Search tips
Search criteria 


Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Immunol. Author manuscript; available in PMC 2017 March 15.
Published in final edited form as:
PMCID: PMC4780223

Genetic and epigenetic regulation of PD-1 expression1


The inhibitory immune receptor Programmed cell death-1 (PD-1) is intricately regulated. In T cells, PD-1 is expressed in response to most immune challenges, but is rapidly down regulated in acute settings, allowing for normal immune responses. On chronically stimulated antigen-specific T cells, PD-1 expression remains high, leading to an impaired response to stimuli. Antibody blockade of PD-1 interactions during chronic antigen settings partially restores immune function and is now used clinically to treat a variety of devastating cancers. Understanding the regulation of PD-1 expression may be useful for developing novel immune based therapies. Here, the molecular mechanisms that drive dynamic PD-1 expression during acute and chronic antigenic stimuli are reviewed. An array of cis-DNA elements, transcription factors, and epigenetic components, including DNA methylation and histone modifications, control PD-1 expression. The interplay between these regulators fine-tunes PD-1 expression in different inflammatory environments and across numerous cell types to modulate immune responses.

Keywords: Transcription Factors, Gene Regulation, PD-1


The inhibitory receptor Programmed cell death-1 (PD-1) is a mediator of central and peripheral immune tolerance and immune exhaustion (16). The immune inhibitory function of PD-1 was demonstrated in PD-1 and PD-L1 knock-out mice, which presented hyperactive immune phenotypes (4, 7, 8), and mutations in PD-1 have been associated with disease progression in multiple human autoimmune disorders (911). High levels of PD-1 were linked to CD8 T cell exhaustion during chronic viral infections (5, 6, 1218). Exhausted CD8 T cells are unable to secrete normal amounts of cytokines, proliferate, or perform immune functions such as initiating cellular cytotoxicity (12, 1922). Although the PD-1 pathway represents a major contributing factor to cellular exhaustion, other inhibitory receptors also contribute (23, 24). PD-1 expression was also found on poorly functional tumor infiltrating cells during multiple types of cancers (2529). Thus, the expression of PD-1 is critical to the development and maintenance of a healthy and robust immune response.

PD-1 expression is tightly and dynamically regulated. On resting naïve T cells, as well as in certain populations of developing thymocytes, PD-1 is expressed at low basal levels (30, 31). This low level has been linked to immune tolerance (3, 30, 31). Following an initial immune stimulus, PD-1 is transiently expressed on multiple immune cells types, including CD4 and CD8 T cells, B cells, macrophages, and dendritic cells (30, 3238). In the case of acute antigen exposure, PD-1 is down regulated in a time course that is concurrent with or prior to antigen clearance. During chronic immune stimulation PD-1 remains highly expressed, which can lead to functional exhaustion (5, 6, 1218). Functional exhaustion can be partially reversed by blocking PD-1/PD-L interactions with antibodies. These antibody-based immune checkpoint blockade therapies [nivolumab (under the trade name Opdivo) or pembrolizumab (Keytruda)] have been shown to be highly efficacious in reinvigorating the anti-tumor immune response in patients with advanced cancers, including melanomas, non-small-cell lung cancer, colorectal cancer, and renal-cell cancer (3945). In addition, high PD-1 expression is necessary for regulatory T cell (Treg) development, and follicular helper T (TFH) cells also constitutively express high PD-1 (1, 2, 46, 47), although PD-1 regulation has not been studied in this population.

In this review, the mechanisms that drive the initial PD-1 induction and its continued expression during chronic antigen exposure will be discussed. In addition to providing an understanding of which active immune environments may induce and be affected by PD-1’s function, knowledge of the molecular mechanisms regulating PD-1 may help tailor future immunotherapies for fighting cancer, chronic HIV and HCV infections, or prevention of allergic responses, transplant rejection, and autoimmunity (48), as well as boosting long-lived memory responses to vaccines (49).

Models for Studying PD-1 Regulation

The expression and regulation of PD-1 has been studied in a variety of model systems. In culture, PD-1 has been studied using both the EL4 mouse T cell line and isolated mouse and human primary immune cells. A variety of stimuli can activate these cells, including the small molecule drugs phorbol 12-myristate 13-acetate (PMA) and ionomycin (Io), concanavalin A, or anti-CD3/CD28 antibodies, which acutely activate immune cells and transiently induce PD-1 expression (30, 5053). In vivo, PD-1 expression is probably most studied and best understood during infection with lymphocytic choriomeningitis virus (LCMV) (12, 19, 20, 5457). The LCMV infection model includes two strains that differ by 2 amino acids (22). Infection with the Armstrong strain results in an acute infection, correlating with transient up-regulation and subsequent loss of PD-1 that coincides with viral clearance. In contrast, establishing a chronic infection with the Clone-13 strain results in durable PD-1 expression and concurrent immune cell dysfunction and exhaustion. Side-by-side analysis of these two infections has provided direct comparisons between the transient/acute vs. the chronic prolonged modalities of PD-1 expression in CD8 T cells. Additionally, prolonged PD-1 expression during an anti-tumor response in mice has been studied using the B16.f10 melanoma cell line or Lewis lung carcinoma (LLC) cell line, both of which are terminally tumorigenic but nonetheless immunogenic in C57Bl/6 mice (25, 58, 59). Although these different models have largely been used to study separate aspects of PD-1 regulation, in vivo infection models have recapitulated findings from in vitro activated cell lines. While most of the studies to date have been performed on murine cells and cell lines (36, 5254, 5964), those performed with human cells have yielded similar findings (65, 66). As described below, this is likely due to conservation of important regulatory elements at the PD-1 locus.

Identifying cis regulatory elements of the Pdcd1 gene

PD-1 is encoded in the Pdcd1 gene. At least 8 cis-elements regulate Pdcd1 expression. Strong mammalian DNA sequence conservation coupled with DNAse I hypersensitivity assays in EL4 cells and CD8 T cells initially identified two conserved regions (CR-B and CR-C) associated with Pdcd1 activation (52). These elements, which are located 100bp and 1.1kb upstream of the transcription start site (TSS), each contains multiple transcription factor binding sites (Figure 1a). An activator protein (AP)-1 binding site is encoded within CR-B (59). CR-C contains an interferon-stimulated response element (ISRE) (60), a nuclear factor of activated T cells (NFAT)c1 binding site (52), a FoxO1 binding site (61), and an NF-κB binding site (36). Notably, reporter constructs that utilize the PD-1 promoter but do not contain the CR-C region failed to induce PD-1 expression in response to a variety of stimuli (36, 52). Collectively, this suggests that CR-C is of critical importance to the observed expression patterns of the gene.

Figure 1
Schematic models of Pdcd1 gene regulation

Two conserved, DNase I hypersensitive elements located −3.7 and +17.1 kb from the TSS enhanced transcriptional activity following TCR and IL-6 or IL-12 cytokine stimulation (Figure 1a and e). These elements encode STAT binding sites and were found to interact directly with the Pdcd1 promoter following ex vivo cell activation and cytokine treatment (62). Additional elements at −26.7 and +17.5 kb bind the mammalian transcriptional insulator CCCTC-binding factor (CTCF) and form constitutively interacting chromatin loops (Figure 1) (62). Because transcriptional insulators prevent the actions of distant enhancers from controlling a downstream gene (67), these CTCF sites likely define the extreme ends of the Pdcd1 regulatory locus.

