GSE125734
DNA methylation profiles reveal possible role of highly methylated TLR signaling on Fasciola gigantica excretory/secretory products (FgESPs) modulation of buffalo DCs [MeDIP-seq]
Purpose: To investigate whether FgESP affects the (hydroxyl)methylation level of DCs Methods: we have profiled the DNA methylome  by using methylated DNA immunoprecipitation sequencing (MeDIP-Seq) in the current study Results: DNA methylation and hydroxymethylation profiles revealed significant changes in the 5-methylcytosine (5-mC) levels in the promoter regions of 5432 genes and significant changes in the 5-hydroxymethylcytosine (5hmC) levels in 360 genes when DCs were treated with FgESPs. These differentially expressed genes were highly enriched in pathways associated with immune function. The characterizations of DCs were assessed using scanning and transmission electron microscopy (SEM/TEM) and quantitative reverse transcriptional PCR (qRT-PCR). Our results demonstrated that FgESPs could markedly suppress DC maturation by down-regulating the expression of membrane phenotypic markers, such as CD1a, MHC II. The functional enrichment analysis found hypermethylation of genes, especially in the NF-?B signaling pathway, and transcription was unchanged or low for the TLR2, TLR4, and IL-12 genes in DCs. Thus, we suggest a possible mechanism of FgESPs in suppressing TLR signaling pathway-dependent DC maturation and function. Moreover, there were 111 genes demonstrating changes in both 5-mC and 5-hmC levels, and 12 of which were enriched and interconnected in pathways associated with the inflammatory response. It is interesting to note that certain cancer-related pathways were indicated in our analysis, such as 'pathways in cancer'. Conclusion: For the first time, our study provides a genome-wide mapping of DNA (hydroxyl)methylation for DCs that interacted with FgESPs. Our study also suggests a possible immunoregulatory mechanism of FgESPs that acts by increasing DNA methylation levels on genes and pathways associated with TLR signaling. Overall design: In the current study, we have profiled the DNA methylome and hydroxymethylome by using high-throughput sequencing. Total DNA was extracted from buffalo PBMC DCs that were treated with FgESP, which was followed byFgESPs, and then performed (hydroxy)methylated DNA immunoprecipitation sequencing [(h)MeDIP-Seq].