DNA methylation and autoimmune disease

Epigenetic therapeutics in autoimmune disease

Several lines of evidence suggest the involvement of disturbance in epigenetic processes in autoimmune disease. Most noteworthy is the global DNA hypomethylation seen in lupus. Epigenetic states in difference from genetic lesions are potentially reversible and hence candidates for pharmacological intervention. Potential targets for drug development are histone modification and DNA methylating and demethylating enzymes. The most advanced set of drugs in clinical development are histone deacetylase (HDAC) inhibitors. However, the prevalence of DNA hypomethylation in lupus suggests that we should shift our attention from HDAC inhibitors to DNA demethylation inhibitors. MBD2 was recently proposed to be involved in demethylation in T cells in lupus and is, therefore, a candidate target. Although this field is at its infancy, it carries great promise.

Global DNA methylation, DNMT1, and MBD2 in patients with systemic lupus erythematosus

To investigate the associations of DNA methylation levels and mRNA expressions of DNA cytosine-5-methyltransferase 1 (DNMT1) and methyl CpG-binding domain 2 (MBD2) with systemic lupus erythematosus (SLE), 108 patients with SLE and 97 healthy controls were enrolled in this study. DNA and total RNA were extracted from the peripheral blood mononuclear cells of the SLE patients and the controls. The global methylation levels of DNA were measured in 63 patients with SLE and 68 healthy controls by the ELISA method. DNMT1 and MBD2 mRNA were also detected in 108 SLE patients and 97 controls using the quantitative real-time polymerase chain reaction method. The global methylation level of DNA was significantly decreased in the SLE patients in comparison with that in the controls ( p < 0.001, 95% CI = 0.1573–0.5052). The patients with SLE have higher expressions of DNMT1 and MBD2 mRNA than the controls ( p < 0.001, 95% CI = −0.0049 – −0.0019 and p = 0.001, 95% CI = −0.0119 – −0.0029, respectively). We also found that there were no significant differences in the methylation level and the expression of DNMT1 and MBD2 mRNA between the active and the inactive SLE patients. A positive correlation was also found between DNMT1 and MBD2 mRNA expressions in the SLE patients ( p < 0.001). This study demonstrated that the patients with SLE had a significantly lower level of DNA methylation than the controls. The expression of both DNMT1 and MBD2 mRNA was significantly increased in the SLE patients compared with the controls. This study also showed a positive correlation between DNMT1 and MBD2 mRNA levels in the patients with SLE.

Global DNA methylation, DNMT1, and MBD2 in patients with rheumatoid arthritis

OBJECTIVES

To investigate the associations of DNA methylation levels and mRNA expressions of DNA cytosine-5-methyltransferase 1 (DNMT1) and methyl CpG-binding domain 2 (MBD2) with rheumatoid arthritis (RA).

METHODS

The global methylation status of DNA was measured in 65 patients with RA and 64 healthy controls by the ELISA method. DNMT1 and MBD2 mRNA were also detected in 177 RA patients and 95 controls using the quantitative real-time polymerase chain reaction method.

RESULTS

The global methylation of DNA was significantly decreased in the RA patients compared to the controls (p=0.005, 95% CI=0.0835-0.4503). The patients with RA had higher expressions of DNMT1 and MBD2 mRNA than the controls (p<0.001, 95% CI=-0.0024 to -0.0053 and p<0.001, 95% CI=-0.0079 to -0.0167, respectively). We also found that the MBD2 mRNA level was not related to the disease activity of RA. However, the expression of DNMT1 mRNA tended to be associated with the disease activity of RA (p=0.08). The levels of DNA methylation and DNMT1 mRNA were significantly decreased in the patients with anti-CCP antibody compared with those without (p=0.005, 95% CI=-0.7333 to -0.1373 and p=0.003, 95% CI=-0.0071 to -0.0022, respectively). The differences in the methylation level and expressions of DNMT1 and MBD2 were not significant between the patients treated with and without anti-TNFα biological agents (Enbrel or Humira).

CONCLUSION

This study demonstrated that the RA patients have a significantly lower level of DNA methylation than the controls. Moreover, RA patients have higher expressions of DNMT1 and MBD2 mRNA. The anti-TNFα biological agents do not seem to affect DNA methylation and mRNA expressions of DNMT1 and MBD2 in RA patients.

Fused-core silica column ultra-performance liquid chromatography-ion trap tandem mass spectrometry for determination of global DNA methylation status

Epigenetic modifications, such as DNA methylation, play key roles in transcriptional regulation of gene expression. More recently, global DNA methylation levels have been documented to be altered in several diseases, including cancer, and as the result of exposure to environmental toxicants. Based on the potential use of global DNA methylation status as a biomarker of disease status and exposure to environmental toxicants, we sought to develop a rapid, sensitive, and precise analytical method for the quantitative measurement of global DNA methylation status using ultra-performance liquid chromatography with detection by ion trap tandem mass spectrometry. Using a fused-core silica column, 2'-deoxyguanosine (2dG) and 5-methyl-2'-deoxycytidine (5mdC) were resolved in less than 1 min with detection limits of 0.54 and 1.47 fmol for 5mdC and 2dG, respectively. The accuracy of detection was 95% or higher, and the day-to-day coefficient of variation was found to be 3.8%. The method was validated by quantification of global DNA methylation status following treatment of cells with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine, which reduced DNA methylation from 3.1% in control cells to 1.1% in treated cells. The sensitivity and high throughput of this method rend it suitable for large-scale analysis of epidemiological and clinical DNA samples.

The -283C/T polymorphism of the DNMT3B gene influences the progression of joint destruction in rheumatoid arthritis

The objective of this study is to investigate the association between the -283C/T polymorphism at the promotor of DNMT3B gene and susceptibility to rheumatoid arthritis (RA) and to evaluate the effect of the polymorphism on clinical features such as progression of joint destruction in RA. A total of 309 patients with RA were compared with 297 control subjects. Genotyping of the -283C/T polymorphism was performed by real-time sequencing using Pyrosequencer. The genotype frequencies of the polymorphism at position -283 were not significantly different between patients with RA and controls. There were significantly positive correlations between the modified Sharp score and the disease duration for carriers of each genotype (y = 9.546x + 19.998, p < 0.001, for T allele carriers, y = 6.185x + 34.424, p < 0.001 for CC homozygotes). The slope of regression line of the T allele carriers was significantly steeper than that of the CC homozygotes (p = 0.014). In conclusion, our results suggest that the -283C/T polymorphism of the DNMT3B gene is a genetic marker related to the joint destruction of RA.

Overexpression of the growth arrest and DNA damage-induced 45alpha gene contributes to autoimmunity by promoting DNA demethylation in lupus T cells

OBJECTIVE

Demethylation of CD11a and CD70 regulatory regions in CD4+ T cells contributes to the development of autoreactivity and overstimulation of autoantibodies. Because growth arrest and DNA damage-induced 45alpha (GADD45alpha) reduces epigenetic silencing of genes by removing methylation marks, this study examined whether the gadd45A gene could contribute to autoimmunity by promoting DNA demethylation in T cells from patients with systemic lupus erythematosus (SLE).

