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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Autoimmun. Author manuscript; available in PMC May 1, 2013.
Published in final edited form as:
PMCID: PMC3313010

Sex-specific differences in the relationship between genetic susceptibility, T cell DNA demethylation and lupus flare severity

Amr H. Sawalha, MD,1,3 Lu Wang, PhD,4 Ajay Nadig, BS,3 Emily C. Somers, PhD, ScM,4,5 W. Joseph McCune, MD,5 the Michigan Lupus Cohort,5 Travis Hughes, BS,3 Joan T. Merrill, MD,6 R. Hal Scofield, MD,1,3 Faith Strickland, PhD,5 and Bruce Richardson, MD, PhD5,7


Lupus is less common in men than women, and the reason is incompletely understood. Current evidence indicates that lupus flares when genetically predisposed individuals encounter environmental agents that trigger the disease, and that the environmental contribution is mediated at least in part by T cell DNA demethylation. We hypothesized that lupus disease activity is directly related to total genetic risk and inversely related to T cell DNA methylation levels in each patient. Since women are predisposed to lupus in part because of their second X chromosome, we also hypothesized that men would require a greater genetic risk, a greater degree of autosomal T cell DNA demethylation, or both, to achieve a lupus flare equal in severity to women. Genetic risk was determined by genotyping men and women with lupus across 32 confirmed lupus susceptibility loci. The methylation status of two T cell autosomal genes known to demethylate in proportion to disease activity, KIR2DL4 (KIR) and PRF1, was measured by bisulfite sequencing. Lupus disease activity was determined by the SLEDAI. Interactions between genetic score, T cell DNA demethylation, and the SLEDAI score were compared between the men and women by regression analysis. Combining the degree of DNA demethylation with the genetic risk score for each patient demonstrated that the (genetic risk)/(DNA methylation) ratio increased directly with disease activity in both men and women with lupus. Importantly, men required a greater (genetic risk)/(DNA methylation) ratio to achieve a SLEDAI score equivalent to women (p=0.010 for KIR and p=0.0054 for PRF1). This difference was not explained by a difference in the genetic risk or T cell DNA demethylation alone, suggesting a genetic-epigenetic interaction. These results suggest that genetic risk and T cell DNA demethylation interact in lupus patients to influence the severity of lupus flares, and that men require a higher genetic risk and/or greater degree of T cell DNA demethylation to achieve a lupus flare equal in severity to women.

Keywords: Genetic risk, epigenetics, DNA methylation, lupus, genetic-epigenetic interaction, sex-disparity

1. Introduction

Systemic lupus erythematosus (SLE or lupus) is a chronic, relapsing autoimmune disease. While the causes of lupus are incompletely understood, persuasive evidence indicates that genetic and environmental factors are required for the disease to flare. The genetic requirement is evidenced by an increased concordance of lupus in identical twins [1], as well as in families with lupus relative to the general population [2], and by the validation of multiple risk loci that predispose to lupus [3]. More recent studies indicate that multiple predisposing genes are required to develop lupus, each contributing a distinct relative risk, and that the number of genes varies between lupus patients to influence the age of disease onset[4], as well as its clinical manifestations [5].

However, genetic predisposition alone is not sufficient to cause lupus. Indeed, there is strong evidence that epigenetic mechanisms play an important role in the pathogenesis of lupus [6-7]. The relapsing course, incomplete concordance in identical twins [1],and evidence that exogenous agents like UV light, procainamide and hydralazine can activate lupus [8], indicate that environmental exposures are required to trigger lupus flares in people with sufficient genetic risk. Evidence that UV light, procainamide and hydralazine are DNA methylation inhibitors, that these agents cause demethylation and aberrant gene overexpression in T cells resulting in autoreactivity and altered effector functions, and that T cells treated with these and other DNA demethylating agents are sufficient to cause lupus in animal models, suggests that the environment can contribute to lupus flares through demethylation of DNA in T lymphocytes and perhaps other cells as well[8]. A role for DNA demethylation in causing lupus flares is also supported by evidence that the same genes demethylate and are overexpressed in T cells from lupus patients as in T cells treated with DNA methylation inhibitors, and that these genes demethylate in direct relation to disease activity as measured by the SLEDAI [8]. Further, in identical twins discordant for lupus, the twin with lower leukocyte DNA methylation levels has the disease [9].Together, these reports suggest that genes and environmentally induced DNA demethylation each provide a distinct but essential contribution to the development and severity of human lupus flares.

