The human glucocorticoid receptor as an RNA-binding protein: global analysis of glucocorticoid receptor-associated transcripts and identification of a target RNA motif

Posttranscriptional regulation is emerging as a key factor in glucocorticoid (GC)-mediated gene regulation. We investigated the role of the human GC receptor (GR) as an RNA-binding protein and its effect on mRNA turnover in human airway epithelial cells. Cell treatment with the potent GC budesonide accelerated the decay of CCL2 mRNA (t(1/2) = 8 ± 1 min versus 62 ± 17 min in DMSO-treated cells) and CCL7 mRNA (t(1/2) = 15 ± 4 min versus 114 ± 37 min), but not that of CCL5 mRNA (t(1/2)=231 ± 8 min versus 266 ± 5 min) in the BEAS-2B cell line. This effect was inhibited by preincubation with an anti-GR Ab, indicating that GR itself plays a role in the turnover of these transcripts. Coimmunoprecipitation and biotin pulldown experiments showed that GR associates with CCL2 and CCL7 mRNAs, but not CCL5 mRNA. These methods confirmed CCL2 mRNA targeting by GR in human primary airway epithelial cells. Association of the GR was localized to the 5' untranslated region of CCL2 mRNA and further mapped to nt 44-60. The collection of transcripts associated with GR, identified by immunoprecipitation of GR-mRNA complexes followed by microarray analysis, revealed 479 transcripts that associated with GR. Computational analysis of the primary sequence and secondary structures of these transcripts yielded a GC-rich motif, which was shown to bind to GR in vitro. This motif was used to predict binding of GR to an additional 7889 transcripts. These results indicate that cytoplasmic GR interacts with a subset of mRNA through specific sequences and can regulate turnover rates, suggesting a novel posttranscriptional role for GR as an RNA-binding protein.

RNA-binding protein HuR coordinately regulates genes essential for Th2 polarization and function at the posttranscriptional level (99.7)

Posttranscriptional gene regulation controls the expression of genes implicated in a variety of processes, including those of the immune system. The RNA-binding protein HuR regulates many early response genes as well as cytokines such as IL-4 and IL-13. Therefore, HuR has been implicated in regulating Th2 polarization and cytokine production. GATA-3, a transcription factor that is essential for Th2 polarization contains a putative HuR binding site in its 3’UTR. Immunoprecipitation (IP) of ribonucleoprotein complexes with an anti-HuR Ab revealed significant enrichment for GATA-3 mRNA. HuR association with GATA-3 3’UTR was confirmed by biotin pull-downs. To understand the role of HuR in Th2 polarization in vivo we generated a transgenic HuR CD4+ T-cell mouse model. Th2-skewed cells over-expressing HuR displayed increases in both numbers of GATA3-expressing cells, and in overall GATA-3 expression. The frequency of Th2-polarized cells, but not of Th1, increased in CD4+ T cell HuR transgenic cells and the levels of secreted IL-4 and IL-13, but not IFN-γ, also increased significantly in both activated splenocytes and polarized cells. Furthermore, a knockdown of HuR in Jurkat cells decreased protein levels of GATA-3. Hence, HuR may be functioning to coordinately posttranscriptionally regulate genes essential for Th2 polarization and function. Better understanding of posttranscriptional regulation may elucidate control mechanisms of naïve CD4+ Th2 polarization.

Principles and applications of polymerase chain reaction: basic science for the practicing physician

OBJECTIVE

To review the technology of polymerase chain reaction (PCR) and its use in diagnostic medicine and biomedical research.

DATA SOURCES

A literature review was performed using the PubMed database for English-language articles published between January 1, 1985, and November 31, 2007, using the following keywords: polymerase chain reaction, real-time polymerase chain reaction, and applications of real-time polymerase chain reaction.

STUDY SELECTION

Select review articles and primary articles relevant to medical applications of PCR were chosen.

RESULTS

As a revolutionary technique, PCR provides a rapid and accurate means of amplifying DNA. It has enabled the cloning and manipulation of genes for biomedical research and has facilitated the diagnosis of genetic, infectious, and oncologic diseases. The use of reverse transcriptases to evaluate RNA levels and the extension of PCR technology to quantify DNA amplification in real time has brought major advances to the application of PCR. By allowing the determination and quantification of changes in gene expression, these techniques have provided a greater understanding of disease processes and now serve as a foundation for diagnostics and basic science research.