METHODS

Levels of GADD45alpha, CD11a, and CD70 messenger RNA (mRNA) and protein were detected by real-time reverse transcription-polymerase chain reaction and Western blotting or flow cytometry. Global DNA methylation was evaluated using Methylamp global DNA methylation quantification kits. Detection of CD4+ T cell proliferation and autologous B cell IgG antibodies was performed using commercially available kits. CD11a and CD70 promoter methylation was determined with bisulfite sequencing.

RESULTS

Elevated gadd45A mRNA expression and global DNA hypomethylation were observed in CD4+ T cells from SLE patients. The levels of gadd45A mRNA were inversely proportional to the levels of DNA methylation. Positive correlations were found between gadd45A and CD11a/CD70 mRNA levels. Expression of gadd45A mRNA was increased in CD4+ T cells following ultraviolet B irradiation, and this was accompanied by increased levels of CD11a and CD70 mRNA. Moreover, increased expression of gadd45A, CD11a, and CD70 mRNA was accompanied by increased autoreactivity and excessive B cell stimulation in gadd45A-transfected CD4+ T cells. CD11a promoter methylation was also significantly reduced in transfected cells. Transfection of gadd45A small interfering RNA inhibited the autoreactivity of SLE CD4+ T cells and led to significant increases in the methylation levels of the CD11a and CD70 promoter regions.

CONCLUSION

These findings indicate that gadd45A may contribute to lupus-like autoimmunity by promoting DNA demethylation in SLE CD4+ T cells.

DNA methylation and not allelic variation regulates STAT6 expression in human T cells

STAT6 transcription factor, which has been implicated in commitment to Th2, is known to be activated by IL-4 and IL-13. Accordingly, STAT6 is primarily responsible for the transcriptional effects of IL-4 and IL-13. STAT6-deficient mice are known to have defective IL-4-mediated functions, such as B cell proliferation, Th2 cell development and IgE secretion; therefore, they primarily contain the Th1 phenotype. However, the mechanism responsible for regulation of STAT6 expression transcriptionally and post-transcriptionally has yet to be elucidated. Here, we characterized the human STAT6 promoter gene and found that the transcriptional regulatory elements CCAAT and ATF were important for the STAT6 promoter activity. Direct sequencing analysis revealed that the 13 GT repeat allelic variation in noncoding exon 1 of the STAT6 gene appeared more frequently in 91 patients with asthma or rheumatoid arthritis than the 15 GT repeat variation, which is the dominant phenotype in healthy controls. However, it appears that this allelic variation did not affect the STAT6 transcriptional activity. Interestingly, treatment with a DNA methyltransferase inhibitor markedly increased the expression of STAT6 mRNA and protein in human primary T cells. In contrast, IFN-gamma treatment significantly repressed the STAT6 transcriptional activity. Therefore, the present study provides insight into the molecular basis of STAT6 expression, and in particular, demonstrates that STAT6 expression is associated with DNA hypermethylation rather than promoter polymorphisms or allelic variations.

Organ and gestational age effects of maternal nutrient restriction on global methylation in fetal baboons

BACKGROUND

A sub-optimal intrauterine environment alters the trajectory of fetal development with profound effects on life-time health. Altered methylation, a proposed epigenetic mechanism responsible for these changes, has been studied in non-primate species but not nonhuman primates. We tested the hypotheses that global methylation in fetal baboon demonstrates organ specificity, gestational age specificity, and changes with maternal nutritional status.

METHODS

We measured global DNA methylation in fetuses of control fed (CTR) and nutrient restricted mothers fed 70% of controls (MNR) for brain, kidney, liver and heart at 0.5 and 0.9 gestation (G).

RESULTS

We observed organ and gestation specific changes that were modified by maternal diet. Methylation in CTR fetuses was highest in frontal cortex and lowest in liver. MNR decreased methylation in 0.5G kidney and increased methylation in 0.9G kidney and frontal cortex.

CONCLUSION

These results demonstrate a potential epigenetic mechanism whereby reduced maternal nutrition has long-term programming effects on fetal organ development.

DNA hypomethylation in the origin and pathogenesis of human diseases

The pathogenesis of any given human disease is a complex multifactorial process characterized by many biologically significant and interdependent alterations. One of these changes, specific to a wide range of human pathologies, is DNA hypomethylation. DNA hypomethylation signifies one of the major DNA methylation states that refers to a relative decrease from the "normal" methylation level. It is clear that disease by itself can induce hypomethylation of DNA; however, a decrease in DNA methylation can also have an impact on the predisposition to pathological states and disease development. This review presents evidence suggesting the involvement of DNA hypomethylation in the pathogenesis of several major human pathologies, including cancer, atherosclerosis, Alzheimer's disease, and psychiatric disorders.

Folic acid, methylation and neural tube closure in humans

This review provides a brief description of folate use and folic acid metabolism in relation to neural tube defect (NTD) risk. First, a meta-analysis of reduction in NTD recurrence and occurrence risk with periconceptional folic acid supplementation is presented. Second, an overview of the complex folate metabolism is given. Third, SNPs for genes involved in folate and homocysteine metabolism that have been studied in relation to NTD riskare discussed. Fourth, the questions whether folate receptor autoantibodies or hampered methylation are mechanisms underlying NTDs are briefly discussed.

X chromosome reactivation perturbs intracellular self/not-self discrimination

New reports indicate a chromosomal rather than hormonal basis for the susceptibility of females to autoimmune disease. It is held that if females reactivate an inactivated X chromosome, there will be overexpression of certain X-located genes affecting immune function. Hence, normal mechanisms of self/not-self discrimination might be impaired resulting in immune reaction to self antigens. However, the data are also consistent with the long-held view that the demands of intracellular self/not-self discrimination have driven the evolution of X-chromosome dosage compensation. It was proposed that, whether cells are in male or female bodies, concentrations of proteins are fine-tuned up to their aggregation thresholds. A disruption of this equilibrium, by agents originating either externally (for example, virus) or internally (for example, reactivated X chromosome), generates homoaggregates that trigger responses against the respective not-self or self antigens. Thus, female susceptibility to autoimmune disease may not be because certain immune system genes happen to be X-located, but because self/not-self discrimination was the raison d'être for X-chromosome dosage compensation in the first place.