Transcription factors inducing acute PD-1 expression

PD-1 expression on CD8 T cells correlates with the strength of TCR signaling (12, 54, 68). TCR stimulation initiates a signaling cascade through the calcineurin pathway, resulting in activation and translocation of the transcription factor NFATc1 (also known as NFAT2) (69). NFATc1 binds strongly to the CR-C region (Figure 1b) and is likely one of the first steps in activating Pdcd1 gene expression (52, 53). Blocking this pathway using the calcineurin inhibitor cyclosporine A or the NFATc1-specific inhibitor peptide VIVIT abrogated PD-1 expression (52). Thus, NFATc1 is necessary for initial activation-induced expression of PD-1 in CD4 and CD8 T cells. PMA/Io mediated NFATc1 binding and transcriptional activity was also found at the −3.7 and +17.1 sites, suggesting that multiple NFATc1 elements are required for driving Pdcd1 expression or that there is genetic redundancy in the mechanism by which Pdcd1 is induced (62). Intriguingly, NFATc1 expression is repressed at extended time points after induction and this is likely part of the mechanism for restricting PD-1 expression during acute antigen exposure (53). During chronic LCMV infection, NFATc1 translocation is also impaired (70). These observations suggest that while NFATc1 may be necessary to initially induce PD-1, another mechanism is required to maintain or augment expression during chronic antigen exposure.

AP-1 frequently couples with NFAT activity during T cell activation (71). TCR-mediated stimulation of the Protein kinase C/Raf pathway activates the MAP kinase cascade, ultimately leading to AP-1 activity (71). Notably, PMA/Io stimulation, originally used to identify NFATc1 binding and activity at CR-C, concurrently triggers this same pathway. In an LLC tumor model, over expression of the AP-1 subunit c-Fos was found to inhibit anti-tumor T cell responses by direct binding to the AP-1 site in the CR-B region of Pdcd1 (Figure 1b). This resulted in induction of PD-1 expression in CD4 and CD8 T cells (59). A mouse containing a mutation of this AP-1 site had less PD-1 expression on tumor-infiltrating T cells and demonstrated increased anti-tumor immunity (59). Unlike other NFAT-coupled AP-1 sites, which are typically adjacent (71), the Pdcd1 AP-1 site was located over 1 kb away from the NFATc1 binding site (52).

Additionally, the Notch pathway, which regulates T cell effector functions (72, 73), also regulates PD-1 expression in acute antigen settings (64). In an in vitro experiment, blockade of the Notch pathway showed a moderate, dose-dependent reduction of PD-1 expression, without affecting the overall activation of the T cell (64). Corroborating this, the Notch intracellular domain and the recombination signal binding protein for immunoglobulin kappa J (RBPJκ), two critical components of the Notch signaling pathway, were bound to the Pdcd1 locus within six hours of in vitro peptide-mediated TCR stimulation (Figure 1b). Similarly, in T cells of patients experiencing sepsis-induced immunosuppression, Notch pathway activation also correlated with PD-1 expression (74). In a model using IL-10 and LPS to cause sepsis-induced immunosuppression in CD4 T cells and macrophages, inhibition of Notch signaling again reduced PD-1 expression. Thus, the Notch pathway appears to directly augment PD-1 expression during T cell activation settings.

Inhibitors of PD-1 expression

T-box expressed in T cells (T-bet) was the first identified inhibitor of PD-1 (63). T-bet expression influences CD8 T cell differentiation with high T-bet levels associated with short-lived effector cells and intermediate levels with memory precursor cells (75). Following TCR stimulation or in PD-1lo memory CD8 T cells from acutely infected mice, T-bet binds 500 bp upstream of the Pdcd1 TSS (Figure 1c) (63). In a chronic LCMV infection, T-bet over-expression (normally only expressed at intermediate levels) was inversely correlated with PD-1 expression, resulting in a PD-1int phenotype (63). Furthermore, PD-1 expression was further increased in this infection model in a T-bet knockout mouse. In acute LCMV infections, CD8 T cells from T-bet knockout mice only showed moderately higher expression of PD-1 compared to controls, rather than the PD-1hi phenotype seen during chronic or peak acute infection. Collectively, these data suggest that while T-bet does repress PD-1, T-bet alone is neither sufficient nor necessary to completely down regulate PD-1, and other factors may synergize with T-bet following an acute infection to silence gene expression.

In acute LCMV viral infection, expression of the inhibitory factor B lymphocyte induced maturation protein 1 (Blimp-1 encoded by Prdm1) is induced by day 8 after T cell activation, and like T-bet is necessary for terminal T cell differentiation and functional memory formation (76, 77). At day 8, Blimp-1 was bound between CR-C and CR-B (Figure 1c) (53). In this system, Blimp-1 binding resulted in the direct loss of NFATc1 occupancy at CR-C. Blimp-1 also directly down regulated PD-1 expression in tissue culture cells. Blimp-1 mediated repression of PD-1 occurred irrespective of whether NFATc1 was overexpressed from an exogenous vector. Moreover, acute LCMV infection of a Blimp-1 KO mouse resulted in prolonged PD-1 expression on virus-specific CD8 T cells (53). These experiments indicate that Blimp-1 is necessary for normal loss of PD-1 expression following an acute infection. Furthermore, TFH cells, which express high levels of PD-1, are also noted for their lack of Blimp-1 expression (46). In germinal centers, retrovirus-mediated exogenous expression of Blimp-1 resulted in a failure to generate PD-1hi TFH subsets, again showing an inverse correlation between Blimp-1 and PD-1 (46). Notably, BCL6, an antagonist of Blimp-1 (78), was necessary for generation of a PD-1hi TFH population (46). However, a direct role for BCL6 inducing PD-1 expression has not been reported. Surprisingly, Blimp-1 is expressed in exhausted CD8 T cells, where PD-1 levels are at their highest (79). In exhausted CD8 T cells of Blimp-1 KO mice, the high levels of PD-1 expression were slightly reduced (79), suggesting a different role for Blimp-1 in regulating Pdcd1 in these cells. The molecular mechanism for how Blimp-1 could function differentially as a repressor or activator of gene expression is unclear. As a repressor, Blimp-1 is known to recruit additional transcriptional repressors that result in silencing the local chromatin environment (8082). In the case where expression is increased in the presence of high levels of Blimp-1 in the cell, several possibilities exist. First, Blimp-1 may not bind to its site in the Pdcd1 gene and PD-1 expression continues to be active. Second, Blimp-1 could bind but fail to recruit the repressive cofactors necessary to silence the gene. This could be due to novel post-translational modifications that control its function. Third, Blimp-1 could function indirectly by repressing a co-repressor necessary for silencing. Lastly, under the exhausted conditions, an additional activating factor may override the Blimp-1 repressor pathway.