CONCLUSIONS

Both PCR and real-time PCR have dramatically changed the field of basic science and diagnostic medicine. These technologies are now a well-established, indispensable part of research and clinical laboratories.

Role of the RNA-binding protein tristetraprolin in glucocorticoid-mediated gene regulation

Glucocorticoids (GCs) are the mainstay of anti-inflammatory therapy. Modulation of posttranscriptional regulation (PTR) of gene expression by GCs is a relevant yet poorly characterized mechanism of their action. The RNA-binding protein tristetraprolin (TTP) plays a central role in PTR by binding to AU-rich elements in the 3'-untranslated region of proinflammatory transcripts and accelerating their decay. We found that GCs induce TTP expression in primary and immortalized human bronchial epithelial cells. To investigate the importance of PTR and the role of TTP in GC function, we compared the effect of GC treatment on genome-wide gene expression using mouse embryonic fibroblasts (MEFs) obtained from wild-type and TTP(-/-) mice. We confirmed that GCs induce TTP in MEFs and observed in TTP(-/-) MEFs a striking loss of up to 85% of GC-mediated gene expression. Gene regulation by TNF-alpha was similarly affected, as was the antagonistic effect of GC on TNF-alpha-induced response. Inflammatory genes, including cytokines and chemokines, were among the genes whose sensitivity to GCs was affected by lack of TTP. Silencing of TTP in WT MEFs by small interfering RNA confirmed loss of GC response in selected targets. Immunoprecipitation of ribonucleoprotein complexes revealed binding of TTP to several validated transcripts. Changes in the rate of transcript degradation studied by actinomycin D were documented for only a subset of transcripts bound to TTP. These results reveal a strong and previously unrecognized contribution of PTR to the anti-inflammatory action of GCs and point at TTP as a key factor mediating this process through a complex mechanism of action.

Posttranscriptional regulation of IL-13 in T cells: role of the RNA-binding protein HuR

BACKGROUND

IL-13, a critical cytokine in allergy, is regulated by as-yet-elusive mechanisms.

OBJECTIVE

We investigated IL-13 posttranscriptional regulation by HuR, a protein associating with adenylate-uridylate-rich elements in the 3' untranslated regions (UTRs) of mRNA, promoting mRNA stability and translation.

METHODS

IL-13 mRNA decay was monitored in human T(H)2-skewed cells by using the transcriptional inhibitor actinomycin D. The IL-13 3'UTR was subcloned into an inducible beta-globin reporter transiently expressed in H2 cells in the absence or presence of overexpressed HuR. Association of HuR with IL-13 mRNA was detected by means of immunoprecipitation of ribonucleoprotein complexes and a biotin pull-down assay. The effects of HuR transient overexpression and silencing on IL-13 expression were investigated.

RESULTS

IL-13 mRNA half-life increased significantly in restimulated T(H)2-skewed cells compared with baseline values. Decay of beta-globin mRNA was significantly faster in H2 cells transfected with the IL-13 3'UTR-containing plasmid than in those carrying a control vector. HuR overexpression increased the beta-globin IL-13 3'UTR reporter half-life. Significant enrichment of IL-13 mRNA was produced by means of immunoprecipitation of Jurkat cell ribonucleoprotein complexes with anti-HuR. HuR binding to the IL-13 3'UTR was confirmed by means of pull-down assay of biotin-labeled RNA probes spanning the IL-13 3'UTR. Two-dimensional Western blot analysis showed stimulus-induced posttranslational modification of HuR. In Jurkat cells mitogen-induced IL-13 mRNA was significantly affected by HuR overexpression and silencing.

CONCLUSIONS

Mitogen-induced IL-13 expression involves changes in transcript turnover and a change in phosphorylation of HuR and its association with the mRNA 3'UTR.

Glucocorticoid actions on airway epithelial responses in immunity: functional outcomes and molecular targets

Research on the biology of airway epithelium in the last decades has progressively uncovered the many roles of this cell type during the immune response. Far from the early view of the epithelial layer simply as a passive barrier, the airway epithelium is now considered a central player in mucosal immunity, providing innate mechanisms of first-line host defense as well as facilitating adaptive immune responses. Alterations of the epithelial phenotype are primarily involved in the pathogenesis of allergic airways disease, particularly in severe asthma. Appreciation of the epithelium as target of glucocorticoid therapy has also grown, because of studies defining the pathways and mediators affected by glucocorticoids, and studies illustrating the relevance of the control of the response from epithelium in the overall efficacy of topical and systemic therapy with glucocorticoids. Studies of the mechanism of action of glucocorticoids within the biology of the immune response of the epithelium have uncovered mechanisms of gene regulation involving both transcriptional and posttranscriptional events. The view of epithelium as therapeutic target therefore has plenty of room to evolve, as new knowledge on the role of epithelium in immunity is established and novel pathways mediating glucocorticoid regulation are elucidated.

