![]() This association was not detected when the effect of HLA-DQB1*06:02 was considered, suggesting that the hypomethylation was possibly derived from HLA-DQB1*06:02. ![]() We then performed an association analysis, and found that several CpG sites in the HLA class II region of the patients were significantly hypomethylated in CD4 + and CD8 + T cells. We confirmed that 90.3% of the probes after general filtering in the HLA region do not include frequent SNPs, and are thus suitable for analysis, particularly in Japanese subjects. The criteria were based on a previous study reporting that the presence of frequent SNPs, especially on the 3′ side of the probe, makes the probe unreliable. ![]() As the large number of SNPs in the HLA region might interfere with the affinity of the array probes, we conducted a comprehensive assessment of the reliability of each probe. We analyzed array-based DNA methylation and gene expression data for the HLA region in CD4 + and CD8 + T cells that were separated from the peripheral blood mononuclear cells of Japanese subjects (NT1, N = 42 control, N = 42). Although NT1 showed a strong association with human leukocyte antigen ( HLA) -DQB1*06:02, the responsible antigens remain unidentified. Narcolepsy type 1 (NT1) is caused by a loss of hypothalamic orexin-producing cells, and autoreactive CD4 + and CD8 + T cells have been suggested to play a role in the autoimmune mechanism.
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