Bacteria cause problems for genetic research

March 18, 2020

A puzzling modification of DNA that is common in bacteria is not present in humans or other mammals. This has been shown in a new study by scientists at Linköping University in Sweden, published in Science Advances. The study shows that detection of the epigenetic mark 6mdA in animals was probably the result of limitations of the technology used and bacterial contamination of samples.

A few years ago, some studies were published that aroused considerable interest among researchers in genetics. These studies had examined a particular epigenetic mark, or modification of the DNA that influences how the DNA sequence is used in different cells. This mark had not previously been observed in multicellular organisms. The mark, known as "6mdA", is, in contrast, common in bacteria, where it plays an important role in protecting the bacteria against viruses. Reports from numerous research groups stating that they had found 6mdA in various animal species, and even in human cells, stimulated not only major interest among the research community, but also some questions. One of these concerned the levels of 6mdA detected, which were so low that scientists wondered whether such a rare epigenetic signal could truly have a function. Following these initial reports, some other published studies were unable to detect 6mdA in animals.

Just as many other research groups, Colm Nestor's group at Linköping University started to study this puzzling epigenetic signal. They were, however, unable to detect it in human or mouse cells. Eventually, they detected 6mdA in two samples of human cells, but it turned out that both of the samples were contaminated with mycoplasma bacteria. The researchers suspected that the epigenetic mark came from the bacteria and not the human cells. They treated the cells with antibiotics against mycoplasma and saw the 6mdA signal disappear.

The LiU researchers believe that contamination with mycoplasma bacteria is an underestimated problem in epigenetic research. The particular strain of mycoplasma they found is common in healthy people and typically does not cause any negative health effects. Since mycoplasma bacteria can exist not only outside cells but also inside cells in the body, it may be that this bacterium is present, but undetected, in human samples. For most types of bacteria, researchers can easily detect if cells cultured in the laboratory are contaminated. However, this is not the case for mycoplasma contamination, which requires special testing.

The LiU researchers soon discovered that it is not only mycoplasma bacteria that cause problems for researchers studying the 6mdA mark. They also found problems with several methods used to detect this epigenetic modification.

"We realised that the 6mdA 'signals' detected by these techniques were simply noise. However, as a consequence of several complex technical problems the background noise in several of the methods was not random, but appeared to be a true signal. Now we can say without a doubt that 6mdA is not present in mammals", says Colm Nestor, research fellow in the Department of Biomedical and Clinical Sciences at Linköping University, and leader of the study.

Colm Nestor maintains that the reports of 6mdA in mammals are from well-executed studies published in reputable scientific journals. It is extremely unusual that several methods give similar misleading results as a result of completely different artefacts.

"When we analyse very rare phenomena, we must be extremely careful and consider whether we truly can measure them using the methods we have chosen. With respect to 6mdA, a lot of time and money can be saved, and a lot of disappointment avoided, if researchers stop studying something that is simply not there", says Colm Nestor.
-end-
The research has received financial support from the Swedish Research Council, the LiU Cancer Network and the Swedish Cancer Society.

The article: "No evidence for DNA N6-methyladenine in mammals", Karolos Douvlataniotis, Maike Bensberg, Antonio Lentini, Björn Gylemo and Colm E. Nestor, (2020), Science Advances, published online on 18 March 2020, doi: 10.1126/sciadv.aay3335

Link: https//doi.org/10.1126/sciadv.aay3335

Linköping University

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