Chronic regulators of PD-1 and factors in other cell types

The transcription factor FoxO1 promotes transcription of a number of genes necessary for homeostatic maintenance of naïve and memory T cells (83). FoxO1 antagonizes the transcription factor T-bet (84), and as such is a candidate for preventing PD-1 down-regulation. In chronic LCMV infections, FoxO1 protein is highly expressed and retained within the nucleus (61). Despite FoxO1 promoting homeostatic division and relative viral control by supporting high T cell numbers, it was also necessary to generate PD-1hi T cells in the chronic infection model as FoxO1 knockout mice have lower PD-1 expression. FoxO1 acted directly on the Pdcd1 locus by binding to a region in CR-C, and therein induced promoter activity and PD-1 expression (Figure 1d). Interestingly, the putative FoxO1 binding site overlaps with one of the NFATc1 binding sites in CR-C. This may indicate a molecular system in which FoxO1 replaces NFATc1 and can override Blimp-1’s repressive activity.

To partially replicate in vitro some of the immune microenvironments seen in chronic infection, CD8 T cells were activated with anti-CD3/CD28 beads and treated with IL-6 or IL-12, resulting in the activation of STAT3 and STAT4 (62). Under these conditions, STAT3 and STAT4 bound the −3.7 and +17.1 regulatory regions and were able to increase PD-1 expression in conjunction with TCR signaling (Figure 1e). The STAT proteins alone were not sufficient, as cytokine stimulation of naïve T cells without concurrent TCR stimulation did not induce PD-1 expression (62). However, this could be due in part to the low levels of IL-12 receptor on naïve CD8 T cells (85). Intriguingly, preconditioning CD8 T cells with IL-12 and/or IFN-α (which induces STAT1/STAT2/IRF9 activity) resulted in higher expression of the repressor T-bet and subsequently led to lower expression of PD-1 upon later antigen encounter (86). Thus, cytokine exposure prior to antigen-mediated TCR signaling may have profound effects on the level of PD-1 expressed.

Due to the immune reinvigoration potential related to PD-1 expression on exhausted CD8 T cells, most of the above transcription factors have been studied in CD8 T cells alone or in a combination of CD4 and CD8 T cells. When queried in B cells, a similar NFATc1-based regulatory system was implicated for PMA/Io- or BCR-mediated induction of PD-1 (36). However, in macrophages the calcineurin and MAP kinase pathways stimulated by PMA/Io did not induce PD-1, and blockade of these pathways had no effect on PD-1 expression induced in macrophages by TLR ligands (36, 87). It was instead found that NF-κB is necessary to induce PD-1 in response to TLR stimulation (36). Inhibition of NF-κB binding to DNA using a small molecule inhibitor resulted in a total loss of PD-1 expression. Further, the NF-κB p65 subunit was bound to a site in CR-C in response to TLR stimulation of macrophages (Figure 1f), and a mutation of this site abrogated transcriptional activity of the region in reporter assays (36). The ability of NF-κB to induce PD-1 directly in cell types other than macrophages has not been studied.

PD-1 regulation in macrophages in response to cytokine stimuli has also been examined. Interferon-α stimulation of macrophages resulted in interferon-stimulated gene factor (ISGF)3 complex binding to the ISRE in the CR-C region (Figure 1f) and induction of PD-1 expression (60). ISGF3 is a complex composed of STAT1, STAT2, and interferon regulatory factor 9 (IRF9) (88), again implicating the STAT family of transcription factors as key members of PD-1 regulation in addition to IRF9. Type I interferon activity was subsequently examined for its effects on cultured T cells (66). In T cells, IFN-α alone had no effect on PD-1 expression. However, although it could not autonomously induce expression, IFN-α administered concurrently with TCR stimulation induced IRF9 binding to the ISRE (Figure 1e) and enhanced TCR-mediated PD-1 expression (66). Much like the cytokine-induced STAT3 and STAT4 activity, interferon-stimulated STAT1, STAT2, and IRF9 seem to have supplementary roles in increasing PD-1 expression that require additional TCR-mediated signals.

Thus, collectively, to date ten transcription factor/complexes are known to modulate PD-1, including eight activators (NFATc1, c-fos/AP-1, Notch, FoxO1, STAT3, STAT4, ISGF3, and NF-κB) and two inhibitory molecules (Blimp-1 and T-bet), which all interact with the locus in response to different stimuli. The complexity and variability of the Pdcd1 regulome, the entire set of transcription factors and genetic elements that affect this one gene, may contribute not only to a differential expression in response to different inflammatory stimuli, including the difference between acute and chronic infection, but may also account for differential patterns seen across multiple cell types in response to the same infection.

Epigenetic regulation of Pdcd1

Epigenetics refers to a stable, heritable mechanism by which cells may maintain transcriptional profiles and corresponding states of differentiation across cell generations without modifying the underlying genetic code. Such epigenetic mechanisms include DNA methylation, histone protein modifications, and overall chromatin looping and organization, which individually or together alter the chromatin state/accessibility and control transcriptional activity of a gene (89). These processes are widely used by the immune system to control immune cell differentiation, fate and gene expression (9093).

Exhausted T cells, even upon total removal of antigen, stably maintain their exhausted phenotype during subsequent divisions (94). This has been demonstrated in exhausted CD8 T cells adoptively transferred from chronic LCMV-infected mice into naïve mice, in which the cells proliferated yet remained functionally exhausted and PD-1hi upon re-challenge with an acute virus (LCMV Armstrong), which otherwise would not induce exhaustion (94). Similarly, PD-1 levels remain high on the CD8 T cells of human patients infected with HIV but undergoing anti-retroviral therapy, which drastically decreases viral loads (65). These data indicate that a heritable epigenetic mechanism establishes and maintains both the exhausted phenotype and expression of PD-1 itself after the exhaustion-inducing stimulus has been removed.

DNA methylation of Pdcd1

The DNA modification 5-methylcytosine (5mC) at CpG sites in transcriptional enhancers or at gene promoters is associated with silencing gene expression (95). In mice, two CpG-rich regions upstream of the Pdcd1 TSS (CR-C itself and a regulatory region starting approximately 300 bp upstream of the promoter and labeled as CR-B) were dynamically methylated in CD8 T cells responding to an acute LCMV infection (54). Both of these regions were fully methylated in resting, naïve CD8 T cells that do not express PD-1. At day 4 following acute LCMV infection, both regions showed a profound loss of methylation that was restored at day 8. DNA methylation was inversely correlated to both PD-1 expression and viral load. By contrast, during chronic LCMV infection, the regions remained unmethylated at day 8 and later time points (Figure 1). Similarly, in a model of antigen tolerance induced by peptide immunotherapy, it was found that de-methylation of the Pdcd1 locus and corresponding induction of PD-1 was necessary for tolerizing T cells (48). This inverse correlation between DNA methylation and PD-1 expression strongly indicates a role for DNA methylation in regulating Pdcd1 gene expression.

