Distinct cell types can be identified by their DNA methylation patterns. Much research over the last decade has focused on DNA methylation changes that occur in cancer or biomarkers that utilise cell-free circulating DNA. However, there has been little research into the differential methylation patterns between leukocytes and other tissues as a detection tool for inflammation in various contexts.
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. Moreover, using TCGA datasets we show a strong, positive linear relationship between infiltrating leukocytes and DNA methylation levels at the HOXA3 locus in six cancer types. We hypothesise this is due to leukocyte infiltration rather than a feature of the diseased cells themselves.
Our data emphasise the importance of considering cellular composition when undertaking DNA methylation analysis and demonstrates the feasibility of developing new diagnostic tests to detect inflammation and immune cell infiltration in both cancerous and non-cancerous diseases.