On the stochastic regulation of interleukin-2 transcription

Expression Efficiency of Multiple Il9 Reporter Alleles Is Determined by Cell Lineage

Generation of allelic gene reporter mice has provided a powerful tool to study gene function in vivo. In conjunction with imaging technologies, reporter mouse models facilitate studies of cell lineage tracing, live cell imaging, and gene expression in the context of diseases. Although there are several advantages to using reporter mice, caution is important to ensure the fidelity of the reporter protein representing the gene of interest. In this study, we compared the efficiency of two Il9 reporter strains Il9^citrine and Il9^GFP in representing IL-9-producing CD4⁺ T_H9 cells. Although both alleles show high specificity in IL-9-expressing populations, we observed that the Il9^GFP allele visualized a much larger proportion of the IL-9-producing cells in culture than the Il9^citrine reporter allele. In defining the mechanistic basis for these differences, chromatin immunoprecipitation and chromatin accessibility assay showed that the Il9^citrine allele was transcriptionally less active in T_H9 cells compared with the wild-type allele. The Il9^citrine allele also only captured a fraction of IL-9-expressing bone marrow-derived mast cells. In contrast, the Il9 ^citrine reporter detected Il9 expression in type 2 innate lymphoid cells at a greater percentage than could be identified by IL-9 intracellular cytokine staining. Taken together, our findings demonstrate that the accuracy of IL-9 reporter mouse models may vary with the cell type being examined. These studies demonstrate the importance of choosing appropriate reporter mouse models that are optimal for detecting the cell type of interest as well as the accuracy of conclusions.

Logic of the inflammation-associated transcriptional response

Immune response to pathogens depends on coordinated regulation of numerous genes that contribute collectively to pathogen elimination and restoration of the integrity of the affected tissue. The pathogen-induced gene expression is governed largely by the signal-induced posttranslational histone modifications that facilitate assembly of the functionally distinct chromatin complexes. In this review, we describe the principles of chromatin-based gene regulation during innate immune responses. We discuss the ability of pathogens to hijack the host response by interfering with various arms of transcriptional machinery involved in the responses. In particular, we discuss the phenomenon of the histone mimicry where interaction between histones and transcriptional regulators is targeted by pathogens that carry the histone-like sequences (histone mimics). We show how the principle of isotone mimicry as an efficient way to control host gene expression has been sued for the development of novel anti-inflammatory pharmacological approaches.

Stochastic expression of the interferon-β gene

The analysis of stochastic interferon-beta gene expression in virus-infected mammalian cells reveals that the levels of components required for virtually every step in the virus induction pathway are limiting.

Virus infection of mammalian cells induces the production of high levels of type I interferons (IFNα and β), cytokines that orchestrate antiviral innate and adaptive immunity. Previous studies have shown that only a fraction of the infected cells produce IFN. However, the mechanisms responsible for this stochastic expression are poorly understood. Here we report an in depth analysis of IFN-expressing and non-expressing mouse cells infected with Sendai virus. Mouse embryonic fibroblasts in which an internal ribosome entry site/yellow fluorescent protein gene was inserted downstream from the endogenous IFNβ gene were used to distinguish between the two cell types, and they were isolated from each other using fluorescence-activated cell sorting methods. Analysis of the separated cells revealed that stochastic IFNβ expression is a consequence of cell-to-cell variability in the levels and/or activities of limiting components at every level of the virus induction process, ranging from viral replication and expression, to the sensing of viral RNA by host factors, to activation of the signaling pathway, to the levels of activated transcription factors. We propose that this highly complex stochastic IFNβ gene expression evolved to optimize both the level and distribution of type I IFNs in response to virus infection.

Eukaryotic cells can respond to extracellular signals by triggering the activation of specific genes. Viral infection of mammalian cells, for example, induces a high level of expression of type I interferons (IFNα and β), proteins required for antiviral immunity that protects cells from the infection. Previous studies have shown that the expression of the IFNβ gene is stochastic, and under optimal conditions only a fraction of the infected cells express the IFNβ gene. At present neither the mechanisms nor functions of this interesting phenomenon are well understood. We have addressed this question by analyzing IFN-expressing and non-expressing mouse cells that were infected with the highly transmissible Sendai virus. We show that stochastic IFNβ gene expression is a consequence of cell-to-cell differences in limiting levels and/or activities of virus components at every level of the virus induction process, from viral replication to expression. These differences include the sensing of viral RNA by host factors, the activation of the signaling pathway, and the levels of activated transcription factors. Our findings reveal the complexity of the regulatory mechanisms controlling stochastic IFNβ gene expression. We propose that the stochastic expression of IFN allows for an even distribution of IFN, thus avoiding over-expression of IFN in infected cells.