Immune-mediated adverse drug reactions

Many adverse drug reactions are mediated by the immune system. This can be because the therapeutic effect of the drug targets the immune system. For example, immunosuppressive drugs increase the risk of infections. It is paradoxical that some immunosuppressive drugs can lead to autoimmune reactions. Another mechanism by which drugs can cause an adverse reaction involves an idiosyncratic response to the drug such as an immune-mediated skin rash. These idiosyncratic drug reactions (IDRs) are difficult to study because of the paucity of valid animal models and their unpredictable nature. Therefore, much of our mechanistic knowledge of IDRs is based on inferences from the clinical characteristics of IDRs rather than on controlled mechanistic studies. In general, IDRs are associated with a delay between starting the drug and the onset of the adverse reaction, and the typical delay is different for different types of IDRs. In contrast, on rechallenge, there is usually a rapid onset of the adverse reaction, which is characteristic of an amnestic immune response. The absence of such a rapid response is usually considered evidence that an IDR is not immune-mediated; yet, there are immune-mediated IDRs that do not have an amnestic response. One possible reason for the lack of an amnestic response is if the IDR has a strong autoimmune component leading to deletion of autoimmune memory cells when the drug is withdrawn. Another interesting characteristic of IDRs is that there are many drugs that can cause different types of IDRs in different patients. A possible explanation is that although the immune response is induced by a drug, it is directed against an autoantigen, and interindividual differences in the immune repertoire determine which autoantigen and target organ are affected. Although testing these hypotheses represents a difficult challenge, the importance of these adverse reactions makes it a high priority.

Hypermethylation of estrogen receptor-alpha gene in atheromatosis patients and its correlation with homocysteine

OBJECTIVE

To investigate the aberrant DNA methylation in promoter region of estrogen receptor alpha (ERalpha) in atherosclerosis (As) and the possible involvement of homocysteine (Hcy) in its pathogenesis.

METHODS

The blood samples were collected from 54 patients with As approved by carotid colorized ultrasound examination and 28 healthy control subjects. The methylation status of CpG islands in ER-alpha gene promoter region of genome DNA was analyzed by nested-methylation-specific PCR (nMSP). tHcy was examined by fluorescent-biochemical method. Spearman rank correlation was used to analyse the relationship between the degree of methylation in ER-alpha gene and the level of tHcy. Cultured smooth muscle cells of Homo sapiens were treated by Hcy with different concentrations and different treating time, again the DNA methylation status was assayed by nMSP, and the proliferation of SMC was assayed by MTT.

RESULTS

Hypermethylation of ER-alpha gene promoter region was found in 38 cases of atherosclerosis patients, and the methylation frequency was 70.4%. While in healthy controls, just 8 of 28 samples hypermethylation was found, only 28.6% methylation frequency was detected, much lower than the one in atherosclerosis group (p<0.05). Meanwhile, the level of tHcy in atherosclerosis group was significantly higher than that in control group (p<0.05). The spearman rank correlation analysis explored an obvious correlation between the degree of methylation in ER-alpha gene and the level of tHcy (r=0.809, p<0.05), and the severity of atherosclerotic lesion was also heightened along with the increment of plasma level of tHcy. The cultured SMCs treated by Hcy resulted in de novo methylation in promoter region of ERalpha gene with a concentration and treating time-dependent manner, and a dose-dependent promoting effect on SMC proliferation. The in vivo and in vitro data coincidently showed that the Hcy could promote the hypermethylation of ERalpha gene, which may be an important mechanism for the pathogenesis of As.

CONCLUSION

Hypermethylation of CpG islands in ER-alpha gene promoter region was found in much higher frequency in atherosclerosis patients, which is positively correlated with the increased level of plasma tHcy and the severity of atherosclerotic lesion, and the in vitro experimental results further extended above clinical data that HHcy can lead to the hypermethylation of ER-alpha gene, and hence to promote the occurrence and development of As.

A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation

Causes underlying inter-individual variations in DNA methylation profiles among normal healthy populations are not thoroughly understood. To investigate the contribution of genetic variation in DNA methyltransferase (DNMT) genes to such epigenetic variation, we performed a systematic search for polymorphisms in all known human DNMT genes [DNMT1, DNMT3A, DNMT3B, DNMT3L and DNMT2 (TRDMT1)] in 192 healthy males and females. One hundred and eleven different polymorphisms were detected. Of these, 24 were located in coding regions and 10 resulted in an amino acid change that may affect the corresponding DNMT protein structure or function. Association analysis between all major polymorphisms (frequency > 1%) and quantitative DNA methylation profiles did not return significant results after correction for multiple testing. Polymorphisms leading to an amino acid change were further investigated for changes in global DNA methylation by differential methylation hybridization. This analysis revealed that a rare change at DNMT3L (R271Q) was associated with significant DNA hypomethylation. Biochemical characterization confirmed that DNMT3L(R271Q) is impaired in its ability to stimulate de novo DNA methylation by DNMT3A. Methylated DNA immunoprecipitation based analysis using CpG island microarrays revealed that the hypomethylation in this sample preferentially clustered to subtelomeric genomic regions with affected loci corresponding to a subset of repetitive CpG islands with low predicted promoter potential located outside of genes.

MAGE-B2 autoantibody: a new biomarker for pediatric systemic lupus erythematosus

OBJECTIVE

Melanoma-associated antigen gene B2 (MAGE-B2) encodes an embryonic antigen normally silenced after birth except in testis and placenta. We identified the MAGE-B2 gene and autoantibodies in pediatric patients with systemic lupus erythematosus (SLE) glomerulonephritis. We investigated the prevalence of MAGE-B2 autoantibodies in association with active SLE, to determine a pathogenetic role of MAGE-B2 protein through its distribution in cells and tissues.

METHODS

A cross-sectional study analyzed the frequency of MAGE-B2 autoantibodies in 40 patients with pediatric SLE, 23 adult controls, and 16 patients with pediatric juvenile rheumatoid arthritis (JRA) using Western blots containing recombinant MAGE-B2. SLE Disease Activity Index 2000 (SLEDAI-2K) and British Isles Lupus Assessment Group (BILAG) index measured SLE disease activity. Tissue distribution of MAGE-B2 protein was assessed by immunohistochemistry, immunofluorescence, and Western blots.

RESULTS

Seventeen (43%) of 40 pediatric SLE patients had MAGE-B2 autoantibodies as compared to 0 of 16 JRA patients and 2 of 23 adult controls. SLE disease activity was significantly higher in MAGE-B2 autoantibody-positive versus autoantibody-negative patients (SLEDAI-2K, mean 10.9 vs 5.2, p = 0.013; BILAG, mean 15.3 vs 6.3, p = 0.023). Active nephritis was more prevalent (60% vs 24%) in MAGE-B2 autoantibody-positive than autoantibody-negative SLE patients. MAGE-B2 protein was visualized in SLE kidney proximal convoluted tubules and in tumor epithelial cells, but not in lymphoblastoid cells.

CONCLUSION

MAGE-B2 autoantibody appears to be a clinically relevant biomarker for pediatric SLE disease activity and nephritis.