In patients with chronic HIV, the PD-1 regulatory region was similarly demethylated in PD-1hi virus-specific cells, and unmethylated in naïve, non-exhausted PD-1lo cells from the same donors (65). Intriguingly, patients who were on anti-retroviral therapy at the time showed no re-methylation of DNA at the PD-1 locus, despite significantly lower viral loads. This indicates that there is no mechanism to reverse DNA methylation changes at the Pdcd1 locus in exhausted cells, regardless of changes in viral burden. Notably, one instance has been found in which DNA methylation is not linked to PD-1 expression. In macrophages, transient induction of PD-1 through TLR signaling and NF-κB was not accompanied by a corresponding demethylation of the Pdcd1 locus (36). However, TLR-mediated PD-1 induction in macrophages was much shorter in duration and not as robust as that in CD8 T cells during acute infection. Together these data suggest that demethylation may only be necessary for high or prolonged PD-1 expression.

There are two general models for how a gene loses DNA methylation. In the passive model, following DNA replication a locus fails to remethylate hemimethylated CpG-containing DNA, resulting in dilution of the methylation mark over successive divisions. In an active model, CpG loci are targeted by members of the ten-eleven translocase (TET) family, resulting in an initial catalytic oxidation of the 5mC to 5-hydroxymethyl cytosine (5hmC) as an intermediate (96, 97). Continued oxidation and base removal results in replacement of the cytosine with a non-methylated cytosine. It should be noted that the data discussed above (54, 65) used bisulfite sequencing, which does not distinguish between 5mC and the 5hmC modification. Intriguingly, 5hmC was enriched at the Pdcd1 locus (albeit at low levels compared to 5mC) in naïve mouse CD4 T cells (48). Both 5hmC and 5mC were lost upon CD4 T cell activation and induction of PD-1 (48). This result would argue that demethylation of the Pdcd1 locus upon gene induction occurs through an active and targeted mechanism. The occurrence of this transitional mark in naïve cells may indicate that the Pdcd1 locus rests in a state capable of rapid demethylation.

The histone landscape of PD-1

Modifications to histone proteins within a chromatin region can change chromatin accessibility and affect promoter and enhancer activity, leading to changes in gene transcription. On a genomic level, enhancers are marked by histones enriched for histone H3 lysine 4 monomethylation (H3K4me1) and when considered “active”, also contain H3K27 acetylation (ac) (98). When PD-1 expression was induced on CD8 T cells in vitro, H3K9ac (another activation specific mark) and H3K27ac were present at CR-C and the promoter (48, 53). The other cis elements −3.7 and +17.1 did not contain active histone marks following TCR stimulation alone even though Pdcd1 expression was induced (62), suggesting that these elements do not play a role unless cytokine stimulation occurs. In agreement, treatment of CD8 T cells ex vivo with the cytokines IL-6 or IL-12 alone resulted in the enrichment of the histone mark H3K4me1 at both the −3.7 and +17.1 regulatory sites (62). Cytokine stimulation did not result in the appearance of H3K27ac at these sites nor induction of Pdcd1 expression, suggesting that cytokine treatment was in effect “licensing” the elements for activity. When cytokine treatment and TCR stimulation were combined, both H3K4me1 and H3K27ac were enriched at these elements, indicating the formation of an active chromatin state at these elements that contributed to increased PD-1 expression (62). Thus, distinct cytokine profiles elicited during infections are capable of manipulating the epigenetic program governing Pdcd1 gene expression.

Following resolution of an acute CD8 T cell activation, the CR-C region of Pdcd1 was enriched for the repressive histone modifications H3K9me3, H3K27me3, and H4K20me3, as summarized in Figure 1 (53). However, H3K9me3 and H3K27me3 were absent from the locus at the same time point in chronic infection or in tolerized cells expressing high levels of PD-1, showing a correlation between appearance of these inhibitory histone profiles and loss of PD-1 expression (48, 54). Exogenous expression of Blimp-1 in acutely activated T cells was capable of inducing these repressive modifications, and driving down PD-1 expression (53). Although Blimp-1 itself is not known to directly modify histone proteins, it does recruit other repressive histone modifying enzymes, including the histone deacetylases HDAC1 and HDAC2, the histone methyltransferase G9a, and the H3K4me2/me1 lysine specific demethylase LSD1 (81, 82, 99). It is important to note that both repressive and activating marks are absent from the locus in naïve cells (53, 54), indicating that active repression is employed only after PD-1 induction, and that the low PD-1 expression in naïve cells may be maintained exclusively by the absence of transcriptional activators and DNA methylation.


The reviewed data suggest that cell specific and cytokine micro-environmental regulation of PD-1 allows for multiple expression paradigms. Exhaustion and high levels of PD-1 are correlated with antigen exposure and prolonged TCR stimulation. How prolonged TCR stimulation and cytokine exposure drive the distinct epigenetic states of the locus remain to be discovered. Because these induction pathways are common to other immune system genes, careful consideration of the transcription factors and epigenetic parameters governing Pdcd1 expression is necessary to be able to control the regulation of PD-1 expression in therapeutic settings. Nonetheless, such pathways offer the prospect of novel targets to intervene with or augment PD-1 controlled immune responses.


We would like to thank the members of the lab for their critical input and feedback for this work.


5 hydroxymethylcytosine
B lymphocyte-induced maturation protein-1
Chromatin Immunoprecipitation
CCCTC binding factor
conserved region B/C
Cyclosporine A
histone H3
Interferon-stimulated gene factor
Interferon-stimulated response element
lysine 4 monomethylation
lysine 4 trimethylation
lysine 27 acetylation
lymphocytic choriomeningitis virus
Lewis Lung carcinoma
programmed death-1
PD-1 ligand 1/ligand 2
phorbol 12-myristate 13-acetate
Follicular helper T cell
regulatory CD4 T cell
transcription start site


1This work was supported by NIH RO1AI113021 to JMB. APRB was supported in part by NIH T32AI007610-12. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.


None of the authors have a financial conflict of interest.