Nuclear export of NF90 to stabilize IL-2 mRNA is mediated by AKT-dependent phosphorylation at Ser647 in response to CD28 costimulation

IL-2 is one of the most important cytokines required for T cell-mediated immune responses. Costimulation of CD28 in T cells up-regulates IL-2 mRNA levels via transcription activation and mRNA stabilization. Upon T cell activation, NF90, an AU-rich element (ARE)-binding protein, translocates from the nucleus into the cytoplasm, where it binds to the ARE-containing 3' untranslated regions of IL-2 mRNA and slows down degradation of IL-2 mRNA. The translocation of NF90 is mediated through a nuclear export signal at its N terminus, but how it is triggered is still unclear. Phosphorylation of ARE-binding proteins has been reported as a signal transduction pathway to stabilize ARE-containing transcripts. In this study, we demonstrate that AKT phosphorylates NF90 on Ser647 upon CD28 costimulation. This phosphorylation is necessary for nuclear export of NF90 and IL-2 mRNA stabilization by this protein, because a mutation at Ser647 abolished both functions. We observed that treatment of cells with CD28 costimulation induced distinct increase in phosphorylation of AKT and NF90 at Ser647 concomitantly. Phosphorylation at Ser647 of NF90 up-regulated IL-2 production in response to CD28 costimulation. In vivo and in vitro data support a model in which CD28 costimulation activates AKT to phosphorylate NF90 at Ser647 and phosphorylation triggers NF90 to relocate to the cytoplasm and stabilize IL-2 mRNA.

Control of interleukin-2 gene transcription: a paradigm for inducible, tissue-specific gene expression

Interleukin-2 (IL-2) is a key cytokine that controls immune cell function, in particular the adaptive arm of the immune system, through its ability to control the clonal expansion and homeostasis of peripheral T cells. IL-2 is produced almost exclusively by T cells in response to antigenic stimulation and thus provides an excellent example of a cell-specific inducible gene. The mechanisms that control IL-2 gene transcription have been studied in detail for the past 20 years and our current understanding of the nature of the inducible and tissue-specific controls will be discussed.

Modeling embryogenesis and cancer: an approach based on an equilibrium between the autostabilization of stochastic gene expression and the interdependence of cells for proliferation

A large amount of data demonstrating the stochastic nature of gene expression and cell differentiation has accumulated during the last 40 years. These data suggest that a gene in a cell always has a certain probability of being activated at any time and that instead of leading to on and off switches in an all-or-nothing fashion, the concentration of transcriptional regulators increases or decreases this probability. In order to integrate these data in an appropriate theoretical frame, we have tested the relevance of the selective model of cell differentiation by computer simulation experiments. This model is based on stochastic gene expression controlled by cellular interactions. Our results show that it is readily able to produce tissue organization. A model involving only two cells generated a bi-layer cellular structure of finite growth. Cell death was not a drawback but an advantage because it improved the viability of this bi-layer structure. However, our results also show that cellular interactions cannot be simply based on raw selection between cells. Instead, tissue coordination includes at least two basic components: phenotypic autostabilization (differentiated cells stabilize their own phenotype) and interdependence for proliferation (differentiated cells stimulate the proliferation of alien phenotypes). In this modified autostabilization-selection model, cellular organization and growth arrest result from a quantitative equilibrium between the parameters controlling these two processes. An imbalance leads to tissue disorganization and invasive cancer-like growth. These findings suggest that cancer does not result solely from mutations in the cancerous cell but from the progressive addition of several small alterations of the equilibrium between autostabilization and interdependence for proliferation. In this frame, it is not solely the cancerous cell that is abnormal. The whole organism is involved. Tumor growth is a local effect of an imbalance between all the factors involved in tissue organization.