Endogenous retroviruses in systemic response to stress signals

Infection of germline cells with retroviruses initiates permanent proviral colonization of the germline genome. The germline-integrated proviruses, called endogenous retroviruses (ERVs), are inherited to offspring in a Mendelian order and belong to the transposable element family. Endogenous retroviruses and other long terminal repeat retroelements constitute ~8% and ~10% of the human and mouse genomes, respectively. It is likely that each individual has a distinct genomic ERV profile. Recent studies have revealed that a substantial fraction of ERVs retains the coding potentials necessary for virion assembly and replication. There are several layers of potential mechanisms controlling ERV expression: intracellular transcription environment (e.g., transcription factor pool, splicing machinery, hormones), epigenetic status of the genome (e.g., proviral methylation, histone acetylation), profile of transcription regulatory elements on each ERV's promoter, and a range of stress signals (e.g., injury, infection, environment). Endogenous retroviruses may exert pathophysiologic effects by infection followed by random reintegration into the genome, by their gene products (e.g., envelope, superantigen), and by altering the expression of neighboring genes. Several studies have provided evidence that ERVs are associated with a range of pathogenic processes involving multiple sclerosis, systemic lupus erythematosus, breast cancer, and the response to burn injury. For instance, the proinflammatory properties of the human ERV-W envelope protein play a central role in demyelination of oligodendrocytes. As reviewed in this article, recent advances in ERV biology and mammalian genomics suggest that ERVs may have a profound influence on various pathogenic processes including the response to injury and infection. Understanding the roles of ERVs in the pathogenesis of injury and infection will broaden insights into the underlying mechanisms of systemic immune disorder and organ failure in these patients.

Decreased DNA methyltransferase 3A and 3B mRNA expression in peripheral blood mononuclear cells and increased plasma SAH concentration in adult patients with idiopathic thrombocytopenic purpura

OBJECTIVE

DNA methylation is known to play an important role in gene transcription and alterations of methylation contribute to the development of certain disorders such as cancer and immunodeficiency. Recent years have found an increasing interest in the role of epigenetic modifications in the etiology of human autoimmune diseases, such as systemic lupus erythromatosus (SLE) and rheumatoid arthritis (RA). DNA methyltransferases (DNMTs) are involved in the epigenetic control of DNA methylation processes. S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), as the substrate and product of essential cellular methyltransferase reactions, have important indicator action of cellular methylation status. The aim of this study is to explore if DNA methylation plays a role in the pathogenesis of idiopathic thrombocytopenic purpura (ITP).

METHODS

DNMT1, DNMT3A, and DNMT3B mRNA expression in peripheral blood mononuclear cells (PBMCs) of adult ITP patients were analyzed by real-time quantitative polymerase chain reaction. Plasma SAM and SAH levels were assayed with reversed-phase high performance liquid chromatography (HPLC).

RESULTS

DNMT3A and DNMT3B mRNA expressions were significantly lower in ITP patients than in healthy controls (p < 0.001), while DNMT1 mRNA expression was not significantly different between the two groups (p = 0.774). Plasma SAH concentration was significantly elevated in ITP patients than in healthy controls (p < 0.05), while the plasma SAM and SAM/SAH were not significantly different between the two groups (p = 0.133, p = 0.624 respectively).

CONCLUSIONS

Our observations suggest that aberrant DNA methylation status reflected by increased plasma SAH concentration and decreased mRNA expression levels of DNMT3A and 3B are possibly involved in the pathogenesis of ITP although the precise mechanisms need further study.

Single nucleotide polymorphism in DNMT3B promoter and the risk for idiopathic thrombocytopenic purpura in Chinese population

OBJECTIVE

Epigenetic changes in gene expression, including DNA methylation and histone modifications, might contribute to autoimmunity. DNA methylation is mediated by a family of DNA methyltransferases. Polymorphisms of the DNA methyltransferase 3B (DNMT3B) gene may influence DNMT3B activity on DNA methylation, thereby modulating the susceptibility to some diseases. The purpose of this study was to investigate the association between the single nucleotide polymorphism (SNP) in promoter of the DNMT3B gene and the risk for development of idiopathic thrombocytopenic purpura (ITP).

METHODS

In this hospital-based case-control study, the DNMT3B SNP was genotyped in 201 patients with ITP and 136 healthy controls by polymerase chain reaction-restriction fragment length polymorphism.

RESULTS

The C/C genotype was not detected in both the patients with ITP and the controls. In the controls, the frequencies of T/T and C/T genotypes and T and C alleles were 97.8%, 2.2%, 98.9%, and 1.1%, respectively. There was no significant difference in genotype and allele distribution between the patients with ITP and the controls (P = 0.745 and 0.747, respectively). No significant difference was observed in genotype and allele distribution between the two groups when stratified by the age. The similar results were shown among the four groups of patients with ITP: acute childhood, chronic childhood, acute adult, and chronic adult.

CONCLUSION

This polymorphism was distributed similarly between the patients with ITP and the controls. It demonstrated that it may not be used as a stratification marker to predict the susceptibility to ITP, at least in the population of North China.

Intra-individual change over time in DNA methylation with familial clustering

CONTEXT

Changes over time in epigenetic marks, which are modifications of DNA such as by DNA methylation, may help explain the late onset of common human diseases. However, changes in methylation or other epigenetic marks over time in a given individual have not yet been investigated.

OBJECTIVES

To determine whether there are longitudinal changes in global DNA methylation in individuals and to evaluate whether methylation maintenance demonstrates familial clustering.

DESIGN, SETTING, AND PARTICIPANTS

We measured global DNA methylation by luminometric methylation assay, a quantitative measurement of genome-wide DNA methylation, on DNA sampled at 2 visits on average 11 years apart in 111 individuals from an Icelandic cohort (1991 and 2002-2005) and on average 16 years apart in 126 individuals from a Utah sample (1982-1985 and 1997-2005).

MAIN OUTCOME MEASURE

Global methylation changes over time.

RESULTS

Twenty-nine percent of Icelandic individuals showed greater than 10% methylation change over time (P < .001). The family-based Utah sample also showed intra-individual changes over time, and further demonstrated familial clustering of methylation change (P = .003). The family showing the greatest global methylation loss also demonstrated the greatest loss of gene-specific methylation by a separate methylation assay.

CONCLUSION

These data indicate that methylation changes over time and suggest that methylation maintenance may be under genetic control.

Abnormal transmethylation/transsulfuration metabolism and DNA hypomethylation among parents of children with autism

An integrated metabolic profile reflects the combined influence of genetic, epigenetic, and environmental factors that affect the candidate pathway of interest. Recent evidence suggests that some autistic children may have reduced detoxification capacity and may be under chronic oxidative stress. Based on reports of abnormal methionine and glutathione metabolism in autistic children, it was of interest to examine the same metabolic profile in the parents. The results indicated that parents share similar metabolic deficits in methylation capacity and glutathione-dependent antioxidant/detoxification capacity observed in many autistic children. Studies are underway to determine whether the abnormal profile in parents reflects linked genetic polymorphisms in these pathways or whether it simply reflects the chronic stress of coping with an autistic child.