1. Francisco LM, Sage PT, Sharpe AH. The PD-1 pathway in tolerance and autoimmunity. Immunol Rev. 2010;236:219–242. [PMC free article] [PubMed]
2. Boussiotis VA, Chatterjee P, Li L. Biochemical signaling of PD-1 on T cells and its functional implications. Cancer J. 2014;20:265–271. [PMC free article] [PubMed]
3. Nishimura H, Honjo T, Minato N. Facilitation of beta selection and modification of positive selection in the thymus of PD-1-deficient mice. J Exp Med. 2000;191:891–898. [PMC free article] [PubMed]
4. Nishimura H, Okazaki T, Tanaka Y, Nakatani K, Hara M, Matsumori A, Sasayama S, Mizoguchi A, Hiai H, Minato N, Honjo T. Autoimmune dilated cardiomyopathy in PD-1 receptor-deficient mice. Science. 2001;291:319–322. [PubMed]
5. Day CL, Kaufmann DE, Kiepiela P, Brown JA, Moodley ES, Reddy S, Mackey EW, Miller JD, Leslie AJ, DePierres C, Mncube Z, Duraiswamy J, Zhu B, Eichbaum Q, Altfeld M, Wherry EJ, Coovadia HM, Goulder PJ, Klenerman P, Ahmed R, Freeman GJ, Walker BD. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature. 2006;443:350–354. [PubMed]
6. Trautmann L, Janbazian L, Chomont N, Said EA, Gimmig S, Bessette B, Boulassel MR, Delwart E, Sepulveda H, Balderas RS, Routy JP, Haddad EK, Sekaly RP. Upregulation of PD-1 expression on HIV-specific CD8+ T cells leads to reversible immune dysfunction. Nat Med. 2006;12:1198–1202. [PubMed]
7. Nishimura H, Nose M, Hiai H, Minato N, Honjo T. Development of lupus-like autoimmune diseases by disruption of the PD-1 gene encoding an ITIM motif-carrying immunoreceptor. Immunity. 1999;11:141–151. [PubMed]
8. Rui Y, Honjo T, Chikuma S. Programmed cell death 1 inhibits inflammatory helper T-cell development through controlling the innate immune response. Proc Natl Acad Sci U S A. 2013;110:16073–16078. [PubMed]
9. Kroner A, Mehling M, Hemmer B, Rieckmann P, Toyka KV, Maurer M, Wiendl H. A PD-1 polymorphism is associated with disease progression in multiple sclerosis. Ann Neurol. 2005;58:50–57. [PubMed]
10. Prokunina L, Castillejo-Lopez C, Oberg F, Gunnarsson I, Berg L, Magnusson V, Brookes AJ, Tentler D, Kristjansdottir H, Grondal G, Bolstad AI, Svenungsson E, Lundberg I, Sturfelt G, Jonssen A, Truedsson L, Lima G, Alcocer-Varela J, Jonsson R, Gyllensten UB, Harley JB, Alarcon-Segovia D, Steinsson K, Alarcon-Riquelme ME. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. Nat Genet. 2002;32:666–669. [PubMed]
11. Nielsen C, Hansen D, Husby S, Jacobsen BB, Lillevang ST. Association of a putative regulatory polymorphism in the PD-1 gene with susceptibility to type 1 diabetes. Tissue antigens. 2003;62:492–497. [PubMed]
12. Barber DL, Wherry EJ, Masopust D, Zhu B, Allison JP, Sharpe AH, Freeman GJ, Ahmed R. Restoring function in exhausted CD8 T cells during chronic viral infection. Nature. 2006;439:682–687. [PubMed]
13. Urbani S, Amadei B, Tola D, Massari M, Schivazappa S, Missale G, Ferrari C. PD-1 expression in acute hepatitis C virus (HCV) infection is associated with HCV-specific CD8 exhaustion. J Virol. 2006;80:11398–11403. [PMC free article] [PubMed]
14. Petrovas C, Casazza JP, Brenchley JM, Price DA, Gostick E, Adams WC, Precopio ML, Schacker T, Roederer M, Douek DC, Koup RA. PD-1 is a regulator of virus-specific CD8+ T cell survival in HIV infection. J Exp Med. 2006;203:2281–2292. [PMC free article] [PubMed]
15. Grakoui A, John Wherry E, Hanson HL, Walker C, Ahmed R. Turning on the off switch: regulation of anti-viral T cell responses in the liver by the PD-1/PD-L1 pathway. Journal of hepatology. 2006;45:468–472. [PubMed]
16. Golden-Mason L, Palmer B, Klarquist J, Mengshol JA, Castelblanco N, Rosen HR. Upregulation of PD-1 expression on circulating and intrahepatic hepatitis C virus-specific CD8+ T cells associated with reversible immune dysfunction. Journal of virology. 2007;81:9249–9258. [PMC free article] [PubMed]
17. Peng G, Li S, Wu W, Tan X, Chen Y, Chen Z. PD-1 upregulation is associated with HBV-specific T cell dysfunction in chronic hepatitis B patients. Mol Immunol. 2008;45:963–970. [PubMed]
18. Fuller MJ, Callendret B, Zhu B, Freeman GJ, Hasselschwert DL, Satterfield W, Sharpe AH, Dustin LB, Rice CM, Grakoui A, Ahmed R, Walker CM. Immunotherapy of chronic hepatitis C virus infection with antibodies against programmed cell death-1 (PD-1) Proc Natl Acad Sci U S A. 2013;110:15001–15006. [PubMed]
19. Zajac AJ, Blattman JN, Murali-Krishna K, Sourdive DJ, Suresh M, Altman JD, Ahmed R. Viral immune evasion due to persistence of activated T cells without effector function. J Exp Med. 1998;188:2205–2213. [PMC free article] [PubMed]
20. Gallimore A, Glithero A, Godkin A, Tissot AC, Pluckthun A, Elliott T, Hengartner H, Zinkernagel R. Induction and exhaustion of lymphocytic choriomeningitis virus-specific cytotoxic T lymphocytes visualized using soluble tetrameric major histocompatibility complex class I-peptide complexes. J Exp Med. 1998;187:1383–1393. [PMC free article] [PubMed]
21. Chen L. Co-inhibitory molecules of the B7-CD28 family in the control of T-cell immunity. Nat Rev Immunol. 2004;4:336–347. [PubMed]
22. Wherry EJ, Ha SJ, Kaech SM, Haining WN, Sarkar S, Kalia V, Subramaniam S, Blattman JN, Barber DL, Ahmed R. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity. 2007;27:670–684. [PubMed]
23. Odorizzi PM, Pauken KE, Paley MA, Sharpe A, Wherry EJ. Genetic absence of PD-1 promotes accumulation of terminally differentiated exhausted CD8+ T cells. J Exp Med. 2015;212:1125–1137. [PMC free article] [PubMed]
24. Turnis ME, Andrews LP, Vignali DA. Inhibitory receptors as targets for cancer immunotherapy. European journal of immunology. 2015;45:1892–1905. [PMC free article] [PubMed]
25. Blank C, Brown I, Peterson AC, Spiotto M, Iwai Y, Honjo T, Gajewski TF. PD-L1/B7H-1 inhibits the effector phase of tumor rejection by T cell receptor (TCR) transgenic CD8+ T cells. Cancer Res. 2004;64:1140–1145. [PubMed]