Functional analysis of the chemokine receptor CCR3 on airway epithelial cells

The function of chemokine receptors on structural cells is only partially known. We previously reported the expression of a functional CCR3 receptor on airway epithelial cells (EC). We speculated that CCR3 might drive wound repair and expression of inflammatory genes in epithelium. The human airway EC lines BEAS-2B, 16-HBE, and primary bronchial EC were used to test the effect of in vitro challenge with the CCR3 ligands CCL11/eotaxin, CCL24/eotaxin-2, or CCL26/eotaxin-3 on 1) wound repair, using an established wound model; 2) cell proliferation and chemotaxis, using specific fluorometric assays; and 3) gene expression, using pathway-specific arrays for inflammatory and profibrotic cytokines, chemokines, and chemokine receptor genes. Agonist specificity was tested by cell pretreatment with an AstraZeneca CCR3 antagonist (10(-8) - 10(-6) M). CCL24 challenge significantly accelerated epithelial wound closure, with similar effects exerted by CCL11 and CCL26. This effect was time dependent, submaximal at 1 nM, and comparable in potency to epidermal growth factor. CCL24 induced a concentration-dependent increase in EC proliferation and chemotaxis, with significant effects observed at 10 nM. The AstraZeneca compound selectively inhibited these CCL24-mediated responses. CCL11 induced the up-regulation of several profibrogenic molecules such as fibroblast growth factor 1 and 5 and of several CC and CXC chemokines. Epithelial immunostaining for CCR3 was stronger in bronchial biopsies of asthmatics displaying marked inflammatory changes than in nondiseased samples. Epithelial CCR3 participates in key functions for wound repair, amplifies the expression of profibrogenic and chemokine transcripts, and appears up-regulated in inflamed asthmatic airways.

The role of post-transcriptional regulation in chemokine gene expression in inflammation and allergy

The aim of this review is to discuss recent advances in the understanding of the regulation of chemokine expression occurring during chronic inflammatory conditions, such as allergic diseases. The focus will be on current data, which suggest that post-transcriptional regulation plays a larger role in chemokine gene regulation than previously recognised. In particular, a growing body of data indicates that mechanisms controlling mRNA stability may be relevant in determining, or maintaining, the increased levels of chemokine gene expression in this context. Such regulatory pathways may be important targets of novel anti-inflammatory strategies.

Chemokines: key players in innate and adaptive immunity

Healthy individuals initiate an immediate immune response to microbes by using a set of germline-encoded receptors that recognize common molecular patterns found on the surface of pathogens that are distinct from self-antigens. This innate immune response is the first line of defense against microorganisms in vertebrates, and constitutes the only immune response in plants and invertebrates. The innate immune system includes cellular components, as well as a host of soluble products (antimicrobial peptides, complement fragments, cytokines, and chemokines). The adaptive immune response, which provides long-lasting protection, takes days to develop and requires somatic mutations leading to the development of antigen-specific T cell receptors (cell-mediated immunity) and immunoglobulins (humoral immunity). Members of the chemokine superfamily are crucially involved in both innate and adaptive responses. We review the biological actions of the chemokine superfamily, focusing on several functions that are relevant for both immune responses, such as cell recruitment, microbicidal activity, cell activation, polarization of CD4+ T cells, and effects on structural cells. In particular, we will illustrate the central role that chemokines play in host defense, best demonstrated by the tremendous number of chemokine and chemokine receptor homologs found in microbial genomes, which deflect the immune response of the host.

Post-transcriptional and nongenomic effects of glucocorticoids

The ability of glucocorticoids to interfere with post-transcriptional gene regulation has recently been recognized as a potentially important part of their anti-inflammatory property, and the mechanisms governing such activity are under active investigation. Several studies have shown that glucocorticoids can inhibit inflammatory signaling pathways known to control mRNA turnover and translation. Moreover, several glucocorticoid-sensitive determinants have been identified on mRNA molecules of inflammatory genes, and the RNA-binding factors interacting with them might constitute relevant glucocorticoid targets. Glucocorticoids also exert effects characterized as nongenomic, which occur within minutes of drug administration. The mechanisms of action of nongenomic glucocorticoid effects differ from the classical, transcription-dependent glucocorticoid action and involve the production of second-messenger molecules and activation of signal transduction pathways, either by the nuclear glucocorticoid receptor or by a membrane glucocorticoid receptor that has not yet been fully characterized. Ultimately, the discovery of novel pathways involved in mediating the actions of glucocorticoids should lead to improved targets for anti-inflammatory therapy.

