Honeybees are infamous for their painful, sometimes deadly stings. But they are arguably less known as a model for studying how the environment shapes gene expression in the brain via epigenetic modifications such as DNA methylation. Gene Robinson, a honeybee researcher from the University of Illinois at Urbana-Champaign, teamed up with clinicians, neuroscientists, radiologists, and engineers to develop a new method to find out if gene expression in the brain is shaped by individual human experience (1).
Robinson has spent the better part of two decades analyzing how the intricate and active social life of bees influences gene expression in the brain. He showed that gene expression in honeybee brains can predict behavior such as aggression and change in response to external factors such as stress hormones released by nearby bees. These gene expression changes often result from epigenetic modifications to DNA such as methylation. These dynamic changes in response to stimuli allow the brain to grow and learn over time.
“We still don't know what the physical manifestation of memory or personality is in the brain. Throughout development, people learn more and more things, right? This is encoded in the brain in some form. People have to be physically storing this information and making the connection,” said King Li, a bioimaging researcher from the University of Illinois at Urbana-Champaign who recently published the new method in Proceedings of the National Academy of Sciences with Robinson. “One hypothesis is that this long-term storage and recall mechanism is [stored] through epigenetics.”
Testing this hypothesis in humans is tricky. Collecting samples of RNA and DNA from human brain samples is more complicated than collecting them from bees; researchers use post-mortem brain samples, which don’t perfectly preserve post-translational modifications. The best way to study experience-induced changes in DNA methylation in individuals is to examine methylation patterns in live brains.
Robinson, Li, and a collaborative team of researchers developed their method to do just that. They fed pigs carbon-13, an isotope of the commonly found carbon-12 that comprises less than 1% of total carbon in the human body and can be imaged by MRI. When the methyl group containing carbon-13 from methionine was added to DNA, the researchers could visualize methylated stretches of DNA using MRI. They call the new approach epigenetic MRI (eMRI) and expect to test it in humans within a year.
“The paper is the first to talk about epigenetic MRI as opposed to the traditional MRI measuring neuronal activity in the brain. The paper is a huge step forward in noninvasive measuring of genetic expression in the whole brain,” said Budhachandra Khundrakpam, a neuroimaging researcher at McGill University.
Using this method, the team saw carbon-13 labeled methyl groups light up along the DNA in the brain, and they also saw methylation levels increase as the pigs developed, an observation Robinson and others previously found in other models such as honeybees.
“We are the first group to have actually demonstrated that by giving this diet with this carbon-13 methionine, we can actually see the label on the DNA in the brain of developing piglets,” said Li.
Li noted that the carbon-13 signal was too weak to image in animals with smaller brains such as mice. Visualize the signal in the pigs’ larger, more human-like brains, Li and Robinson recruited electrical and computer engineer Zhi-Pei Liang from the University of Illinois at Urbana-Champaign to develop analysis software to amplify the signal.
Li and Robinson are optimistic that this method will translate to humans after they finish some finetuning in pigs. But some researchers still have questions about the approach.
“It’s a proof-of-concept study,” said Theodora Dorina Papageorgiou, a neuroscience researcher with expertise in MRI methods from Baylor College of Medicine. “They talk about it as a nondestructive study, but they did euthanize the animals to look at the effects in the brain and use tissue sampling from various brain regions. So in the end, tissue sampling occurred after the animals were euthanized.”
Papageorgiou expects to see these results validated in live animals before the team tests the approach in humans.
Li and Robinson are currently validating this method in adult pigs since they hope to develop this imaging technique for adults rather than children. But Li thinks that the method will work better in adults since the carbon-13 signal is amplified in bigger brains.
“We have unpublished results that showed that we can actually see the labeling in adult pigs already. It gives us very high confidence that we can get into humans because the human brain is about eight to ten times the size [of an adult pig brain],” said Li. “If the labeling works the same as in adult pigs, then we are in business.”
Li and his collaborators hope that this method can be used to examine differences in methylation in the brains of patients with neurological disorders such as Alzheimer’s and Parkinson’s diseases. He is currently collaborating with researchers who have animal models of neurological diseases to examine the difference in methylation patterns in animals.
“This could give insight into a variety of diseases including Alzheimer's disease. One of the really important frontiers in Alzheimer's is to look for early markers of the disease before neuronal damage occurs. We're interested in exploring whether changes in epigenetics in the brain can serve as an early marker,” said Robinson.
- Lam, F. et al. Epigenetic MRI: Noninvasive imaging of DNA methylation in the brain. PNAS 119, e2119891119 (2022).