Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine

5-Methylcytosine and 5-hydroxymethylcytosine are epigenetic modifications involved in gene regulation and cancer. We present a new, simple, and high-throughput platform for multi-color epigenetic analysis. The novelty of our approach is the ability to multiplex methylation and de-methylation signals in the same assay. We utilize an engineered methyltransferase enzyme that recognizes and labels all unmodified CpG sites with a fluorescent cofactor. In combination with the already established labeling of the de-methylation mark 5-hydroxymethylcytosine via enzymatic glycosylation, we obtained a robust platform for simultaneous epigenetic analysis of these marks. We assessed the global epigenetic levels in multiple samples of colorectal cancer and observed a 3.5-fold reduction in 5hmC levels but no change in DNA methylation levels between sick and healthy individuals. We also measured epigenetic modifications in chronic lymphocytic leukemia and observed a decrease in both modification levels (5-hydroxymethylcytosine: whole blood 30 %; peripheral blood mononuclear cells (PBMCs) 40 %. 5-methylcytosine: whole blood 53 %; PBMCs 48 %). Our findings propose using a simple blood test as a viable method for analysis, simplifying sample handling in diagnostics. Importantly, our results highlight the assay's potential for epigenetic evaluation of clinical samples, benefiting research and patient management. Dual-color global labelling of 5-hydroxymethylcytosine and umCpG by multi-color fluorescent labelling. We apply an engineered methyltransferase enzyme specific for unmodified CpG to incorporate a modified cofactor that binds to a fluorophore by click chemistry. In combination with 5-hydroxymethylcytosine labelling via enzymatic glycosylation, we incorporate spectrally distinct colour for each epigenetic mark, enabling simultaneous quantification in different cancer types.**image

Automated summary

The article presents a new high-throughput platform for multi-color epigenetic analysis, which allows simultaneous detection of methylation and demethylation signals. By utilizing an engineered methyltransferase enzyme and enzymatic glycosylation, the study achieves simultaneous measurement of 5-hydroxymethylcytosine and 5-methylcytosine. The findings demonstrate the potential of using a simple blood test for epigenetic evaluation in clinical samples, benefiting research and patient management.