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Genome-Wide Assessment of Differential DNA Methylation Associated with Autoantibody Production in Systemic Lupus Erythematosus.

Chung SA, Nititham J, Elboudwarej E, Quach HL, Taylor KE, Barcellos LF, Criswell LA - PLoS ONE (2015)

Bottom Line: Overall, associated CpG sites were hypomethylated in autoantibody positive compared to autoantibody negative cases.Differential methylation of CpG sites within the major histocompatibility region was not strongly associated with autoantibody production.In conclusion, hypomethylation of CpG sites within genes from different pathways is associated with anti-dsDNA, anti-SSA, anti-Sm, and anti-RNP production in SLE, and these associations are not explained by genetic variation.

View Article: PubMed Central - PubMed

Affiliation: Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, University of California San Francisco, San Francisco, California, United States of America.

ABSTRACT
Systemic lupus erythematosus (SLE) is characterized by the development of autoantibodies associated with specific clinical manifestations. Previous studies have shown an association between differential DNA methylation and SLE susceptibility, but have not investigated SLE-related autoantibodies. Our goal was to determine whether DNA methylation is associated with production of clinically relevant SLE-related autoantibodies, with an emphasis on the anti-dsDNA autoantibody. In this study, we characterized the methylation status of 467,314 CpG sites in 326 women with SLE. Using a discovery and replication study design, we identified and replicated significant associations between anti-dsDNA autoantibody production and the methylation status of 16 CpG sites (pdiscovery<1.07E-07 and preplication<0.0029) in 11 genes. Associations were further investigated using multivariable regression to adjust for estimated leukocyte cell proportions and population substructure. The adjusted mean DNA methylation difference between anti-dsDNA positive and negative cases ranged from 1.2% to 19%, and the adjusted odds ratio for anti-dsDNA autoantibody production comparing the lowest and highest methylation tertiles ranged from 6.8 to 18.2. Differential methylation for these CpG sites was also associated with anti-SSA, anti-Sm, and anti-RNP autoantibody production. Overall, associated CpG sites were hypomethylated in autoantibody positive compared to autoantibody negative cases. Differential methylation of CpG sites within the major histocompatibility region was not strongly associated with autoantibody production. Genes with differentially methylated CpG sites represent multiple biologic pathways, and have not been associated with autoantibody production in genetic association studies. In conclusion, hypomethylation of CpG sites within genes from different pathways is associated with anti-dsDNA, anti-SSA, anti-Sm, and anti-RNP production in SLE, and these associations are not explained by genetic variation. Thus, studies of epigenetic mechanisms such as DNA methylation represent a complementary method to genetic association studies to identify biologic pathways that may contribute to the clinical heterogeneity of autoimmune diseases.

No MeSH data available.


Related in: MedlinePlus

Autoantibody distribution of the study participants (n = 326).
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pone.0129813.g001: Autoantibody distribution of the study participants (n = 326).

Mentions: The clinical characteristics of the 326 SLE cases examined in this study are presented in Table 1 and Fig 1. To minimize confounding, we studied only women of European descent who had never smoked. All 326 SLE cases were successfully characterized on the HumanMethylation450 BeadChip and data for 467,314 CpG sites were analyzed.


Genome-Wide Assessment of Differential DNA Methylation Associated with Autoantibody Production in Systemic Lupus Erythematosus.

Chung SA, Nititham J, Elboudwarej E, Quach HL, Taylor KE, Barcellos LF, Criswell LA - PLoS ONE (2015)

Autoantibody distribution of the study participants (n = 326).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508022&req=5

pone.0129813.g001: Autoantibody distribution of the study participants (n = 326).
Mentions: The clinical characteristics of the 326 SLE cases examined in this study are presented in Table 1 and Fig 1. To minimize confounding, we studied only women of European descent who had never smoked. All 326 SLE cases were successfully characterized on the HumanMethylation450 BeadChip and data for 467,314 CpG sites were analyzed.

Bottom Line: Overall, associated CpG sites were hypomethylated in autoantibody positive compared to autoantibody negative cases.Differential methylation of CpG sites within the major histocompatibility region was not strongly associated with autoantibody production.In conclusion, hypomethylation of CpG sites within genes from different pathways is associated with anti-dsDNA, anti-SSA, anti-Sm, and anti-RNP production in SLE, and these associations are not explained by genetic variation.

View Article: PubMed Central - PubMed

Affiliation: Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, University of California San Francisco, San Francisco, California, United States of America.

ABSTRACT
Systemic lupus erythematosus (SLE) is characterized by the development of autoantibodies associated with specific clinical manifestations. Previous studies have shown an association between differential DNA methylation and SLE susceptibility, but have not investigated SLE-related autoantibodies. Our goal was to determine whether DNA methylation is associated with production of clinically relevant SLE-related autoantibodies, with an emphasis on the anti-dsDNA autoantibody. In this study, we characterized the methylation status of 467,314 CpG sites in 326 women with SLE. Using a discovery and replication study design, we identified and replicated significant associations between anti-dsDNA autoantibody production and the methylation status of 16 CpG sites (pdiscovery<1.07E-07 and preplication<0.0029) in 11 genes. Associations were further investigated using multivariable regression to adjust for estimated leukocyte cell proportions and population substructure. The adjusted mean DNA methylation difference between anti-dsDNA positive and negative cases ranged from 1.2% to 19%, and the adjusted odds ratio for anti-dsDNA autoantibody production comparing the lowest and highest methylation tertiles ranged from 6.8 to 18.2. Differential methylation for these CpG sites was also associated with anti-SSA, anti-Sm, and anti-RNP autoantibody production. Overall, associated CpG sites were hypomethylated in autoantibody positive compared to autoantibody negative cases. Differential methylation of CpG sites within the major histocompatibility region was not strongly associated with autoantibody production. Genes with differentially methylated CpG sites represent multiple biologic pathways, and have not been associated with autoantibody production in genetic association studies. In conclusion, hypomethylation of CpG sites within genes from different pathways is associated with anti-dsDNA, anti-SSA, anti-Sm, and anti-RNP production in SLE, and these associations are not explained by genetic variation. Thus, studies of epigenetic mechanisms such as DNA methylation represent a complementary method to genetic association studies to identify biologic pathways that may contribute to the clinical heterogeneity of autoimmune diseases.

No MeSH data available.


Related in: MedlinePlus