There is a better way to decipher the epigenetic code of DNA to identify the disease

A new method of sequencing chemical groups linked to the surface of DNA paves the way for better detection of cancer and other diseases in the blood, according to a Perelman School of Medicine study of the 39, University of Pennsylvania published today in Nature Biotechnology. These chemical groups mark one of the four "letters" of DNA in the genome, and it is the differences between these marks along the DNA that control which genes are expressed or silenced .

To detect diseases earlier and with greater precision, researchers are increasingly interested in the analysis of floating DNA in environments where there is a limited amount, such as the one at hand. extruded from tumors into the blood.

"We hope that this method will provide the ability to decode epigenetic marks on the DNA of small transient cell populations that previously was difficult to study, to determine whether the DNA originates from from a specific tissue or even from a tumor. "Rahul Kohli, co-lead author, MD, Ph.D., assistant professor of biochemistry and biophysics and medicine.

Researchers at Penn and elsewhere have been studying these DNA changes over the past two decades to better understand and diagnose a range of disorders, including cancer. In recent decades, the main methods used to decipher the epigenetic code were based on a chemical called bisulfite. Although bisulfite has been shown to be useful, it also has major limitations: it fails to differentiate the most common changes from cytosine, which is a constituent part of DNA, and more importantly, it destroys a much of the affected DNA, leaving little material to be sequenced in the laboratory.

The new method described in this paper is based on the fact that a class of immune defense enzymes, called APOBEC DNA deaminases, can be reused for biotechnological applications. Specifically, the deaminase-guided chemical reaction is able to achieve what bisulfite could do, but without damaging the DNA.

"This technological breakthrough paves the way for a better understanding of complex biological processes such as how the nervous system develops or the progression of a tumor," said lead co-author, Hao Wu, Ph.D. assistant professor of genetics. Emily Schutsky, a graduate student from Kohli, is the first author of the study.

Using this method, the team showed that determining the epigenetic code of a neuron type used 1,000 times less DNA than it was required by the methods dependent on bisulfite. From there, the new method could also differentiate the two most common epigenetic brands, methylation and hydroxmethylation.

"We have been able to show that the genome sites that seem altered are actually very different in terms of the distribution of these two brands," said Kohli. "This discovery suggests important and distinctive biological roles for both brands on the genome."

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More information:
Non-destructive basal resolution sequencing of 5-hydroxymethylcytosine using a deaminase DNA, Nature Biotechnology (2018). DOI: 10.1038 / nbt.4204, https://www.nature.com/articles/nbt.4204