26. Curiel TJ, Wei S, Dong H, Alvarez X, Cheng P, Mottram P, Krzysiek R, Knutson KL, Daniel B, Zimmermann MC, David O, Burow M, Gordon A, Dhurandhar N, Myers L, Berggren R, Hemminki A, Alvarez RD, Emilie D, Curiel DT, Chen L, Zou W. Blockade of B7-H1 improves myeloid dendritic cell-mediated antitumor immunity. Nat Med. 2003;9:562–567. [PubMed]
27. Sierro SR, Donda A, Perret R, Guillaume P, Yagita H, Levy F, Romero P. Combination of lentivector immunization and low-dose chemotherapy or PD-1/PD-L1 blocking primes self-reactive T cells and induces anti-tumor immunity. European journal of immunology. 2011;41:2217–2228. [PubMed]
28. Winograd R, Byrne KT, Evans RA, Odorizzi PM, Meyer AR, Bajor DL, Clendenin C, Stanger BZ, Furth EE, Wherry EJ, Vonderheide RH. Induction of T-cell Immunity Overcomes Complete Resistance to PD-1 and CTLA-4 Blockade and Improves Survival in Pancreatic Carcinoma. Cancer Immunol Res. 2015;3:399–411. [PMC free article] [PubMed]
29. Taube JM, Klein AP, Brahmer JR, Xu H, Pan X, Kim JH, Chen L, Pardoll DM, Topalian SL, Anders RA. Association of PD-1, PD-1 ligands, and other features of the tumor immune microenvironment with response to anti-PD-1 therapy. Clinical cancer research : an official journal of the American Association for Cancer Research 2014 [PMC free article] [PubMed]
30. Agata Y, Kawasaki A, Nishimura H, Ishida Y, Tsubata T, Yagita H, Honjo T. Expression of the PD-1 antigen on the surface of stimulated mouse T and B lymphocytes. Int Immunol. 1996;8:765–772. [PubMed]
31. Hiroyuki Nishimura YA, Kawasaki Akemi, Sato Masaki, Imamura Sadao, Minato Nagahiro, Yagita Hideo, Nakano Toru, Honjo Tasuku. Developmentally regulated expression of the PD-1 protein on the surface of double-negative (CD4~CD8~) thymocytes. International Immunology. 1996;8:773–780. [PubMed]
32. Haynes NM, Allen CD, Lesley R, Ansel KM, Killeen N, Cyster JG. Role of CXCR5 and CCR7 in follicular Th cell positioning and appearance of a programmed cell death gene-1high germinal center-associated subpopulation. J Immunol. 2007;179:5099–5108. [PubMed]
33. Yao S, Wang S, Zhu Y, Luo L, Zhu G, Flies S, Xu H, Ruff W, Broadwater M, Choi IH, Tamada K, Chen L. PD-1 on dendritic cells impedes innate immunity against bacterial infection. Blood. 2009;113:5811–5818. [PubMed]
34. Zhang Y, Ma CJ, Ni L, Zhang CL, Wu XY, Kumaraguru U, Li CF, Moorman JP, Yao ZQ. Cross-talk between programmed death-1 and suppressor of cytokine signaling-1 in inhibition of IL-12 production by monocytes/macrophages in hepatitis C virus infection. J Immunol. 2011;186:3093–3103. [PubMed]
35. Okazaki T, Maeda A, Nishimura H, Kurosaki T, Honjo T. PD-1 immunoreceptor inhibits B cell receptor-mediated signaling by recruiting src homology 2-domain-containing tyrosine phosphatase 2 to phosphotyrosine. Proc Natl Acad Sci U S A. 2001;98:13866–13871. [PubMed]
36. Bally AP, Lu P, Tang Y, Austin JW, Scharer CD, Ahmed R, Boss JM. NF-kappaB Regulates PD-1 Expression in Macrophages. J Immunol. 2015;194:4545–4554. [PMC free article] [PubMed]
37. Honda T, Egen JG, Lammermann T, Kastenmuller W, Torabi-Parizi P, Germain RN. Tuning of antigen sensitivity by T cell receptor-dependent negative feedback controls T cell effector function in inflamed tissues. Immunity. 2014;40:235–247. [PMC free article] [PubMed]
38. Costa PA, Leoratti FM, Figueiredo MM, Tada MS, Pereira DB, Junqueira C, Soares IS, Barber DL, Gazzinelli RT, Antonelli LR. Induction of Inhibitory Receptors on T Cells During Plasmodium vivax Malaria Impairs Cytokine Production. J Infect Dis 2015 [PMC free article] [PubMed]
39. Topalian SL, Hodi FS, Brahmer JR, Gettinger SN, Smith DC, McDermott DF, Powderly JD, Carvajal RD, Sosman JA, Atkins MB, Leming PD, Spigel DR, Antonia SJ, Horn L, Drake CG, Pardoll DM, Chen L, Sharfman WH, Anders RA, Taube JM, McMiller TL, Xu H, Korman AJ, Jure-Kunkel M, Agrawal S, McDonald D, Kollia GD, Gupta A, Wigginton JM, Sznol M. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med. 2012;366:2443–2454. [PMC free article] [PubMed]
40. Brahmer JR, Tykodi SS, Chow LQ, Hwu WJ, Topalian SL, Hwu P, Drake CG, Camacho LH, Kauh J, Odunsi K, Pitot HC, Hamid O, Bhatia S, Martins R, Eaton K, Chen S, Salay TM, Alaparthy S, Grosso JF, Korman AJ, Parker SM, Agrawal S, Goldberg SM, Pardoll DM, Gupta A, Wigginton JM. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N Engl J Med. 2012;366:2455–2465. [PMC free article] [PubMed]
41. Hamid O, Robert C, Daud A, Hodi FS, Hwu WJ, Kefford R, Wolchok JD, Hersey P, Joseph RW, Weber JS, Dronca R, Gangadhar TC, Patnaik A, Zarour H, Joshua AM, Gergich K, Elassaiss-Schaap J, Algazi A, Mateus C, Boasberg P, Tumeh PC, Chmielowski B, Ebbinghaus SW, Li XN, Kang SP, Ribas A. Safety and tumor responses with lambrolizumab (anti-PD-1) in melanoma. N Engl J Med. 2013;369:134–144. [PMC free article] [PubMed]
42. Topalian SL, Sznol M, McDermott DF, Kluger HM, Carvajal RD, Sharfman WH, Brahmer JR, Lawrence DP, Atkins MB, Powderly JD, Leming PD, Lipson EJ, Puzanov I, Smith DC, Taube JM, Wigginton JM, Kollia GD, Gupta A, Pardoll DM, Sosman JA, Hodi FS. Survival, durable tumor remission, and long-term safety in patients with advanced melanoma receiving nivolumab. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2014;32:1020–1030. [PMC free article] [PubMed]
43. Goding SR, Wilson KA, Xie Y, Harris KM, Baxi A, Akpinarli A, Fulton A, Tamada K, Strome SE, Antony PA. Restoring immune function of tumor-specific CD4+ T cells during recurrence of melanoma. J Immunol. 2013;190:4899–4909. [PMC free article] [PubMed]
44. Jin HT, Anderson AC, Tan WG, West EE, Ha SJ, Araki K, Freeman GJ, Kuchroo VK, Ahmed R. Cooperation of Tim-3 and PD-1 in CD8 T-cell exhaustion during chronic viral infection. Proc Natl Acad Sci U S A. 2010;107:14733–14738. [PubMed]
45. Duraiswamy J, Kaluza KM, Freeman GJ, Coukos G. Dual blockade of PD-1 and CTLA-4 combined with tumor vaccine effectively restores T-cell rejection function in tumors. Cancer Res. 2013;73:3591–3603. [PMC free article] [PubMed]
46. Johnston RJ, Poholek AC, DiToro D, Yusuf I, Eto D, Barnett B, Dent AL, Craft J, Crotty S. Bcl6 and Blimp-1 are reciprocal and antagonistic regulators of T follicular helper cell differentiation. Science. 2009;325:1006–1010. [PMC free article] [PubMed]