Sex also contributes to lupus. Lupus predominantly afflicts women, with a female:male ratio ranging from 4.3 to 13.6 [10]. Estrogen and other hormones might contribute to this female predilection [11-12]. A hormonal influence is evidenced by disease exacerbations during pregnancy [13], increased disease severity in women with prolactinomas [14], and mildly increased flares in women receiving hormonal supplementation [15]. Further, treatment with DHEA, a weak androgen, improves overall quality-of-life and steroid requirements in mild to moderate lupus [16]. However, having 2 X chromosomes also predisposes to lupus. Men with Klinefelter’s syndrome (47, XXY) develop lupus at approximately the same rate as women, indicating an X-linked gene-dosing effect in the female predominance of lupus [17]. Evidence that the X-linked gene CD40LG is overexpressed on T cells from women but not men with active lupus because the gene on the silenced X demethylates, also suggests that women, and men with Klinefelter’s Syndrome, may be predisposed to lupus because their second X can demethylate and become transcriptionally active in response to the environmental triggers [18].

Why men with one X chromosome develop lupus is less clear. Family-based studies indicating that women who have a lupus-afflicted male relative have a more severe disease than women with no affected male relative [19], and that lupus may be more severe in men [20-21], suggest that an increased total genetic risk may contribute to the increased severity of male lupus. However, the disease flares and remits in men as it does in women, indicating an environmental contribution as well.

Since both the degree of T cell DNA demethylation and the total genetic risk contribute to human lupus, we hypothesized that the degree of lupus disease activity in any given patient is directly related to their total genetic risk, and inversely related to their T cell DNA methylation levels. We also hypothesized that women are predisposed to lupus because of hormones and their second, methylated X chromosome, and that men with only one X chromosome require a greater total genetic risk, a greater degree of T cell DNA demethylation or both to achieve a lupus flare equal in severity to women. To test this hypothesis we genotyped men and women with inactive and active lupus for 32 lupus risk loci and calculated the total genetic risk using an additive model. We also measured the DNA methylation of two autosomal genes in CD4+ T cells from the same patients. We then evaluated the associations between genetic risk, DNA methylation levels and sex, controlling for the SLEDAI score.

2. Material and Methods

2.1 Patients and study design

We included 42 and 31 European-American women and men with lupus in this study. All patients were recruited from the rheumatology clinics at the University of Michigan and the Oklahoma Medical Research Foundation (OMRF), and fulfilled the American College of Rheumatology classification criteria for SLE [22-23]. There was no significant difference in age between the two groups (46.8+15.2 years for men and 41.6+12.8 years for women, p=0.12). The study was approved by the Institutional Review Boards at the University of Oklahoma Health Sciences Center, OMRF, and the University of Michigan, and all patients signed an approved informed consent prior to participating. Disease activity was determined for all patients at the time of sample collection using the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI), and scores ranged from 0-14 with a mean of 4. Patients with neurologic involvement were excluded as these criteria are weighted heavily by the SLEDAI; for example, a cerebrovascular event due to thrombosis receives a score of 8 while thrombosis in a leg is not scored. Patients receiving methotrexate were excluded because of possible effects on DNA methylation [24], and those receiving cyclophosphamide within the previous month were excluded because of effects on cell surface protein expression [25]. We have previously reported that other medications commonly used to treat lupus, including nonsteroidal anti-inflammatory medications, corticosteroids, anti-malarials and anti-metabolites like azathioprine do not affect DNA methylation [26-27].

Blood samples were collected and peripheral blood mononuclear cells separated using density gradient centrifugation (Ficoll-Paque PLUS, GE Healthcare Life Sciences). CD4+ T cells were separated with magnetic beads and direct labeling using the CD4+ T Cell Isolation Kit (Miltenyi Biosystems), and DNA was extracted from CD4+ T cells for DNA methylation studies using the Qiagen DNEasy kit. Non-CD4+ T cell DNA was similarly extracted for genotyping. The presence of only one X chromosome in the male lupus patients was confirmed by karyotyping, fluorescence in situ hybridization, or a quantitative PCR-based method [28], and serum prolactin levels were measured in the men by the University of Michigan clinical laboratories.

2.2 Genotyping and DNA methylation

Lupus patients were genotyped across 32 previously confirmed genetic susceptibility loci using TaqMan allelic discrimination assays(Applied Biosystems). Methylation of the KIR2DL4 (KIR) promoter (-250 to +78, 10 CG pairs) and the PRF1promoter (-800 to -600, 6 CG pairs) was measured by Pyrosequencing of bisulfite treated DNA as previously described [27, 29].

2.3 Statistical analysis

Regression models and the corresponding Wald test were used to evaluate the difference between genetic score, DNA methylation and (genetic score)/(DNA methylation) in men and women with lupus while controlling for disease activity as measured by SLEDAI. P values of <0.05 were considered statistically significant. Non-significant interaction terms were dropped from the final models. All statistical analysis was performed using SAS v9.2 and R 2.13.0.

