Undermethylation of interferon-gamma gene in human T cell lines and normal T lymphocytes

Type I interferon induces TCR-dependent and -independent antimicrobial responses in γδ intraepithelial lymphocytes

Intraepithelial lymphocytes (IEL) expressing the γδ T cell receptor (TCR) survey the intestinal epithelium to limit the invasion of microbial pathogens. The production of type I interferon (IFN) is a central component of an antiviral immune response, yet how these pro-inflammatory cytokines contribute to γδ IEL effector function remains unclear. Based on the unique activation status of IELs, and their ability to bridge innate and adaptive immunity, we investigated the extent to which type I IFN signaling modulates γδ IEL function. Using an ex vivo culture model, we find that type I IFN alone is unable to drive IFNγ production, yet low level TCR activation synergizes with type I IFN to induce IFNγ production in murine γδ IELs. Further investigation into the underlying molecular mechanisms of co-stimulation revealed that TCRγδ-mediated activation of NFAT and JNK is required for type I IFN to promote IFNγ expression in a STAT4- dependent manner. Whereas type I IFN rapidly upregulates antiviral gene expression independent of a basal TCRγδ signal, neither tonic TCR triggering nor the presence of a TCR agonist was sufficient to elicit type I IFN-induced IFNγ production in vivo . However, bypassing proximal TCR signaling events synergized with IFNAR/STAT4 activation to induce γδ IEL IFNγ production. These findings indicate that γδ IELs contribute to host defense in response to type I IFN by mounting a rapid antimicrobial response independent of TCRγδ signaling, and under permissive conditions, produce IFNγ in a TCR-dependent manner.

Epigenetic regulation of T cell adaptive immunity

The conceptualization of adaptive immunity, founded on the observation of immunological memory, has served as the basis for modern vaccination and immunotherapy approaches. This fundamental concept has allowed immunologists to explore mechanisms that enable humoral and cellular lymphocytes to tailor immune response functions to a wide array of environmental insults and remain poised for future pathogenic encounters. Until recently, for T cells it has remained unclear how memory differentiation acquires and sustains a gene expression program that grants a cell with a capacity for a heightened recall response. Recent investigations into this critical question have identified epigenetic programs as a causal molecular mechanism governing T cell subset specification and immunological memory. Here, we outline the studies that have illustrated this concept and posit on how insights into T cell adaptive immunity can be applied to improve upon existing immunotherapies.

Distinct Methylation of IFNG in the Gut

Mucosal expression of proinflammatory cytokines plays a pivotal role in inflammatory bowel disease (IBD) pathogenesis. Epigenetic remodeling of chromatin via DNA methylation regulates gene expression. In this study, IFNG DNA methylation was analyzed within the mucosal compartment in both normal and IBD populations and compared to its peripheral counterparts. Overall IFNG methylation (across eight CpG sites) was significantly lower in lamina propria (LP) T cells compared to peripheral blood (PB) T cells. No methylation differences were detected when comparing PB T derived from normal to IBD patients. However, LP T-cell DNA derived from IBD patients displayed different levels of IFNG methylation of the upstream regulatory regions compared to DNA from normal controls. In fact, IFNG DNA promoter methylation levels functionally correlate with IFNG mRNA expression in unstimulated T cells, using quantitative real-time PCR. A 5% decrease in promoter methylation status is associated with nearly a 3-fold increase in IFNG expression. Likewise, methylation of the single -54 bp IFNG SnaB1 site strongly inhibited IFNG promoter expression. These results suggest that the epigenetic methylation status of IFNG may play a mechanistic role in the modulation of cytokine secretion in the mucosa.

Atypical mechanisms regulate the PMA-induced expression of IFN-gamma in a porcine trophectoderm cell line