47. Crotty S. Follicular helper CD4 T cells (TFH) Annu Rev Immunol. 2011;29:621–663. [PubMed]
48. McPherson RC, Konkel JE, Prendergast CT, Thomson JP, Ottaviano R, Leech MD, Kay O, Zandee SE, Sweenie CH, Wraith DC, Meehan RR, Drake AJ, Anderton SM. Epigenetic modification of the PD-1 (Pdcd1) promoter in effector CD4(+) T cells tolerized by peptide immunotherapy. eLife. 2015:4. [PMC free article] [PubMed]
49. Allie SR, Zhang W, Fuse S, Usherwood EJ. Programmed death 1 regulates development of central memory CD8 T cells after acute viral infection. J Immunol. 2011;186:6280–6286. [PMC free article] [PubMed]
50. Chemnitz JM, Parry RV, Nichols KE, June CH, Riley JL. SHP-1 and SHP-2 associate with immunoreceptor tyrosine-based switch motif of programmed death 1 upon primary human T cell stimulation, but only receptor ligation prevents T cell activation. J Immunol. 2004;173:945–954. [PubMed]
51. Vibhakar R, Juan G, Traganos F, Darzynkiewicz Z, Finger LR. Activation-induced expression of human programmed death-1 gene in T-lymphocytes. Exp Cell Res. 1997;232:25–28. [PubMed]
52. Oestreich KJ, Yoon H, Ahmed R, Boss JM. NFATc1 regulates PD-1 expression upon T cell activation. J Immunol. 2008;181:4832–4839. [PMC free article] [PubMed]
53. Lu P, Youngblood BA, Austin JW, Rasheed Mohammed AU, Butler R, Ahmed R, Boss JM. Blimp-1 represses CD8 T cell expression of PD-1 using a feed-forward transcriptional circuit during acute viral infection. J Exp Med. 2014;211:515–527. [PMC free article] [PubMed]
54. Youngblood B, Oestreich KJ, Ha SJ, Duraiswamy J, Akondy RS, West EE, Wei Z, Lu P, Austin JW, Riley JL, Boss JM, Ahmed R. Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8(+) T cells. Immunity. 2011;35:400–412. [PMC free article] [PubMed]
55. Mueller SN, Langley WA, Li G, Garcia-Sastre A, Webby RJ, Ahmed R. Qualitatively different memory CD8+ T cells are generated after lymphocytic choriomeningitis virus and influenza virus infections. J Immunol. 2010;185:2182–2190. [PubMed]
56. West EE, Jin HT, Rasheed AU, Penaloza-Macmaster P, Ha SJ, Tan WG, Youngblood B, Freeman GJ, Smith KA, Ahmed R. PD-L1 blockade synergizes with IL-2 therapy in reinvigorating exhausted T cells. J Clin Invest. 2013;123:2604–2615. [PMC free article] [PubMed]
57. Blackburn SD, Shin H, Haining WN, Zou T, Workman CJ, Polley A, Betts MR, Freeman GJ, Vignali DA, Wherry EJ. Coregulation of CD8+ T cell exhaustion by multiple inhibitory receptors during chronic viral infection. Nat Immunol. 2009;10:29–37. [PMC free article] [PubMed]
58. Overwijk WW, Restifo NP. B16 as a mouse model for human melanoma. In: Coligan John E, et al., editors. Current protocols in immunology. Unit 20. Chapter 20. 2001. p. 21. [PMC free article] [PubMed]
59. Xiao G, Deng A, Liu H, Ge G, Liu X. Activator protein 1 suppresses antitumor T-cell function via the induction of programmed death 1. Proc Natl Acad Sci U S A. 2012;109:15419–15424. [PubMed]
60. Cho HY, Lee SW, Seo SK, Choi IW, Choi I. Interferon-sensitive response element (ISRE) is mainly responsible for IFN-alpha-induced upregulation of programmed death-1 (PD-1) in macrophages. Biochim Biophys Acta. 2008;1779:811–819. [PubMed]
61. Staron MM, Gray SM, Marshall HD, Parish IA, Chen JH, Perry CJ, Cui G, Li MO, Kaech SM. The transcription factor FoxO1 sustains expression of the inhibitory receptor PD-1 and survival of antiviral CD8(+) T cells during chronic infection. Immunity. 2014;41:802–814. [PMC free article] [PubMed]
62. Austin JW, Lu P, Majumder P, Ahmed R, Boss JM. STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells. J Immunol. 2014;192:4876–4886. [PMC free article] [PubMed]
63. Kao C, Oestreich KJ, Paley MA, Crawford A, Angelosanto JM, Ali MA, Intlekofer AM, Boss JM, Reiner SL, Weinmann AS, Wherry EJ. Transcription factor T-bet represses expression of the inhibitory receptor PD-1 and sustains virus-specific CD8+ T cell responses during chronic infection. Nat Immunol. 2011;12:663–671. [PMC free article] [PubMed]
64. Mathieu M, Cotta-Grand N, Daudelin JF, Thebault P, Labrecque N. Notch signaling regulates PD-1 expression during CD8(+) T-cell activation. Immunol Cell Biol. 2013;91:82–88. [PubMed]
65. Youngblood B, Noto A, Porichis F, Akondy RS, Ndhlovu ZM, Austin JW, Bordi R, Procopio FA, Miura T, Allen TM, Sidney J, Sette A, Walker BD, Ahmed R, Boss JM, Sekaly RP, Kaufmann DE. Cutting edge: Prolonged exposure to HIV reinforces a poised epigenetic program for PD-1 expression in virus-specific CD8 T cells. J Immunol. 2013;191:540–544. [PMC free article] [PubMed]
66. Terawaki S, Chikuma S, Shibayama S, Hayashi T, Yoshida T, Okazaki T, Honjo T. IFN-alpha directly promotes programmed cell death-1 transcription and limits the duration of T cell-mediated immunity. J Immunol. 2011;186:2772–2779. [PubMed]
67. Hou C, Zhao H, Tanimoto K, Dean A. CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc Natl Acad Sci U S A. 2008;105:20398–20403. [PubMed]
68. Wherry EJ, Blattman JN, Murali-Krishna K, van der Most R, Ahmed R. Viral persistence alters CD8 T-cell immunodominance and tissue distribution and results in distinct stages of functional impairment. J Virol. 2003;77:4911–4927. [PMC free article] [PubMed]
69. Rao A, Luo C, Hogan PG. Transcription factors of the NFAT family: regulation and function. Annu Rev Immunol. 1997;15:707–747. [PubMed]
70. Agnellini P, Wolint P, Rehr M, Cahenzli J, Karrer U, Oxenius A. Impaired NFAT nuclear translocation results in split exhaustion of virus-specific CD8+ T cell functions during chronic viral infection. Proc Natl Acad Sci U S A. 2007;104:4565–4570. [PubMed]
71. Macian F, Lopez-Rodriguez C, Rao A. Partners in transcription: NFAT and AP-1. Oncogene. 2001;20:2476–2489. [PubMed]
72. Cho OH, Shin HM, Miele L, Golde TE, Fauq A, Minter LM, Osborne BA. Notch regulates cytolytic effector function in CD8+ T cells. J Immunol. 2009;182:3380–3389. [PMC free article] [PubMed]