Single-molecule polymerase chain reaction reduces bias: application to DNA methylation analysis by bisulfite sequencing

The treatment of DNA with bisulfite, which converts C to U but leaves 5-methyl-C unchanged, forms the basis of many analytical techniques for DNA methylation analysis. Many techniques exist for measuring the methylation state of a single CpG but, for analysis of an entire region, cloning and sequencing remains the gold standard. However, biases in polymerase chain reaction (PCR) amplification and in cloning can skew the results. We hypothesized that single-molecule PCR (smPCR) amplification would eliminate the PCR amplification bias because competition between templates that amplify at different efficiencies no longer exists. The amplified products can be sequenced directly, thus eliminating cloning bias. We demonstrated this accurate and unbiased approach by analyzing a sample that was expected to contain a 50:50 ratio of methylated to unmethylated molecules: a region of the X-linked FMR1 gene from a human female cell line. We compared traditional cloning and sequencing to smPCR and sequencing. Sequencing smPCR products gave an expected methylated to unmethylated ratio of 48:52, whereas conventional cloning and sequencing gave a biased ratio of 72:28. Our results show that smPCR sequencing can eliminate both PCR and cloning bias and represents an attractive approach to bisulfite sequencing.

Hypomethylation of interleukin-4 and -6 promoters in T cells from systemic lupus erythematosus patients

AIM

DNA methylation regulates gene expression, and hypomethylation is associated with abnormal T-cell function in systemic lupus erythematosus (SLE). However, little is known about the methylation levels of the interleukin (IL)-4 and -6 promoters in SLE patients.

METHODS

T cells were isolated from 20 SLE patients and 10 healthy controls, activated in vitro in the presence or absence of 5- azacytidine (5-azaC), and their IL-4 and -6 transcripts were characterized using semiquantitative RT-PCR. Following bisulfate modification of their genomic DNA, the levels of DNA methylation in the IL-4 or -6 promoter were determined by nested PCR and direct sequencing.

RESULTS

The levels of IL-4 and -6 mRNA transcripts were significantly higher in SLE T cells, as compared with that in the controls. Furthermore, the treatment of healthy T cells with 5-azaC demethylated the CpG islands in the IL-4 or -6 promoter and increased IL-4 and -6 mRNA transcriptions. Importantly, the hypomethylation of the CpG islands in the IL-4 and -6 promoters displayed in SLE patients was similar to that of healthy T cells treated with 5-azaC. Finally, the hypomethylation levels of the CpG islands in the IL-4 and -6 promoters in lupus patients were significantly correlated to the IL-4 and -6 expressions.

CONCLUSION

The hypomethylation of the CpG islands of the IL-4 and -6 promoters accrued in T cells from SLE patients and was associated with the severity of SLE at the clinic.

Demethylation of CD40LG on the inactive X in T cells from women with lupus

Why systemic lupus erythematosus primarily affects women is unknown. Recent evidence indicates that human lupus is an epigenetic disease characterized by impaired T cell DNA methylation. Women have two X chromosomes; one is inactivated by mechanisms including DNA methylation. We hypothesized that demethylation of sequences on the inactive X may cause gene overexpression uniquely in women, predisposing them to lupus. We therefore compared expression and methylation of CD40LG, a B cell costimulatory molecule encoded on the X chromosome, in experimentally demethylated T cells from men and women and in men and women with lupus. Controls included TNFSF7, a methylation-sensitive autosomal B cell costimulatory molecule known to be demethylated and overexpressed in lupus. Bisulfite sequencing revealed that CD40LG is unmethylated in men, while women have one methylated and one unmethylated gene. 5-Azacytidine, a DNA methyltransferase inhibitor, demethylated CD40LG and doubled its expression on CD4(+) T cells from women but not men, while increasing TNFSF7 expression equally between sexes. Similar studies demonstrated that CD40LG demethylates in CD4(+) T cells from women with lupus, and that women but not men with lupus overexpress CD40LG on CD4(+) T cells, while both overexpress TNFSF7. These studies demonstrate that regulatory sequences on the inactive X chromosome demethylate in T cells from women with lupus, contributing to CD40LG overexpression uniquely in women. Demethylation of CD40LG and perhaps other genes on the inactive X may contribute to the striking female predilection of this disease.

Drug-induced lupus

Drug-induced lupus (DIL) is a rare adverse reaction to a large variety of drugs with features resembling those of idiopathic systemic lupus erythematosus (SLE). It usually develops only after months and, quite commonly, years of treatment with the offending agent, although latencies of days or weeks have been described in some instances. There are some indications that the risk of DIL can increase with higher daily and cumulative doses and with longer duration of therapy. There are no definitive and commonly accepted diagnostic criteria for DIL, but the following guidelines have been proposed: (a) sufficient and continuing exposure to a specific drug, (b) at least one symptom compatible with SLE, (c) no history suggestive of SLE before starting the drug, and (d) resolution of symptoms within weeks (sometimes months) after discontinuation of the putative offending agent. In addition, it is frequently suggested that the presence of ANA is required for the diagnosis of DIL. However, negative ANA test results should not automatically preclude such a diagnosis, particularly if a patient has other autoantibodies associated with SLE/DIL.

DNA Methylation Errors in Cloned Mice Disappear with Advancement of Aging

Cloned animals have various health problems. Aberrant DNA methylation is a possible cause of the problems. Restriction landmark genomic scanning (RLGS) that enabled us to analyze more than 1,000 CpG islands simultaneously demonstrated that all cloned newborns had aberrant DNA methylation. To study whether this aberration persists throughout the life of cloned individuals, we examined genome-wide DNA methylation status of newborn (19.5 dpc, n=2), adult (8-11 months old, n=3), and aged (23-27 months old, n=4) cloned mice using kidney cells as representatives. In the adult and aged groups, cloning was repeated using cumulus cells of the adult founder clone of each group as nucleus donor. Two newborn clones had three with aberrantly methylated loci, which is consistent with previous reports that all cloned newborns had DNA methylation aberrations. Interestingly, we could detect only one aberrantly methylated locus in two of the three adult clones in mid-age and none of four senescent clones, indicating that errors in DNA methylation disappear with advancement of animals' aging.

Phenotypic plasticity and the epigenetics of human disease

It is becoming clear that epigenetic changes are involved in human disease as well as during normal development. A unifying theme of disease epigenetics is defects in phenotypic plasticity--cells' ability to change their behaviour in response to internal or external environmental cues. This model proposes that hereditary disorders of the epigenetic apparatus lead to developmental defects, that cancer epigenetics involves disruption of the stem-cell programme, and that common diseases with late-onset phenotypes involve interactions between the epigenome, the genome and the environment. Increased understanding of epigenetic-disease mechanisms could lead to disease-risk stratification for targeted intervention and to targeted therapies.