Interferon-gamma (IFN-gamma) is a major effector cytokine of the immune system with an expression pattern strictly restricted to cells of the lymphoid lineage. Several years ago, we reported that, during early pregnancy, the trophectoderm of the pig blastocyst, which represents a monolayer of polarized epithelial cells secretes high amount of IFN-gamma in a transient and developmentally regulated manner. In an effort to study the molecular basis of this atypical IFN-gamma gene expression, a pig trophectoderm cell line, TBA B4-3, was established in our laboratory. These cells developed a polarized phenotype with high transepithelial electrical resistance (TER) when grown on a microporous membrane. We found that treatment of polarized TBA B4-3 cells with the strong PKC agonist PMA induced, 3-4 days later, a transient IFN-gamma mRNA expression and vectorial IFN-gamma protein secretion. In order to better understand IFN-gamma gene regulation in TBA B4-3 cells, we examined in this system the effect of several drugs and factors known to affect the inducibility of this cytokine in T lymphocytes, the main source of IFN-gamma in the immunocompetent animal. We found that cyclosporine A (CsA) treatment of TBA B4-3 cells induces a partial inhibition of IFN-gamma secretion, thus indicating a minor role for the calcineurin signaling pathway in IFN-gamma expression. In addition, we found that although PMA alone can induce IFN-gamma secretion, the calcium ionophore A23187 synergizes with PMA for induction. We also analyzed by Southern blot the methylation status of a CpG dinucleotide in the 5' flanking region of IFN-gamma promoter and found that it was unmethylated in TBA B4-3 cells and in several pig epithelial cell lines that do not express IFN-gamma thus indicating the absence of correlation between demethylation and the ability to express IFN-gamma. Taken together, these results indicate that the mechanisms involved in IFN-gamma induction in TBA B4-3 cells are atypical compared to those presently known to operate in the T cell lineage.

Inhibition of DNA methyltransferase stimulates the expression of signal transducer and activator of transcription 1, 2, and 3 genes in colon tumor cells

Inhibitors of DNA methyltransferase, typified by 5-aza-2'-deoxycytidine (5-Aza-CdR), induce the expression of genes transcriptionally down-regulated by de novo methylation in tumor cells. We utilized gene expression microarrays to examine the effects of 5-Aza-CdR treatment in HT29 colon adenocarcinoma cells. This analysis revealed the induction of a set of genes that implicated IFN signaling in the HT29 cellular response to 5-Aza-CdR. Subsequent investigations revealed that the induction of this gene set correlates with the induction of signal transducer and activator of transcription (STAT) 1, 2, and 3 genes and their activation by endogenous IFN-alpha. These observations implicate the induction of the IFN-response pathway as a major cellular response to 5-Aza-CdR and suggests that the expression of STATs 1, 2, and 3 can be regulated by DNA methylation. Consistent with STAT's limiting cell responsiveness to IFN, we found that 5-Aza-CdR treatment sensitized HT29 cells to growth inhibition by exogenous IFN-alpha2a, indicating that 5-Aza-CdR should be investigated as a potentiator of IFN responsiveness in certain IFN-resistant tumors.

Distinct methylation of the interferon gamma (IFN-gamma) and interleukin 3 (IL-3) genes in newly activated primary CD8+ T lymphocytes: regional IFN-gamma promoter demethylation and mRNA expression are heritable in CD44(high)CD8+ T cells

Differential genomic DNA methylation has the potential to influence the development of T cell cytokine production profiles. Therefore, we have conducted a clonal analysis of interferon (IFN)-gamma and interleukin (IL)-3 gene methylation and messenger (m)RNA expression in primary CD8+ T cells during the early stages of activation, growth, and cytokine expression. Despite similar distributions and densities of CpG methylation sites, the IFN-gamma and IL-3 promoters exhibited differential demethylation in the same T cell clone, and heterogeneity between clones. Methylation patterns and mRNA levels were correlated for both genes, but demethylation of the IFN-gamma promoter was widespread across >300 basepairs in clones expressing high levels of IFN-gamma mRNA, whereas demethylation of the IL-3 promoter was confined to specific CpG sites in the same clones. Conversely, the majority of clones expressing low or undetectable levels of IFN-gamma mRNA exhibited symmetrical methylation of four to six of the IFN-gamma promoter CpG sites. Genomic DNA methylation also has the potential to influence the maintenance or stability of T cell cytokine production profiles. Therefore, we also tested the heritability of IFN-gamma gene methylation and mRNA expression in families of clones derived from resting CD44(low)CD8+ T cells or from previously activated CD44(high)CD8+ T cells. The patterns of IFN-gamma gene demethylation and mRNA expression were faithfully inherited in all clones derived from CD44(high) cells, but variable in clones derived from CD44(low) cells. Overall, these findings suggest that differential genomic DNA methylation, including differences among cytokine genes, among individual T cells, and among T cells with different activation histories, is an important feature of cytokine gene expression in primary T cells.