Cytokine mRNA levels in brain and peripheral tissues of the rat: relationships with plus-maze behavior

There is evidence that interleukin (IL)-2 may be related to anxiety as measured in the elevated plus-maze. Recently, we showed that normal adult male Wistar rats can differ systematically in this test of avoidance behavior, that is, time spent on the open arms of the elevated plus-maze. Rats with low open arm time had higher striatal levels of IL-2 mRNA than those with high open arm time, but did not differ significantly in expression of other striatal cytokine mRNA. Here, we investigated whether these expression effects are anatomically specific to the striatum. Therefore, we asked in this double-blind study whether elevated plus-maze behavior may also be related to endogenous levels of cytokine mRNA in other brain regions, which play a role for anxiety, namely the amygdala, hippocampus, and the prefrontal cortex. Additionally, and as peripheral controls, immuno-neuro-endocrine relevant tissues (adrenal glands, spleen) were analyzed. Based on open arm time in the elevated plus-maze, male Wistar rats were divided into sub-groups with either low or high open arm time behavior. Then, IL-1beta, IL-2, IL-6, and tumor necrosis factor (TNF)-alpha cDNA levels were measured post-mortem using semi-quantitative, competitive, reverse transcription polymerase chain reaction. First, we found that cytokine expressions differed considerably between and within these central and peripheral tissues. Secondly, rats with high compared to low open arm time behavior showed higher IL-2 mRNA levels in the prefrontal cortex, which is an inverse pattern to what we recently found in the striatum. These results provide new evidence indicating that cytokine mRNA in the brain can be related to elevated plus-maze behavior and that this relationship is site (prefrontal cortex, striatum)- and cytokine mRNA-specific (IL-2).

CATERPILLER 16.2 (CLR16.2), a novel NBD/LRR family member that negatively regulates T cell function

The newly discovered mammalian CATERPILLER (NOD, NALP, PAN) family of proteins share similarities with the NBD-LRR superfamily of plant disease resistance (R) proteins and are predicted to mediate important immune regulatory function. This report describes the first cloning and characterization of a novel CATERPILLER gene, CLR16.2 that is located on human chromosome 16. The protein encoded by this gene has a typical NBD-LRR configuration. Analysis of CLR16.2 suggests the highest expression among T lymphocytes. Cellular localization studies of CLR16.2 revealed that it is a cytoplasmic protein. Querying microarray studies in the public data base showed that CLR16.2 was significantly (>90%) down-regulated 6 h after anti-CD3 and anti-CD28 stimulation of primary T lymphocytes. Its reduction upon T cell stimulation is consistent with a potential negative regulatory role. Indeed CLR16.2 decreased NF-kappaB, NFAT, and AP-1 induction of reporter gene constructs in response to T cell activation by anti-CD3 and anti-CD28 antibodies or PMA and ionomycin. Following T cell stimulation, the presence of CLR16.2 reduced the levels of the endogenous transcripts for the IL-2 and CD25 proteins that are central in maintaining T cell activation and preventing T cell anergy. This reduction was accompanied by a delay of IkappaBalpha degradation. We propose that CLR16.2 serves to attenuate T cell activation via TCR and co-stimulatory molecules, and its reduction during T cell stimulation allows the ensuing cellular activation.

Tristetraprolin Down-RegulatesIL-2Gene Expression through AU-Rich Element-Mediated mRNA Decay

Posttranscriptional regulation of IL-2 gene expression at the level of mRNA decay is mediated by an AU-rich element (ARE) found in the 3'-untranslated region. We hypothesized that the ARE-binding protein tristetraprolin (TTP) regulates T lymphocyte IL-2 mRNA decay by interacting with the IL-2 ARE and targeting the transcript for decay. rTTP protein expressed in HeLa cells bound specifically to the IL-2 ARE with high affinity in a gel shift assay. In primary human T lymphocytes, TTP mRNA and protein expression were induced by TCR and CD28 coreceptor stimulation. Using a gel shift assay, we identified a cytoplasmic RNA-binding activity that was induced by TCR and CD28 coreceptor stimulation and bound specifically to the IL-2 ARE sequence. Using anti-TTP Abs, we showed by supershift that this inducible activity contained TTP. We also showed that insertion of the IL-2 ARE sequence into the 3'-untranslated region of a beta-globin reporter construct conferred TTP-dependent mRNA destabilization on the beta-globin reporter. To determine whether TTP also regulates IL-2 gene expression in vivo, we examined IL-2 expression in primary cells from wild-type and TTP knockout mice. Compared with their wild-type counterparts, TCR- and CD28-activated splenocytes and T cells from TTP knockout mice overexpressed IL-2 mRNA and protein. Also, IL-2 mRNA was more stable in activated splenocytes from TTP knockout mice compared with wild-type mice. Taken together, these data suggest that TTP functions to down-regulate IL-2 gene expression through ARE-mediated mRNA decay.

