Genome-wide analysis of dna methylation and role of methylation status at line-1 and alu sequences in chronic plaque-type psoriasis

Abstract

Long interspersed element-1 (LINE-1 or L1) and short interspersed elements (Alu) retrotransposons are identified to influence human genome in many fashions such as modifications in gene expression. Alterations in methylation of LINE-1 and Alu have been demonstrated to associate with many diseases, particularly in malignancies and autoimmune diseases. Moreover, level and pattern of LINE-1 hypomethylation were related to high cancer risk, prognosis and aggressiveness of many several cancers. But there is no study in Psoriasis. To evaluate DNA methylated status of repetitive sequence in psoriasis. We determined DNA methylation level and pattern of LINE-1 and Alu in keratinocyte and various hematopoietic cells from psoriasis (n=29) compared to normal controls (n=33) and squamous cell carcinoma (SCC) (n=8), by the improved combined bisulfite restriction analysis of LINE-1 and Alu (COBRA-LINE-1 and Alu). COBRA-LINE-1 classified LINE-1 loci due to methylation patterns of 2 CpG dinucleotides at 5’UTR into four categories: hypermethylated (mCmC), hypomethylated (uCuC), and 2 forms of partially methylated loci (uCmC and mCuC). The consequences of epigenetic changes of psoriatic skin in intragenic LINE-1 in gene expression were tested on 2 expression microarrays (GSE13355 and GSE14905). We found hypomethylation of LINE-1 but not Alu in keratinocyte from psoriasis (p-value=0.044) (% methylation in psoriasis vs. normal = 41.64 VS. 45.15). The percentage of uCuC (%uCuC) of LINE-1 was significantly higher in keratinocyte from psoriasis than healthy subjects (p-value=0.045) (% methylation in psoriasis vs. normal = 41.11 VS. 37.40). A receiver-operating characteristic (ROC) curve analysis demonstrated the cut-off value >39.67% of %uCuC with sensitivity = 69.23% and specificity = 69.23% for psoriasis. Moreover, %uCmC of LINE-1 was significantly lower in severe psoriasis than mild psoriasis (p-value=0.022) (% methylation in severe vs. mild psoriasis = 9.10 VS. 18.80). ROC curve analyses displayed the possible of %uCmC as biomarker for psoriasis severity with a cut-off value of ≤ 10.87% (sensitivity = 83.33% and specificity = 100.00%). Genome-wide expression array analysis revealed a higher prevalence of down regulation when genes containing LINE-1s than without (p-value=3.84 x 10-27 and p-value=2.14 x 10-21, respectively). Changes in LINE-1 pattern and reduction in level can be observed in psoriatic skin. This change is one of the mechanisms that alter gene expression leading to phenotypic change of psoriatic skin. Consequently, certain classes of LINE-1 methylation patterns, %uCuC and %uCmC may be used as novel biomarker for psoriasis.