CD4+, But Not CD8+, T Cells from Mammary Tumor-Bearing Mice Have a Down-Regulated Production of IFN-γ: Role of Phosphatidyl Serine

IFN-γ production is dramatically reduced in T cells from mice bearing large mammary tumors. This inhibition of IFN-γ gene expression occurs mostly in CD4+ T cells, as determined by ELISA and reverse transcriptase-PCR. The effects of known mammary tumor factors in normal T cells and its subsets were evaluated. Pretreatment with granulocyte-macrophage CSF resulted in increased IFN-γ levels by T cells, while PGE2 pretreatment equally decreased the levels of this cytokine in CD4+ and CD8+ T cells from normal mice. Interestingly, phosphatidyl serine (PS) down-regulated the IFN-γ production of CD4+, but not that of CD8+, T cells. Methylation analysis indicated that the CpG dinucleotide in SnaBI site of the IFN-γ 5′ promoter flank region was hypermethylated in CD4+, but not in CD8+, T cells of large tumor bearers and of normal mice pretreated with PS. Electrophoresis mobility shift assay using an oligonucleotide probe corresponding to the IFN-γ promoter core region sequence showed a greatly reduced binding of a 90-kDa nuclear protein in CD4+ T cells from tumor bearers and in those from PS-pretreated normal mice. Since IL-2 production is not affected in either CD4+ or CD8+ T cells from tumor bearers, these studies indicate that IFN-γ production can be regulated independently from that of other type 1 cytokines in vivo. Our data further suggest that PS is involved in IFN-γ gene down-regulation during mammary tumorigenesis and contributes to the generalized immunosuppression associated with tumor growth.

Molecular regulation of cytokine gene expression: interferon-gamma as a model system

The regulation of IFN-gamma transcription appears to be quite complex. In addition to the interaction of numerous regions of the genomic DNA with multiple DNA binding protein family members, DNA methylation may serve to act as an early determinant of the capacity of a cell to initiate transcription. Transcriptional activation occurs in response to both soluble extracellular signals and cell contact, and it appears quite likely that this activation may result from the interaction of different families of DNA binding proteins with different enhancer elements. Furthermore, because chronic IFN-gamma transcription and subsequent expression would likely be detrimental to the host (see 81), mechanisms have evolved to quench expression at both transcriptional and posttranscriptional levels. Given the complexity of cell-to cell interactions in the immune system, it is reasonable to expect that additional mechanisms regulating IFN-gamma transcription, involving previously identified or as yet unidentified DNA binding proteins, remain to be defined.

Hypomethylation of the interferon-gamma gene correlates with its expression by primary T-lineage cells

To determine the potential role of methylation in the regulation of interferon-gamma (IFN-gamma) gene transcription by T cells, primary T-lineage cell populations were analyzed for the extent of methylation of three CpG sites within or near transcriptional activator elements in the 5' flank and first intron of the human IFN-gamma gene. A striking correlation was observed between the capacity of the IFN-gamma gene to be expressed and the degree of hypomethylation. The IFN-gamma gene was virtually completely methylated at all sites in thymocytes, neonatal T cells, and adult CD45RAhiCD45R0lo (antigenically naive) CD4 T cells, cell types that all have a low or undetectable capacity to express the IFN-gamma gene. In contrast, there was substantial hypomethylation in T-lineage cell types with relatively high capacities to express the IFN-gamma gene, including adult CD8 T cells and adult CD45RAloCD45R0hi (memory/effector) CD4 T cells. These results suggest that hypomethylation of the IFN-gamma genetic locus may be an important determinant of IFN-gamma gene expression in vivo by T-lineage cells.