Critical Role of TNF Receptor Type-2 (p75) as a Costimulator for IL-2 Induction and T Cell Survival: A Functional Link to CD28

CD28 provides important signals that lower the threshold of T cell activation, augment the production of IL-2, and promote T cell survival. The recent identification of a second family of costimulatory molecules within the TNFR family has reshaped the "two-signal" model of T cell activation. In this study the role of p75 as a T cell costimulatory molecule in controlling cell fate during TCR/CD28-mediated stimulation was examined. We found that p75-deficient T cells possess a profound defect in IL-2 production in response to TCR/CD28-mediated stimulation. Examination of key signaling intermediates revealed that TCR proximal events such as global tyrosine phosphorylation and ZAP70 phosphorylation, as well as downstream MAPK cascades are unperturbed in p75-deficient T cells. In contrast, p75 is nonredundantly coupled to sustained AKT activity and NF-kappaB activation in response to TCR/CD28-mediated stimulation. Moreover, p75-deficient T cells possess a defect in survival during the early phase of T cell activation that is correlated with a striking defect in Bcl-x(L) expression. These data indicate discrete effects of p75 on the intracellular signaling milieu during T cell activation, and reveal the synergistic requirement of TCR, CD28, and p75 toward optimal IL-2 induction and T cell survival. We propose that p75 acts as one of the earliest of the identified costimulatory members of the TNFR family, and is functionally linked to CD28 for initiating and determining T cell fate during activation.

Genomic imprinting: could the chromatin structure be the driving force?

Genomic imprinting is traditionally defined as an epigenetic process leading to parental origin-dependent monoallelic expression of some genes. The current paradigm considers this unusual expression mode as the biological raison d être of imprinting. The present chapter proposes a critical review of our ideas about genomic imprinting in light of more recent investigatory progress. Many observations are difficult to explain on the basis of the current paradigm. Studies of allelic expression of many imprinted genes and other characteristics of chromatin domains containing clustered imprinted genes, such as replication and chromatin structure, revealed an unexpectedly complex situation that challenged the role of genomic imprinting as a mechanism of transcriptional regulation. The emerging picture is that parental imprinting is a feature of large chromatin domains with their own domain-wide characteristics. The primary biological function of imprinting may reside in the differential chromatin structure of the parental chromosomal regions and not in the monoallelic expression of some of the genes contained within them.

The human IL-2 gene promoter can assemble a positioned nucleosome that becomes remodeled upon T cell activation

Controlled production of the cytokine IL-2 plays a key role in the mammalian immune system. Expression from the gene is tightly regulated with no detectable expression in resting T cells and a strong induction following T cell activation. The IL-2 proximal promoter (+1 to -300) contains many well-defined transcriptional activation elements that respond to T cell stimulation. To determine the role of chromatin structure in the regulation of interleukin-2 gene transcription, nucleosome assembly across the IL-2 promoter region was examined using in vitro chromatin reconstitution assays. The IL-2 promoter assembles a nucleosome that is both translationally and rotationally positioned, spanning some of the major functional control elements. The binding of transcription factors to these elements, with the exception of the architectural protein HMGA1, was occluded by the presence of the nucleosome. Analysis of the chromatin architecture of the IL-2 gene in Jurkat T cells provided evidence for the presence of a similarly positioned nucleosome in vivo. The region encompassed by this nucleosome becomes remodeled following activation of Jurkat T cells. These observations suggest that the presence of a positioned nucleosome across the IL-2 proximal promoter may play an important role in maintaining an inactive gene in resting T cells and that remodeling of this nucleosome is important for gene activation.

Tumor antigen-specific induction of transcriptionally targeted retroviral vectors from chimeric immune receptor-modified T cells

High-level systemic delivery of viral vectors to tumors has proved problematic as a result of immune neutralization, nonspecific adhesion, and clearance of circulating viral particles. Some cell types localize to tumors in response to particular biological properties associated with tumor growth. Their use to deliver viral vectors to tumors would allow precious viral stocks to be protected until they can be released at high local concentrations. Here, we describe a mechanism by which retroviral vector production by T cells can be regulated by a tumor-specific trigger through engagement of a chimeric immune receptor (CIR) with its target antigen. The virus that is released from the T cells can also be transcriptionally targeted. Finally, we show that it is possible to use vector-loaded, antigen-triggered human T cells as therapeutic, tumor-specific vector delivery cells in models of both local intratumoral and systemic delivery to both lung and liver metastases. This strategy incorporates multiple levels of targeting into the delivery system at the stages of surface targeting, viral production, and gene expression.