Correlation Between MRNA Expression And DNA Methylation And RA Activity In PBMC

Rheumatoid arthritis?RA?is a chronic systemic autoimmune disease,which characterized by complex causes and inflammation.Researches showed that the heritability of RA had been estimated to be about 60%.Epigenetic modification,especially DNA methylation,which always happen with the development of the immune cells and differentiation,endogenous and acquired immune response,contribute much to rheumatoid arthritis.Peripheral blood mononuclear cells?PBMC?,including lymphocytes?T cells,B cells and natural killer cells?,monocytes and dendritic cells,play an important role in the immune study.In view of this,we explored the relationship between mRNA and DNA methylation from expression level and geographical position level in peripheral blood mononuclear cells and exploration the biological function of significant genes in analysis in the first part.And we explore the rheumatoid arthritis activity related genes through different expression analysis and Venn diagram based on DAS28 hoping to provide new information for the diagnosis and treatment in the second part.Part OneObjective:To explore the relationship between mRNA and DNA methylation from expression level and geographical position level in PBMC and the biological process influenced by DNA methylation.Methods:We conducted this study in 46 subjects with Agilent LncRNA&mRNA microarray and Illumina 450K.Based on these data,we explored the comprehensive relationship between m RNA and DNA methylation by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus?MeS-eQTL?analysis in PBMCs in 46 unrelated subjects.We also performed an enrichment analysis to discuss biological function of genes under significant methylation regulation both in correlation analyses and eQTL analysis.Results:The distribution of?values?methylation level?is various according to the different gene regions and CpG regions,e.g.,CpG islands have the peak of hypomethylation values,and the farther away from the CpG islands,the less the hypomethylation sites,but the more the hypermethylation sites.Single pair correlation coefficients?rT1?are moderate?-0.63-0.62?in intensity.We found that 19,807methylationsites?6%?were significantly correlated with mRNA expression of 7,968genes?60%??P<0.05?and the negative and positive correlations are nearly equal in quantity.Correlation analysis on each gene?T4?found 60.1%genes presented significant correlation between mRNA and gene-based methylation?P<0.05?and more than 10.0%genes presented very strong correlation(R_T4>0.8).Methylation sites have regulation effects on expression in MeS-eQTL analysis,with more often observation in the region of the transcription start site?TSS?.The genes under significant methylation regulation both in correlation analysis and MeS-eQTL analysis tend to cluster to the categories which are essential for maintaining the basic life activities of cells or the mechanism of some diseases.Conclusions:Gene expression is regulated by DNA methylation and the direction is different.Most methylation sites have regulation effects on expression are in the region of the transcription start site.Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMC.The results increased our understanding on the correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.Part TwoObjective:Analyzing mRNA among different rheumatoid arthritis activity groups based on DAS28 in order to explore rheumatoid arthritis activity related genes and their biological function.Methods:We conducted this study in 28 RA patients and 18 healthy controls with with Agilent LncRNA&mRNA microarray in PBMC.Then,we select pathogenesis related genes among different rheumatoid arthritis activity groups and identify only pathogenesis related genes,only disease activity related genes and pathogenesis and disease activity related genes with Venn diagram and different expression analysis.Then we conduct enrichment analysis and protein-protein interaction analysis.Results:We find 80 only disease activity related genes and 36 pathogenesis related genes.Among them,12 only disease activity related genes,including SOCS3,C12orf44,KIFC1,MRPS18A,GYG1,RAB35,B4GALT5,LRRC41,LILRB4,LILRA5,CR1,PDIA6,show a decline trend and have significant correlations?P<0.05?with DAS28.Gene PPIH is pathogenesis and disease activity related genes,showing a rising trend and having significant correlations?P<0.05?with DAS28.Enrichment analysis find four terms related to methylation and one term related to stress response.Gene HIST1H3D,HIST1H3E,HIST1H3F,HIST1H4F and HIST1H4I were seen in five categories related with methylation and showing experimental,textmining and co-expressional evidence channels.Conclusions:Our study finds 80 only disease activity related genes and 36pathogenesis related genes.We explore rheumatoid arthritis disease activity related genes and their biological functions and their relationship between protein hoping to provide new information for the diagnosis and treatment for rheumatoid arthritis and provide useful clues to the study on other autoimmune diseases.