3. Results

We studied 31 men and 42 women with a range of SLEDAI scores. All were genotyped for the 32 known and confirmed lupus susceptibility loci listed in Table 1. We compared total genetic risk in the men and women using the formula: genetic risk=Σ132(nx.ORx), where n is the number of risk alleles (0, 1 or 2) and OR is the allelic odds ratio for each genetic risk locus examined. In these calculations men with the X chromosome-encoded MECP2 risk allele were considered to be functionally homozygous, so the relative risk was multiplied by 2, making them equivalent to women with two risk alleles in this locus. Men had a slightly higher total genetic risk relative to women (36.36 ± 1.03 versus 34.14 ± 0.78) but this difference is only marginally significant in our sample after controlling for SLEDAI (p=0.053).

Table 1
List of confirmed lupus susceptibility loci and tag SNPs genotyped in this study.

However, men with lupus, like women with lupus, have flares and remissions induced by environmental exposures. Current evidence suggests that the environment triggers lupus flares by inhibiting CD4+ T cell DNA methylation, causing aberrant overexpression of genes that convert normal antigen specific “helper” T cells into autoreactive, cytotoxic, pro-inflammatory cells capable of causing lupus-like autoimmunity in animal models, and that the degree of T cell demethylation correlates with increasing severity of lupus flares [8]. We therefore compared the degree of DNA methylation in the PRF1 and KIR2DL4 (KIR) promoters, previously reported to demethylate in proportion to lupus disease activity as measured by the SLEDAI [27, 29], in the same patients. Figure 1A compares the relationship between KIR promoter methylation and the SLEDAI in the men and women with lupus. The men tend to have slightly lower methylation levels than the women, but the difference is not statistically significant (P= 0.16). Figure 1B similarly compares the relationship between PRF1 methylation and the SLEDAI in the same men and women. Again there is a trend for the men to have lower methylation levels, but the difference is not significant (P= 0.20).

Figure 1
DNA methylation levels (%) in the promoter of KIR (A) and PRF1 (B) in CD4+ T cells from the lupus men and women included in this study. There was no difference between men and women after controlling for SLEDAI (P= 0.16, P= 0.20, respectively).

We then asked if the degree of DNA demethylation interacts with the total genetic risk to determine the severity of lupus flares in men and women with lupus. Since we hypothesize that overall lupus severity would correlate with increased total genetic risk, and the degree of T cell DNA demethylation correlates with the severity of individual flares as determined by the SLEDAI [27, 29], we compared the ratio of (genetic risk)/(DNA methylation) in each of the men and women with lupus at the same level of SLEDAI. Figure 2A shows this relationship using KIR methylation. The mean (genetic risk)/(KIR methylation) ratio overall is 0.0515 lower for women than men, after controlling for SLEDAI, with a p-value of 0.010. Figure 2B similarly shows the effect of PRF1 methylation. The mean (genetic risk)/(PRF1 methylation) overall is 0.0757 lower for women than men, after controlling for SLEDAI, with a p-value of 0.0054. Thus, for both genes, combining the degree of DNA demethylation with the total genetic risk in each subject demonstrates that men require a greater degree of DNA demethylation and/or a greater total genetic risk to achieve a lupus flare equal in severity of women, and the difference is statistically significant in contrast to the effect of the genetic score or DNA methylation level alone in our sample (Table 2). The difference between men and women also widens with increased SLEDAI scores (Figure 2), and is significant in patients with active disease (SLEDAI≥4), but not when the disease is inactive (SLEDAI<4) (Figure 3). These results thus indicate that genetic risk and T cell demethylation interactions correlate strongly with disease severity. These results also support the hypothesis that men require a greater genetic/epigenetic interaction to achieve a flare equal in severity to women.

Figure 2
Ratios of (genetic risk)/(KIR methylation) (A) and (genetic risk)/(PRF1 methylation) (B) versus SLEDAI in men and women with lupus. Linear regression analysis showed that the mean (genetic risk)/(KIR methylation) and (genetic risk)/(PRF1 methylation) ...
Figure 3
(Genetic risk)/(DNA methylation) ratios using KIR methylation (A) and PRF1 methylation (B) in men and women with inactive disease (SLEDAI<4) and active disease (SLEDAI≥4).
Table 2
The linear regression model used to evaluate the association of (genetic risk)/(KIR methylation) ratio, (genetic risk)/(PRF1 methylation) ratio, genetic risk alone, KIR methylation alone, and PRF1 methylation alone, with sex and SLEDAI scores.