73. Maekawa Y, Minato Y, Ishifune C, Kurihara T, Kitamura A, Kojima H, Yagita H, Sakata-Yanagimoto M, Saito T, Taniuchi I, Chiba S, Sone S, Yasutomo K. Notch2 integrates signaling by the transcription factors RBP-J and CREB1 to promote T cell cytotoxicity. Nat Immunol. 2008;9:1140–1147. [PubMed]
74. Pan T, Liu Z, Yin J, Zhou T, Liu J, Qu H. Notch Signaling Pathway Was Involved in Regulating Programmed Cell Death 1 Expression during Sepsis-Induced Immunosuppression. Mediators Inflamm. 2015;2015:539841. [PMC free article] [PubMed]
75. Joshi NS, Cui W, Chandele A, Lee HK, Urso DR, Hagman J, Gapin L, Kaech SM. Inflammation directs memory precursor and short-lived effector CD8(+) T cell fates via the graded expression of T-bet transcription factor. Immunity. 2007;27:281–295. [PMC free article] [PubMed]
76. Kallies A, Xin A, Belz GT, Nutt SL. Blimp-1 transcription factor is required for the differentiation of effector CD8(+) T cells and memory responses. Immunity. 2009;31:283–295. [PubMed]
77. Rutishauser RL, Martins GA, Kalachikov S, Chandele A, Parish IA, Meffre E, Jacob J, Calame K, Kaech SM. Transcriptional repressor Blimp-1 promotes CD8(+) T cell terminal differentiation and represses the acquisition of central memory T cell properties. Immunity. 2009;31:296–308. [PMC free article] [PubMed]
78. Shaffer AL, Yu X, He Y, Boldrick J, Chan EP, Staudt LM. BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. Immunity. 2000;13:199–212. [PubMed]
79. Shin H, Blackburn SD, Intlekofer AM, Kao C, Angelosanto JM, Reiner SL, Wherry EJ. A role for the transcriptional repressor Blimp-1 in CD8(+) T cell exhaustion during chronic viral infection. Immunity. 2009;31:309–320. [PMC free article] [PubMed]
80. Shin HM, V, Kapoor N, Guan T, Kaech SM, Welsh RM, Berg LJ. Epigenetic modifications induced by Blimp-1 Regulate CD8(+) T cell memory progression during acute virus infection. Immunity. 2013;39:661–675. [PMC free article] [PubMed]
81. Su ST, Ying HY, Chiu YK, Lin FR, Chen MY, Lin KI. Involvement of histone demethylase LSD1 in Blimp-1-mediated gene repression during plasma cell differentiation. Mol Cell Biol. 2009;29:1421–1431. [PMC free article] [PubMed]
82. Yu J, Angelin-Duclos C, Greenwood J, Liao J, Calame K. Transcriptional repression by blimp-1 (PRDI-BF1) involves recruitment of histone deacetylase. Mol Cell Biol. 2000;20:2592–2603. [PMC free article] [PubMed]
83. Kerdiles YM, Beisner DR, Tinoco R, Dejean AS, Castrillon DH, DePinho RA, Hedrick SM. Foxo1 links homing and survival of naive T cells by regulating L-selectin, CCR7 and interleukin 7 receptor. Nat Immunol. 2009;10:176–184. [PMC free article] [PubMed]
84. Rao RR, Li Q, Gubbels Bupp MR, Shrikant PA. Transcription factor Foxo1 represses T-bet-mediated effector functions and promotes memory CD8(+) T cell differentiation. Immunity. 2012;36:374–387. [PMC free article] [PubMed]
85. Rogge L, Barberis-Maino L, Biffi M, Passini N, Presky DH, Gubler U, Sinigaglia F. Selective expression of an interleukin-12 receptor component by human T helper 1 cells. J Exp Med. 1997;185:825–831. [PMC free article] [PubMed]
86. Schurich A, Pallett LJ, Lubowiecki M, Singh HD, Gill US, Kennedy PT, Nastouli E, Tanwar S, Rosenberg W, Maini MK. The third signal cytokine IL-12 rescues the anti-viral function of exhausted HBV-specific CD8 T cells. PLoS Pathog. 2013;9:e1003208. [PMC free article] [PubMed]
87. Said EA, Dupuy FP, Trautmann L, Zhang Y, Shi Y, El-Far M, Hill BJ, Noto A, Ancuta P, Peretz Y, Fonseca SG, Van Grevenynghe J, Boulassel MR, Bruneau J, Shoukry NH, Routy JP, Douek DC, Haddad EK, Sekaly RP. Programmed death-1-induced interleukin-10 production by monocytes impairs CD4+ T cell activation during HIV infection. Nat Med. 2010;16:452–459. [PMC free article] [PubMed]
88. Horvath CM, Stark GR, Kerr IM, Darnell JE., Jr Interactions between STAT and non-STAT proteins in the interferon-stimulated gene factor 3 transcription complex. Molecular and cellular biology. 1996;16:6957–6964. [PMC free article] [PubMed]
89. Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet. 2002;3:662–673. [PubMed]
90. Lee PP, Fitzpatrick DR, Beard C, Jessup HK, Lehar S, Makar KW, Perez-Melgosa M, Sweetser MT, Schlissel MS, Nguyen S, Cherry SR, Tsai JH, Tucker SM, Weaver WM, Kelso A, Jaenisch R, Wilson CB. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity. 2001;15:763–774. [PubMed]
91. Araki Y, Wang Z, Zang C, Wood WH, 3rd, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP. Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells. Immunity. 2009;30:912–925. [PMC free article] [PubMed]
92. Scharer CD, Barwick BG, Youngblood BA, Ahmed R, Boss JM. Global DNA methylation remodeling accompanies CD8 T cell effector function. J Immunol. 2013;191:3419–3429. [PMC free article] [PubMed]
93. Shih HY, Sciume G, Poholek AC, Vahedi G, Hirahara K, Villarino AV, Bonelli M, Bosselut R, Kanno Y, Muljo SA, O’Shea JJ. Transcriptional and epigenetic networks of helper T and innate lymphoid cells. Immunol Rev. 2014;261:23–49. [PMC free article] [PubMed]
94. Utzschneider DT, Legat A, Fuertes Marraco SA, Carrie L, Luescher I, Speiser DE, Zehn D. T cells maintain an exhausted phenotype after antigen withdrawal and population reexpansion. Nat Immunol. 2013;14:603–610. [PubMed]
95. Xu J, Pope SD, Jazirehi AR, Attema JL, Papathanasiou P, Watts JA, Zaret KS, Weissman IL, Smale ST. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci U S A. 2007;104:12377–12382. [PubMed]
96. Hashimoto H, Liu Y, Upadhyay AK, Chang Y, Howerton SB, Vertino PM, Zhang X, Cheng X. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 2012;40:4841–4849. [PMC free article] [PubMed]
97. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324:930–935. [PMC free article] [PubMed]
98. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010;107:21931–21936. [PubMed]
99. Gyory I, Wu J, Fejer G, Seto E, Wright KL. PRDI-BF1 recruits the histone H3 methyltransferase G9a in transcriptional silencing. Nat Immunol. 2004;5:299–308. [PubMed]