5-Methylcytosine in genes with methylation-dependent regulation

An asymmetric distribution of deoxy-5-methylcytidylic acid-inhibiting restriction sites (dcm-sites) takes place in ten human genes regulated by 5-methylcytosine. These genes are dcm-site enriched upstream and dcm-site poor downstream. Along them, there is a scattering of hypermethylatable introns and hypomethylatable exons with a common code: the 5mCpG dinucleotides characterize promoters; Gp5mCs characterize introns; Tp5mCs and Cp5mCs are in small concentrations in exons. Housekeeping genes contain more dcm-sites when compared with tissue-specific genes. This depends on the higher number of dcm-sites in their promoters and introns. In exons, the relatively lower number of dcm-sites is almost the same in both housekeeping and tissue-specific genes. Going from 5' to 3', the average frequency of occurrence of these sites per nucleotide units decreases in introns and increases in exons. This difference is highly discriminated for tissue-specific and less discriminated for housekeeping genes.

Certain changes in ornithine decarboxylase gene methylation accompany gene amplification

The ornithine decarboxylase (ODC; EC 4.1.1.17) gene in parental, dexamethasone-resistant and 2-difluoromethylornithine (DFMO)-resistant human IgG-myeloma-cell lines was studied with the aid of methylation-sensitive restriction endonucleases and probes recognizing different parts of the gene. In all cell lines the promoter region of the ODC gene appeared to be heavily methylated, whereas the first long intron was unmethylated. Methylation analyses of several clones from the parental cell line revealed that these cells are heterogeneous with respect to the methylation status of the ODC gene, whereas all clones from DFMO-resistant cell lines displayed the same methylation pattern. Two of the parental clones represented a hypomethylated type very close to that exclusively found among the DFMO-resistant clones with ODC gene amplification. This typical methylation pattern was due to decreased methylation of a few CCGG sequences in the 3'-flanking region of the gene. It is possible that this kind of hypomethylation favours the initiation of the gene-amplification process in certain individual cells. This hypothesis was supported by the finding that no hypomethylation was present in the ODC gene of another human myeloma cell line that had acquired resistance to DFMO without gene amplification. In a dexamethasone-resistant cell line that overproduced ODC mRNA at normal gene dosage there were some minor differences between the methylation pattern of the ODC gene of different clones, but no such hypomethylation could be found in clones from the parental cell line. In dexamethasone-resistant cells the ODC gene was hypomethylated around the two HpaII sites and three CfoI sites in the coding region and also, as well as in cells with amplified ODC sequences, in the 3'-flanking region of the gene. Some hypomethylation in the distant 5'-flanking region was also observed.

Three different mRNAs encoding human granulocyte colony-stimulating factor receptor

Three cDNAs for the human granulocyte colony-stimulating factor (G-CSF) receptor were isolated from the cDNA libraries of human U937 leukemia cells and placenta by using a murine G-CSF receptor cDNA as the probe. The human G-CSF receptor containing 813 amino acids had a marked homology (62.5%) with its murine counterpart and consisted of extracellular, transmembrane, and cytoplasmic domains. The WSXWS motif found in members of the newly identified growth factor receptor family was also present in the extracellular domain of the human G-CSF receptor. Expression of the cloned cDNA in monkey COS cells gave rise to a protein that could specifically bind G-CSF with a high affinity (Kd, 550 pM). Two other classes of the human G-CSF receptor were also identified, one of which had a deletion of the transmembrane domain and seemed to encode a secreted, soluble receptor. The third class of the G-CSF receptor contained a 27-amino acid insertion in the cytoplasmic domain and was highly expressed in placenta.

The methylation state of the T cell antigen receptor beta chain gene in subpopulations of mouse thymocytes

Previous analyses of T cell receptor beta chain (TcR beta) genomic DNA from subsets of human peripheral blood leukocytes suggested that the TcR beta methylation pattern might reflect distinct differentiation pathways. The studies presented here, using murine thymocyte subsets, have specifically addressed the question of whether methylation of TcR beta DNA is related to the cellular maturity and type of TcR beta mRNA expressed in the different subsets. We have observed that the DNA isolated from either CD4+ or CD8+ thymocytes, the more mature thymic subsets, is less methylated in the TcR beta region than DNA isolated from the CD4-CD8-, double-negative population containing the more immature thymocytes. In addition, this pattern of DNA methylation is directly related to the ratio of 1.3-kb to 1.0-kb TcR beta mRNA seen in these different cell types. Although a quantitative difference in the level of TcR beta mRNA was noted for the two mature subsets, no qualitative difference in the ratio of 1.3-kb to 1.0-kb mRNA was detected. Furthermore, these DNA methylation patterns appear to be lineage related, because the TcR beta region of genomic DNA isolated from mouse macrophages is heavily methylated.