4. Discussion

The reason that women develop lupus more often than men is incompletely understood. Estrogen might contribute to the female predilection, but prepubertal girls develop lupus at a higher rate than age matched boys [30], and even after menopause women still develop lupus more often than men [31].Therefore, estrogen alone is not responsible for the sexual dimorphism in lupus. Further, most men with lupus have normal sex hormone levels [32]. The possibility that the male Y chromosome is protective has been considered [33], but sequencing of the relatively gene-poor Y chromosome has provided no evidence for immune genes [34-35].While a translocation of TLR7 to the Y chromosome causes a male-predominant form of lupus in BXSB mice [36], similar translocations have not been reported in human lupus. In addition, it has been reported that elevated prolactin levels may contribute to the development of lupus in a small subset of men [37]. In this study we measured prolactin levels in 26 of the 31 men and all were normal (data not shown), suggesting a minimal if any effect of prolactin on disease activity in this cohort. Finally, data from male lupus patients with Klinefelter’s syndrome (47, XXY) suggest that having more than one X chromosome predisposes to lupus [17]. The presence of an extra X chromosome was excluded in all men included in our study.

We have previously found that men with lupus are significantly more likely to carry the lupus-risk alleles in the HLA region and in IRF5 compared to women, suggesting a role for sex-gene interaction in the pathogenesis of lupus [38]. Similar finding have been previously reported for lupus-associated polymorphisms in the SPP1 and TLR7 genetic loci [39-40]. However, the currently known genetic susceptibility loci for lupus do not entirely explain the heritability of this disease. The reason for this “missing heritability” is currently obscure, and may be unmasked by studies directed into epigenetics, discovery of rare genetic variants, and gene-gene or gene-environment interaction.

We modeled the associations between genetic risk, DNA methylation levels and SLEDAI, controlling for sex, and tested possible interactions between genetic risk, DNA methylation, and sex through statistical modeling. We found that men with lupus overall have a higher (genetic risk)/(DNA methylation) ratio compared to women with a similar SLEDAI score. This supports an interaction between the genetic risk and CD4+ T cell DNA methylation in lupus, and suggests that this interaction may contribute to the sex bias in lupus. Thus genetic-epigenetic interactions might play a role in explaining the sex discrepancy in this disease. We also found that while overall DNA methylation is not significantly different between men and women with lupus, a ratio between genetic risk and DNA methylation is much more predictive of sex than would be explained by the difference in genetic score alone.

It should be noted that DNA methylation in our study was quatified using two independent previously known methylation-sensitive genes in CD4+ T cells, and genetic risk score was determined using an additive model. Recent work suggests wide-spread DNA methylation changes in lupus CD4+ T cells [41], and evidence for gene-gene epistatic interaction in lupus is emerging [42-43]. Therefore, a more comprehensive study to examine genetic-epigenetic interaction in lupus using global DNA methylation changes, and exploring gene-gene interactions in calculating genetic risk would be feasible and of great interest in the future. Genetic-epigenetic interaction in lupus has been also suggested by the finding of lupus susceptibility alleles in the genetic locus containing methyl-CpG-binding protein 2 (MECP2) [44]. The MECP2-encoded protein plays a crucial role in DNA methylation-regulated gene expression [45]. Taken together, we propose that genetic-epigenetic interaction studies should be considered in exploring the “missing heritability” in lupus.

A potential role for epigenetics in sex disparity in lupus and other autoimmune diseases is intriguing. In a mouse model for lupus with an inducible T cell DNA methylation defect, we demonstrated that demethylation resulting in activation of gene expression from the two X chromosomes is necessary for the development of autoimmunity [46]. Recent findings suggest that global genomic DNA methylation in peripheral blood is significantly different by sex and ethnicity [47]. Healthy normal women had lower DNA methylation compared to men, and African-Americans have lower DNA methylation compared to European-Americans [47]. DNA methylation defects are associated with the development of lupus, therefore, if validated in specific cell subsets, these findings might shed more light on why lupus is more common in women and perhaps also help explain the higher frequency of lupus in African-Americans.

5. Conclusions

Our findings provide evidence of a genetic/epigenetic interaction in the pathogenesis of lupus, and demonstrate that men require a higher genetic score and lower T cell DNA methylation to develop a lupus flare of an equal severity to women. Future work should focus on exploring the mechanisms behind this interaction. Genetic-epigenetic modeling might also help to better understand the pathogenesis of other autoimmune or chronic diseases with genetic and epigenetic etiologies.


  • Genetic/epigenetic interaction influences disease severity in lupus patients
  • Higher genetic risk score to DNA methylation ratio correlated with increased severity of lupus flares
  • Men with lupus require a higher genetic risk to DNA methylation ratio to achieve a lupus flare of equal severity to women
  • Understanding the mechanisms behind genetic/epigenetic interaction might help to explain the missing heritability and sex disparity in lupus.


This work was supported by a grant from the Lupus Foundation of America made possible through support from the Wallace H. Coulter Foundation, NIH grants AR42525, ES015214, UL1RR024986, and a Merit grant from the Department of Veterans Affairs and a grant from the Lupus Research Institute.


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Financial conflict of interest: None of the authors has any financial conflict of interest to report.


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