Leukocyte-specific DNA methylation biomarkers and their implication for pathological epigenetic analysis

Abstract

Background Distinct cell types can be identified by their DNA methylation patterns. Much research over the last decade has focused on DNA methylation changes in cancer or the use of cell-free circulating DNA in plasma to identify damaged tissue in cases of trauma or organ transplantation. However, there has been little research into the differential methylation patterns between leukocytes and other tissues and how they can be used as a detection tool for immune activity in a range of contexts. Results We have identified several loci that are fully methylated in leukocytes but virtually devoid of methylation in a range of other mesoderm-, ectoderm-, and endoderm-derived tissues. We validated these biomarkers using amplicon-bisulphite-sequencing on saliva and in vitro mixing of peripheral blood mononuclear cells and intestinal organoid cells combined at a defined range of ratios. Interestingly, these methylation biomarkers have previously been identified as altered in various inflammatory diseases, including Alzheimer disease, inflammatory bowel disease, and psoriasis. We hypothesise this is due to leukocyte infiltration rather than being a feature of the diseased cells themselves. Moreover, we show a positive linear relationship between infiltrating leukocytes and DNA methylation levels at the HOXA3 locus in six cancer types, indicative of further immune cell infiltration. Conclusions Our data emphasise the importance of considering cellular composition when undertaking DNA methylation analysis and demonstrate the feasibility of developing new diagnostic tests to detect inflammation and immune cell infiltration.

Methylomic, Proteomic, and Metabolomic Correlates of Traffic-Related Air Pollution in the Context of Cardiorespiratory Health: A Systematic Review, Pathway Analysis, and Network Analysis

“…Peripheral blood mononuclear cells (PBMCs), however, are a specific subset of leukocytes. The choice to utilize PBMCs or leukocytes in methylomic research depends on research goals and the cell type of interest; however, both are sufficient [ 122 , 123 ]. For proteomic papers, serum and plasma were the most common biological matrices (34 and 21 papers, respectively).…”