Drug-induced liver injury at an Asian center: a prospective study

BACKGROUND/AIMS

The aetiology of drug-induced liver injuries (DILI) in Asia is different from that in the West, as anecdotal studies have shown that traditional complementary and alternative medicines (CAM) accounted for a major proportion of offending drugs in DILI in Asia. We aimed to study DILI in Asia prospectively, and to test whether DILI caused by traditional CAM was related to adulterants.

METHODS

A collaborative group consisting of a tertiary-hospital hepatology department, a pharmaceutical laboratory, and a pharmacovigilance unit was formed to study patients with DILI at a tertiary hospital over a 26-month period prospectively. Traditional medicines that were implicated were tested for the presence of adulterants.

RESULTS

Thirty-one patients with DILI were enrolled: age 51+/-3 (18-79) years, 17 (55%) male. Twenty-three (74%) had hepatocellular, six (19%) had cholestatic, and two (7%) had a mixed pattern of injury. Chinese traditional CAM was the most common medication type implicated, accounting for 17 (55%) patients, followed by Malay CAM in five (16%). Thirty-one traditional medicines from 17 patients were available for chemical analysis. Adulterants were found in nine (29%) of them.

CONCLUSIONS

DILI in Asia has a different aetiology as compared with the West, and could be related to presence of adulterants in traditional CAM.

Complete response of deep neutrophilic dermatosis associated with myelodysplastic syndrome to 5-azacytidine

Cutaneous manifestations of myelodysplastic syndromes (MDS) may predict disease progression and a poorer prognosis. We describe a patient in whom a deep neutrophilic dermatosis preceded evolution of disease from refractory anaemia to RAEB (refractory anaemia with excess blasts) and resolved completely on treating the disease with 5-azacytidine. The dermatological response was accompanied by complete bone marrow remission and trilineage haematological improvement. We suggest that 5-azacytidine should be considered in the treatment of immune mediated cutaneous manifestations of MDS.

Different effects of homocysteine and oxidized low density lipoprotein on methylation status in the promoter region of the estrogen receptor alpha gene

We investigated the effects of homocysteine (Hcy) and oxidized low density lipoprotein (ox-LDL) on DNA methylation in the promoter region of the estrogen receptor alpha (ERalpha) gene, and its potential mechanism in the pathogenesis of atherosclerosis. Cultured smooth muscle cells (SMCs) of humans were treated by Hcy and ox-LDL with different concentrations for different periods of time. The DNA methylation status was assayed by nested methylation-specific polymerase chain reaction, the lipids that accumulated in the SMCs and foam cell formations were examined with Oil red O staining. The proliferation of SMCs was assayed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method. The results showed that ox-LDL in moderate concentrations (10-40 mg/L) induced de novo methylation in the promoter region of the ERalpha gene of SMCs. However, high concentrations (50 mg/L) of ox-LDL, resulted in demethylation of ERalpha. The Hcy treatment resulted in de novo methylation in the promoter region of the ERalpha gene with a concentration- and treating time-dependent manner, and a dose-dependent promoting effect on SMC proliferation. These data indicated that the two risk factors for atherosclerosis had the function of inducing de novo methylation in the promoter region of the ERalpha gene of SMCs. However, high concentrations (50 mg/L) of ox-LDL induced demethylation, indicating that different risk factors of atherosclerosis with different potency might cause different aberrant methylation patterns in the promoter region of the ERalpha gene. The atherogenic mechanism of Hcy might involve the hypermethylation of the ERalpha gene, leading to the proliferation of SMCs in atherosclerotic lesions.

Systemic lupus erythematosus: multiple immunological phenotypes in a complex genetic disease

Systemic lupus erythematosus (SLE) is a complex polygenic autoimmune disease characterized by the presence of anti-nuclear autoantibodies (ANAs) that are often detectable years prior to the onset of clinical disease. The disease is associated with a chronic activation of the immune system, with the most severe forms progressing to inflammatory damage that can impact multiple organ systems in afflicted individuals. Current therapeutic strategies poorly control disease manifestations and are generally immunosuppressive. Recent studies in human patient populations and animal models have associated elements of the innate immune system and abnormalities in the immature B lymphocyte receptor repertoires with disease initiation. A variety of cytokines, most notably type I interferons, play important roles in disease pathogenesis and effector mechanisms. The genetic basis for disease susceptibility is complex, and analyses in humans and mice have identified multiple susceptibility loci, several of which are located in genomic regions that are syntenic between humans and mice. The complexities of the genetic interactions that mediate lupus have been investigated in murine model systems by characterizing the progressive development of disease in strains expressing various combinations of susceptibility alleles. These analyses indicate that genetic epistasis dramatically impact disease development and support the feasibility of identifying molecular pathways that can suppress disease progression without completely impairing normal immune function.

Immunoepigenetics: the unseen side of cancer immunoediting

Cancer immunosurveillance representing, till recently, the explanatory framework relating cancer and the immune system, does not convincingly explain tumor escape. At the beginning of the decade, a new theory emerged, namely the immunoediting theory, and it comprehensively defines the role of the immune system in carcinogenesis. The core of this theory embraces the concept that the immune system on the one hand protects the body from cancer and on the other it shapes the immunogenicity of these cancers, thus presents a persuasive rationalization of the resistance of tumors against the immune response. With the immune system playing, in this context, such a pivotal role in shaping the tumor immune profile and in subsequent oncogenesis, it seems rather paradoxical to accept the immunocompetent host's immune system as a constant moiety. While DNA mutations of immune genes create a rather polymorphic condition, their frequency is much lower than that of other genetic events. Of these, epigenetic alterations give rise to new epialleles, which can reach up to 100% per locus. Bearing in mind that cancer is characterized by a tremendous amount of epigenetic aberrations, in both gene and global level, it is reasonable to postulate that, for the same unknown causes, analogous aberrations could affect the immune genes. Should this be the case, the relation between oncogenesis and the immune system appears much more dynamic and complex. Such an immunoepigenetic approach to carcinogenesis could improve our understanding of a series of common cancer-related aspects, such as environmental risk factors, effectiveness of demethylating agents, failure of current immunotherapies, etc. Moreover, this immunoepigenetic paradigm will take the current perception of the immune system and cancer interrelation further and beyond, constituting that the immunoresistant cancer cell phenotype is not shaped by the immune system acting as a steady and rigid evolutionary pressure, but rather as an extremely dynamic variable.

Implication of abnormal epigenetic patterns for human diseases

Significant evidences have brought new insights on the mechanisms by which epigenetic machinery proteins regulate gene expression, leading to a redefinition of chromatin regulation in terms of modification of core histones, DNA methylation, RNA-mediated silencing pathways, action of methylation-dependent sensitive insulators and Polycomb/Trithorax group proteins. Consistent with these fundamental aspects, an increasing number of human pathologies have been found to be associated with aberrant epigenetics regulation, including cancer, mental retardation, neurodegenerative symptoms, imprinting disorders, syndromes involving chromosomal instabilities and a great number of human life-threatening diseases. The possibility of reversing epigenetic marks, in contrast to genetic code, may provide new pharmacological targets for emerging therapeutic intervention.

