencing, we identify the activator protein 1 (AP1) as a major partner for productive GR-chromatin interactions. AP1 is critical for GR-regulated transcription and recruitment to co-occupied regulatory elements, illustrating an extensive AP1-GR interaction network. Importantly, the maintenance of baseline chromatin accessibility facilitates GR recruitment and is dependent on AP1 binding. We propose a model in which the basal occupancy of transcription factors acts to prime chromatin and direct inducible transcription factors to select regions in the genome.
Biological differences among metazoans and between cell types in a given organism arise in large part due to differences in gene expression patterns. Gene-distal enhancers are key contributors to these expression patterns, exhibiting both sequence diversity and cell type specificity. Studies of long-range interactions indicate that enhancers are often important determinants of nuclear organization, contributing to a general model for enhancer function that involves direct enhancer-promoter contact. However, mechanisms for enhancer function are emerging that do not fit solely within such a model, suggesting that enhancers as a class of DNA regulatory element may be functionally and mechanistically diverse.
Cell differentiation entails early lineage choices leading to the activation, and the subsequent maintenance, of the gene expression program characteristic of each cell type. Alternative lineage choices involve the activation of different regulatory and coding regions of the genome, a process instructed by lineage-determining transcription factors, and at least in part mediated by the deposition of chromatin marks that modify functionality and accessibility of the underlying genome. According to classic epigenetics, subsequent maintenance of chromatin marks across mitoses and in spite of environmental perturbations occurs largely through autonomous and unsupervised mechanisms. However, paradigmatic genetic and biochemical studies in immune system and hematopoietic cells strongly point to the concept that both induction and maintenance of the differentiated state require constant supervision by lineage-determining transcription factors, which may act to globally organize the genome in both the one- and the three-dimensional space.
A multiply redundant genetic switch ?locks in? the transcriptional signature of regulatory T cells
- W Fu
- A Ergun
- T Lu
- Etal