Assessment of signal transducer and activator of transcription 6 as a target of glucocorticoid action in human airway epithelial cells

BACKGROUND

Activation of signal transducer and activator of transcription (STAT)6 by IL-4 and IL-13 is essential in many key epithelial responses in the asthmatic airway including expression of numerous chemokines, goblet cell differentiation and mucus production and expression of other allergic inflammatory genes. While these responses are all inhibited by glucocorticoids (GC) administered systemically or by inhalation, the inhibitory mechanisms are unknown.

OBJECTIVE

To test the hypothesis that GC suppress allergic responses by blocking IL-4-induced STAT6 signalling in airway epithelial cells.

METHODS

Western blotting and reporter gene assays were used to determine whether GC could inhibit STAT6 production, phosphorylation or nuclear translocation, or whether GC could affect STAT6 transcriptional activity in the BEAS-2B airway epithelial cell line.

RESULTS

Our results showed that GC had no inhibitory effect on the total cellular or nuclear levels of STAT6 or phospho-STAT6. GC did not inhibit transcription from three different STAT6-driven reporter constructs, indicating that GC also did not inhibit STAT6 function.

CONCLUSION

We conclude that airway epithelial STAT6 is not the central target of GC in allergic inflammation and that the inhibitory effect of GC on STAT6-mediated IL-4- and IL-13-induced responses is exerted by targeting pathways distinct from STAT6.

Sequence variants of the gene encoding chemoattractant receptor expressed on Th2 cells (CRTH2) are associated with asthma and differentially influence mRNA stability

The gene, CRTH2, encoding a receptor for prostaglandin D(2) (PGD(2)), is located within the peak linkage region for asthma on chromosome (Chr.) 11q reported in African American families. Family-based analysis of asthma and two common SNPs [G1544C and G1651A (rs545659)] in the 3'-untranslated region of CRTH2 showed significant evidence of linkage in the presence of disequilibrium for the 1651G allele (P = 0.003) of SNP rs545659. Haplotype analysis yielded additional evidence of linkage disequilibrium for the 1544G-1651G haplotype (P < 0.001). Population-based case-control analyses were conducted in two independent populations, and demonstrated significant association of the 1544G-1651G haplotype with asthma in an African American population (P = 0.004), and in a population of Chinese children (P < 0.001). Moreover, in the Chinese children the frequency of the 1651G allele in near-fatal asthmatics was significantly higher than mild-to-moderate asthmatics (P = 0.001) and normal controls (P < 0.001). The 1651G allele of SNP re545659 was also associated with a higher degree of bronchial hyperresponsiveness (P < 0.027). Transcriptional pulsing experiments showed that the 1544G-1651G haplotype confers a significantly higher level of reporter mRNA stability, when compared with a non-transmitted haplotype (1544C-1651A), suggesting that the CRTH2 gene on Chr. 11q is a strong candidate gene for asthma.

Interferon-gamma inhibits STAT6 signal transduction and gene expression in human airway epithelial cells

The activating and inhibitory cytokine signals that act upon epithelial cells in the human lung are critically important for controlling the production of inflammatory mediators from those cells in the context of allergic disease. The cytokines interleukin (IL)-4 and IL-13, derived from T helper (Th)-2 cells and other cell types, are potent inducers of epithelial cell expression of a host of inflammatory molecules, including the chemokines eotaxin-1, -2 and -3. Intracellular signal transduction in response to IL-4/IL-13 occurs largely through activation of signal transducer and activator of transcription 6 (STAT6). Interferon (IFN)-gamma, a Th1-type cytokine, has opposing effects to IL-4/IL-13 in various cell types, including T cells, B-cells, endothelium, and epithelium. In this study, we demonstrate that IL-4-induced STAT6 activation was inhibited profoundly by 24 h pretreatment with IFN-gamma in human primary airway epithelial cell cultures. Using Western blotting, we showed that the levels of both cytoplasmic and nuclear-localized phospho-STAT6 were reduced by IFN-gamma pretreatment, and this effect was dependent on the concentration of IFN-gamma and time of exposure to IFN-gamma. The functional activity of STAT6 was also completely inhibited by IFN-gamma: IL-4-induced luciferase activity from a STAT6-driven reporter construct was suppressed, as was IL-4-induced expression of messenger RNA (mRNA) and protein for eotaxin-3, a STAT6-dependent gene implicated in allergic inflammation. We found that mRNA for suppressor of cytokine signaling (SOCS)-1 and (SOCS)-3, known inhibitors of IL-4 signaling, and IL-13 receptor alpha2, a potential inhibitor of IL-4 signaling, were both strongly induced by IFN-gamma pretreatment. IFN-gamma also increased the rate of decay of IL-4-induced eotaxin-3 mRNA. We conclude that there are multiple mechanisms by which IFN-gamma regulates IL-4- and STAT6-dependent signaling and gene expression in airway epithelial cells. These observations have important implications for the regulation of epithelial cell activation by the balance of Th1/Th2-type cytokines in the airways in allergic disease.