DNA hypomethylation and human diseases

Changes in human DNA methylation patterns are an important feature of cancer development and progression and a potential role in other conditions such as atherosclerosis and autoimmune diseases (e.g., multiple sclerosis and lupus) is being recognised. The cancer genome is frequently characterised by hypermethylation of specific genes concurrently with an overall decrease in the level of 5 methyl cytosine. This hypomethylation of the genome largely affects the intergenic and intronic regions of the DNA, particularly repeat sequences and transposable elements, and is believed to result in chromosomal instability and increased mutation events. This review examines our understanding of the patterns of cancer-associated hypomethylation, and how recent advances in understanding of chromatin biology may help elucidate the mechanisms underlying repeat sequence demethylation. It also considers how global demethylation of repeat sequences including transposable elements and the site-specific hypomethylation of certain genes might contribute to the deleterious effects that ultimately result in the initiation and progression of cancer and other diseases. The use of hypomethylation of interspersed repeat sequences and genes as potential biomarkers in the early detection of tumors and their prognostic use in monitoring disease progression are also examined.

Methylation of endogenous human retroelements in health and disease

Retroelements constitute approximately 45% of the human genome. Long interspersed nuclear element (LINE) autonomous retrotransposons are predominantly represented by LINE-1, nonautonomous small interspersed nuclear elements (SINEs) are primarily represented by ALUs, and LTR retrotransposons by several families of human endogenous retroviruses (HERVs). The vast majority of LINE and HERV elements are densely methylated in normal somatic cells and contained in inactive chromatin. Methylation and chromatin structure together ensure a stable equilibrium between retroelements and their host. Hypomethylation and expression in developing germ cells opens a "window of opportunity" for retrotransposition and recombination that contribute to human evolution, but also inherited disease. In somatic cells, the presence of retroelements may be exploited to organize the genome into active and inactive regions, to separate domains and functional regions within one chromatin domain, to suppress transcriptional noise, and to regulate transcript stability. Retroelements, particularly ALUs, may also fulfill physiological roles during responses to stress and infections. Reactivation and hypomethylation of LINEs and HERVs may be important in the pathophysiology of cancer and various autoimmune diseases, contributing to chromosomal instability and chronically aberrant immune responses. The emerging insights into the pathophysiological importance of endogenous retroelements accentuate the gaps in our knowledge of how these elements are controlled in normal developing and mature cells.

Aging in heterozygous Dnmt1-deficient mice: effects on survival, the DNA methylation genes, and the development of amyloidosis

We previously reported that heterozygous DNA methyltransferase 1-deficient (Dnmt1(+/-)) mice maintain T-cell immune function and DNA methylation levels with aging, whereas controls develop autoimmunity, immune senescence, and DNA hypomethylation. We therefore compared survival, cause of death, and T-cell DNA methylation gene expression during aging in Dnmt1(+/-) mice and controls. No difference in longevity was observed, but greater numbers of Dnmt1(+/-) mice developed jejunal apolipoprotein AII amyloidosis. Both groups showed decreased Dnmt1 expression with aging. However, expression of the de novo methyltransferases Dnmt3a and Dnmt3b increased with aging in stimulated T cells from control mice. MeCP2, a methylcytosine binding protein that participates in maintenance DNA methylation, increased with age in Dnmt1(+/-) mice, suggesting a mechanism for the sustained DNA methylation levels. This model thus provides potential mechanisms for DNA methylation changes of aging, and suggests that changes in DNA methylation may contribute to some forms of amyloidosis that develop with aging.

Epigenetics and human disease: translating basic biology into clinical applications

Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an "extra" layer of transcriptional control that regulates how genes are expressed. These mechanisms are critical components in the normal development and growth of cells. Epigenetic abnormalities have been found to be causative factors in cancer, genetic disorders and pediatric syndromes as well as contributing factors in autoimmune diseases and aging. In this review, we examine the basic principles of epigenetic mechanisms and their contribution to human health as well as the clinical consequences of epigenetic errors. In addition, we address the use of epigenetic pathways in new approaches to diagnosis and targeted treatments across the clinical spectrum.

STAT4 expression in human T cells is regulated by DNA methylation but not by promoter polymorphism

STAT4, which plays a pivotal role in Th1 immune responses, enhances IFN-gamma transcription in response to the interaction of IL-12 with the IL-12R. Mice deficient in STAT4 lack IL-12-induced IFN-gamma production and Th1 differentiation and display a predominantly Th2 phenotype. Although these findings indicate that STAT4 expression levels are important for the development of cytokine-producing Th1 cells, the transcriptional and posttranscriptional mechanisms regulating STAT4 expression are unknown. We sought to identify and characterize the transcriptional regulatory elements in the promoter region of the human STAT4 gene. We found that disruption of multiple transcriptional regions covering the CREB, OCT1, and SP1 motifs significantly reduced STAT4 promoter activity. However, genomic DNA isolated from 91 patients with asthma or rheumatoid arthritis showed no evidence of mutations in the defined STAT4 essential promoter region. The 5' flanking region of the promoter was found to contain a -149A/G change in approximately 20-35% of patients, but this polymorphism had no effect on promoter activity. Interestingly, STAT4 expression was drastically increased in human T cells following treatment with a DNA methyltransferase inhibitor, and truncation of methylation sites in the proximal regulatory elements of the STAT4 promoter markedly enhanced transcriptional activity. Thus, our findings provide molecular insight into STAT4 expression and suggest that, in human T cells, STAT4 expressional regulation is associated with DNA hypermethylation, but not promoter polymorphisms.

Targeting Toll-like receptor signaling in plasmacytoid dendritic cells and autoreactive B cells as a therapy for lupus

This review focuses on the role of Toll-like receptors (TLRs) in lupus and on possibilities to treat lupus using TLR modulating inhibitory oligodeoxynucleotides (INH-ODNs). TLRs bridge innate and adaptive immune responses and may play an important role in the pathogenesis of systemic lupus erythematosus. Of particular interest are TLR3, -7, -8, and -9, which are localized intracellularly. These TLRs recognize single-stranded or double-stranded RNA or hypomethylated CpG-DNA. Exposure to higher order CpG-DNA ligands or to immune complexed self-RNA triggers activation of autoreactive B cells and plasmacytoid dendritic cells. INH-ODNs were recently developed that block all downstream signaling events in TLR9-responsive cells. Some of these INH-ODNs can also target TLR7 signaling pathways. Based on their preferential cell reactivity, we classify INH-ODNs into class B and class R. Class B ('broadly reactive') INH-ODNs target a broad range of TLR-expressing cells. Class R ('restricted') INH-ODNs easily form DNA duplexes or higher order structures, and are preferentially recognized by autoreactive B cells and plasmacytoid dendritic cells, rather than by non-DNA specific follicular B cells. Both classes of INH-ODNs can block animal lupus. Hence, therapeutic application of these novel INH-ODNs in human lupus, particularly class R INH-ODNs, may result in more selective and disease-specific immunosuppression.