Molecular genetics of ornithine decarboxylase in human tumor cells

As the molecular biology of mammalian ornithine decarboxylase is coming of age, more and more interesting features of this unique protein are being uncovered. Ornithine decarboxylase belongs to those 20 or so enzymes or binding proteins, the genes for which are easily amplified under suitable selection pressure. This also applies to the human enzyme. Gene amplification of ornithine decarboxylase is not the only means to acquire resistance to inhibitors of the enzyme, as its overproduction can occur through an enhanced transcription or even through a more efficient translation of normal mRNA amounts. The resistance in human tumors can likewise be acquired by activating other enzymes, such as arginase. In contrast to the multigene family in mouse, it appears that in the human genome only two ornithine decarboxylase genes are present mapping to the chromosomes 2 and 7. Out of these, at least the sequences in the short arm of chromosome 2 are transcriptionally active and amplifiable. Human ornithine decarboxylase also belongs to those proteins which show a positive correlation between gene hypomethylation and expression. The genes of human ornithine decarboxylase are methylated to varying extents and distinct hypomethylation is seen in certain malignant cells, most notably human lymphatic leukemia cells. The human ornithine decarboxylase gene is easily transferrable into other mammalian cells in which it is efficiently expressed. Some indirect evidence seems to indicate that overproduction of ornithine decarboxylase may confer a growth advantage to mammalian cells. A further piece of information suggesting an important role for the enzyme is the fact that the structure of the ornithine decarboxylase gene is extremely well conserved during evolution. This does not apply only to the coding region but also to the overall organization of the gene itself.

Human T-lymphoblastoid cell lines with high and low abilities to produce interferon-gamma constitutively and their susceptibilities to interferon

A human T-lymphoblastoid cell line, TCL-Fuj, produces large amounts of interferon (IFN)-gamma constitutively. A variant cell line, 2M, was derived from it. Both cell lines express similar surface antigen markers, but differ in surface morphology. Compared with the parent TCL-Fuj cell line, 2M produced less IFN-gamma constitutively but more in response to IFN inducers. The IFNs produced constitutively and on stimulation with inducers were analyzed by SDS-polyacrylamide gel electrophoresis. In TCL-Fuj cells, the constitutive and induced IFNs consisted of the same molecular species (22K and 39K). In 2M cells, smaller IFNs were produced constitutively (18K and 32K) and induction resulted in a marked increase of 22K molecules. These two cell lines also differed in sensitivity to the antiviral activity of IFN. Other T-lymphoblastoid cell lines, HPB-ALL and TCL-Fuj 4 cells, which did not produce IFN-gamma were permissive for vesicular stomatitis virus (VSV) replication; its growth was markedly suppressed by IFN-gamma and -alpha. TCL-Fuj cells were also permissive for VSV, but were not susceptible to the antiviral effect of the IFNs. In contrast, in 2M cells the multiplication of VSV was restricted; the viral yield was further reduced by the IFNs and increased by treatment with anti-human IFN-gamma serum. Several clonal cell lines derived from TCL-Fuj and 2M cells had characteristics similar to the respective parent cell lines. The growth of both cell lines was not affected by IFN-gamma or by -alpha. The separation of antiviral and anti-proliferative susceptibilities was peculiar to 2M cells unlike other cell lines.

Chronic exposure to dexamethasone induces hypomethylation of ornithine decarboxylase genes in a human myeloma cell line

Chronic exposure of a human myeloma cell line to dexamethasone resulted in a selection of cells resistant to the growth-inhibitory action of the glucocorticoid. Upon acute exposure of the parental myeloma cells to dexamethasone growth inhibition was associated with depression of ornithine decarboxylase (ODC, EC 4.1.1.17) activity. However, in cells adapted to grow in the presence of micromolar concentrations of dexamethasone, ODC activity was fully comparable to that in the parental cells. Restriction enzyme analyses with the two isoschizomers HpaII and MspI as well as with the methylation-sensitive CfoI, indicated that the otherwise heavily methylated ODC gene(s) were rendered hypomethylated in the myeloma cells resistant to dexamethasone. This hypomethylation within and/or around ODC genes was associated with a 2-4-fold enhancement of accumulation of ODC mRNA.