Regulation of eotaxin gene expression by TNF-alpha and IL-4 through mRNA stabilization: involvement of the RNA-binding protein HuR

During inflammatory responses, a major posttranscriptional regulation of early response and inflammatory gene expression occurs through modulation of mRNA turnover. We report that two potent inducers of the CC chemokine eotaxin, TNF-alpha and IL-4, regulate its production in airway epithelial cells by increasing eotaxin mRNA stability. In experiments using the transcriptional inhibitor actinomycin D, eotaxin mRNA half-life was significantly prolonged by cell stimulation with TNF-alpha or IL-4, with the combination of the two cytokines being the most effective in extending the mRNA half-life. Involvement of the eotaxin 3' untranslated region in the mRNA-stabilizing effect was tested by transient transfection of a construct expressing a chimeric transcript carrying a serum-inducible beta-globin reporter linked to the eotaxin 3' untranslated region. The half-life of the chimeric mRNA was markedly increased in cells stimulated with TNF-alpha and IL-4. Evidence that the mRNA-stabilizing protein HuR participated in the cytokine effect was obtained: first, HuR presence in the cytoplasm, believed to be required for HuR-mediated mRNA stabilization, increased in both transformed (BEAS-2B cell line) and primary bronchial epithelial cells following treatment with TNF-alpha and IL-4. Second, endogenous eotaxin mRNA was found to bind to HuR in vivo, as detected by immunoprecipitation of HuR-containing messenger ribonucleoprotein complexes followed by real-time RT-PCR analysis; such association increased after cell treatment with TNF-alpha and IL-4. Third, overexpression of HuR in BEAS-2B cells significantly increased the expression of eotaxin mRNA and protein. Our findings implicate mRNA stabilization in the cytokine-mediated increase in eotaxin expression and strongly suggest a role for HuR in this effect.

Differential regulation of eotaxin expression by IFN-gamma in airway epithelial cells

BACKGROUND

Eotaxin is a chemokine that binds with high affinity and specificity to the chemokine receptor CCR3 and plays an important role in the pathogenesis of allergic disease.

OBJECTIVE

We studied the regulation of eotaxin expression by the T(H)1 cytokine IFN-gamma and analyzed its molecular mechanisms.

METHODS

Levels of eotaxin mRNA and protein expression in the airway epithelial cell line BEAS-2B were determined with RT-PCR and ELISA. Mechanisms of transcriptional regulation were assessed by means of electrophoretic mobility shift assays and luciferase assay with eotaxin promoter-luciferase reporter plasmids.

RESULTS

Although IFN-gamma did not directly induce the expression of eotaxin protein, it increased the induction by TNF-alpha when these cytokines were added simultaneously. In contrast, preincubation of cells with IFN-gamma for 24 hours profoundly inhibited the production induced by TNF-alpha. IFN-gamma did not influence the TNF-alpha-induced binding of nuclear factor kappaB to a DNA probe derived from the eotaxin promoter. IFN-gamma did not increase the ability of TNF-alpha to activate the eotaxin promoter. Studies of eotaxin mRNA levels indicate that IFN-gamma combined with TNF-alpha increased the expression of eotaxin mRNA. When cells were preincubated with IFN-gamma, there was no inhibition of the appearance of eotaxin mRNA.

CONCLUSION

These studies demonstrate that IFN-gamma enhances eotaxin expression when added in combination with TNF-alpha and profoundly inhibits eotaxin expression after preincubation. In both cases the available data indicate that the effect is mediated by a posttranscriptional mechanism.