Reducing the immunostimulatory activity of CpG-containing plasmid DNA vectors for non-viral gene therapy

The mammalian innate immune system has the ability to recognise and direct a response against incoming foreign DNA. The primary signal that triggers this response is unmethylated CpG motifs present in the DNA sequence of various disease-causing pathogens. These motifs are rare in vertebrate DNA, but abundant in bacterial and some viral DNAs. Because gene therapy generally involves the delivery of DNA from either plasmids of bacterial origin or recombinant viruses, an acute inflammatory response of variable severity inevitably results. The response is most serious for non-viral gene delivery vectors composed of cationic lipid-DNA complexes, producing adverse effects at lower doses and lethality at higher doses of complex. This review examines the role of immunostimulatory CpG motifs in the acute inflammatory response to non-viral gene therapy vectors. Strategies to neutralise or eliminate CpG motifs within plasmid DNA vectors, and the existing limitations of CpG reduction on improving the safety profile of non-viral vectors, will be discussed.

Immune cells and cytokines in systemic lupus erythematosus: an update

PURPOSE OF REVIEW

Systemic lupus erythematosus is characterized by overactive B cells that differentiate into autoantibody-forming cells, aberrant T cell function that provides help to B cells, and the production of pro-inflammatory cytokines. This article reviews recent studies unraveling the complex interplay between cytokines and lymphocytes in systemic lupus erythematosus.

RECENT FINDINGS

In systemic lupus erythematosus, T cells are characterized by heightened calcium responses early after activation of their surface receptor. Alterations of the T cell receptor/CD3 complex, namely the substitution of the FcepsilsonRgamma for the T cell receptor zeta chain, and increased mitochondrial potentials can account for this 'overexcitable' phenotype. At the same time, this heightened calcium signal leads to a block of the transcription of the IL-2 gene, a pivotal cytokine for the immune response. The end result is increased spontaneous apoptosis and decreased activation-induced cell death of T cells in systemic lupus erythematosus that in turn leads to enhanced help to B cells and potentially decreased regulatory function. The B cells, on the other hand, are shown to be directly activated by immune complexes by way of Toll-like receptors independently of T cells. Finally, recent studies have tried to elucidate the role of cytokines such as interferon-alpha in systemic lupus erythematosus and, following the paradigm of rheumatoid arthritis, to establish targets for treatment.

SUMMARY

The increased apoptosis and aberrant T cell activation coupled with nonspecific activation of B cells lead to the production of auto-antigen: auto-antibody complexes that are the hallmark of systemic lupus erythematosus. Future treatments aiming at correcting the intracellular and intercellular signaling abnormalities may prove effective in restoring immune tolerance in systemic lupus erythematosus.

A Toll for lupus

Toll-like receptor (TLR)-9 recognizes CpG motifs in microbial DNA. TLR9 signalling stimulates innate antimicrobial immunity and modulates adaptive immune responses including autoimmunity against chromatin, e.g., in systemic lupus erythematosus (SLE). This review summarizes the available data for a role of TLR9 signalling in lupus and discusses the following questions that arise from these observations: 1) Is CpG-DNA/TLR9 interaction involved in infection-induced disease activity of lupus? 2) What are the risks of CpG motifs in vaccine adjuvants for lupus patients? 3) Is TLR9 signalling involved in the pathogenesis of lupus by recognizing self DNA?

Causes and consequences of DNA hypomethylation in human cancer

While specific genes are hypermethylated in the genome of cancer cells, overall methylcytosine content is often decreased as a consequence of hypomethylation affecting many repetitive sequences. Hypomethylation is also observed at a number of single-copy genes. While global hypomethylation is highly prevalent across all cancer types, it often displays considerable specificity with regard to tumor type, tumor stage, and sequences affected. Following an overview of hypomethylation alterations in various cancers, this review focuses on 3 hypotheses. First, hypomethylation at a single-copy gene may occur as a 2-step process, in which selection for gene function follows upon random hypo methylation. In this fashion, hypomethylation facilitates the adaptation of cancer cells to the ever-changing tumor tissue microenvironment, particularly during metastasis. Second, the development of global hypomethylation is intimately linked to chromatin restructuring and nuclear disorganization in cancer cells, reflected in a large number of changes in histone-modifying enzymes and other chromatin regulators. Third, DNA hypomethylation may occur at least partly as a consequence of cell cycle deregulation disturbing the coordination between DNA replication and activity of DNA methyltransferases. Finally, because of their relation to tumor progression and metastasis, DNA hypomethylation markers may be particularly useful to classify cancer and predict their clinical course.

DNA methylation and human disease

DNA methylation is a crucial epigenetic modification of the genome that is involved in regulating many cellular processes. These include embryonic development, transcription, chromatin structure, X chromosome inactivation, genomic imprinting and chromosome stability. Consistent with these important roles, a growing number of human diseases have been found to be associated with aberrant DNA methylation. The study of these diseases has provided new and fundamental insights into the roles that DNA methylation and other epigenetic modifications have in development and normal cellular homeostasis.

G-rich DNA suppresses systemic lupus

Whereas the role of immune complexes in mediating renal cell and immune cell activation is well established, the contribution of sequence-specific immunomodulatory actions of the chromatin part remains unclear. Toll-like receptor-9 (TLR-9) mediates immunostimulatory effects of unmethylated microbial CpG-DNA. It was hypothesized that hypomethylated CpG-DNA in vertebrates may have similar effects and may contribute to disease progression in lupus nephritis. A synthetic G-rich DNA, known to block CpG-DNA effects, was used in this study. In macrophages, G-rich DNA suppressed CpG-DNA-but not LPS-induced production of CCL5 in a dose-dependent manner. Injections of G-rich DNA suppressed lymphoproliferation induced by CpG-DNA injections in mice. In MRL(lpr/lpr) mice with lupus nephritis, labeled G-rich DNA co-localized to glomerular immune complexes and was taken up into endosomes of TLR-9-positive infiltrating macrophages. Eleven-week-old MRL(lpr/lpr) mice that received injections of either saline or G-rich DNA for 13 wk revealed decreased lymphoproliferation and less autoimmune tissue injury in lungs and kidneys as compared with saline-treated controls. G-rich DNA reduced the levels of serum dsDNA-specific IgG2a as well as the renal immune complex deposits. This was consistent with the blocking effect of G-rich DNA on CpG-DNA-induced proliferation of B cells that were isolated from MRL(lpr/lpr) mice. As oligodeoxyribonucleotide 2114-treated MRL(lpr/lpr) mice were not exposed to exogenous CpG-DNA, these effects should relate to a blockade of CpG motifs in endogenous DNA. It is concluded that adjuvant activity of self-DNA contributes to the pathogenesis of lupus nephritis. Modulating the CpG-DNA-TLR-9 pathway may offer new opportunities for the understanding and treatment of lupus.