In 2006, an international team of scientists published the complete genome sequence of the honeybee, revealing striking insights into the complex social behavior of these insects. According to Ryszard Maleszka, a geneticist at the Australian National University and a collaborator on the project, one of the most exciting discoveries was that honeybees, similar to humans but unlike fruit flies and nematodes, have the full complement of DNA methyltransferase enzymes (DNMTs) that underlie an animal's ability to flexibly adapt to the environment by regulating gene expression.
Royal Jelly Diet
The link between diet and epigenetics can explain how honeybees with identical genomes can take on different social roles within hives. Larvae that are fed royal jelly become queen bees capable of reproducing and living a long time, in contrast to short-lived, sterile worker bees. In 2008, Maleszka and his team reported in Science that silencing the expression of one DNMT in young honeybee larvae mimics the effects of royal jelly on the fate of honeybee females, resulting in queens with fully developed ovaries (1). And in a study published two years later in PLoS Biology, Maleszka and his team used whole-genome sequencing to show that more than 550 genes have different methylation patterns in the brains of queens and workers (2). Together, the results suggest that the royal jelly diet influences brain methylation patterns to determine the honeybee's caste.
Still, the mechanism by which DNA methylation mediates distinct, diet-controlled developmental trajectories was not well understood. To address this question, Maleszka and his collaborators compared genome-wide methylation patterns in the heads of larval queens and workers. Among the thousands of differentially methylated genes they identified was one that encoded an enzyme called anaplastic lymphoma kinase, which is an important regulator of metabolism. Published in March in Proceedings of the National Academy of Sciences, their results suggest that this enzyme plays a key role in linking the nutritional environment with downstream signaling (3). "The next step is to look in more detail at the key elements of the signaling pathways that are involved in energy metabolism and food processing," says Maleszka.
Because core metabolic pathways are conserved across a range of organisms, the results are likely to generalize to humans. "To a certain extent, there are limitations, especially with regard to behaviors that are unique to mammals or humans," says Maleszka. "But that's not the case with food and nutrients. This is the area that can probably be most fruitful in terms of data transfer from model organisms to humans."
One possible topic of investigation relevant to human health is how high-fructose corn syrup modulates epigenetic responses in the honeybee. "We are hoping that one day we might be able to monitor all those epigenetic modifications in real time in defined tissues or organs," says Maleszka. "Such technologies will make the complex disease challenge more realistic in terms of diagnostics and possible prevention."
Many studies examining the link between nutrition and epigenetics have focused on effects during development, when DNA methylation patterns are established. Studies in humans have shown that maternal nutrient intake during pregnancy can affect DNA methylation in the offspring. For instance, low maternal carbohydrate intake during pregnancy is associated with changes in DNA methylation in the umbilical cord as well as later obesity in children, while maternal folic acid supplementation around the time of conception leads to altered methylation patterns in very young children.
In some cases, epigenetic changes affect disease-related genes. Individuals conceived during the Dutch famine in 1944–1945 show altered methylation in genes implicated in obesity and diabetes, as well as a higher incidence of schizophrenia and heart disease compared with their unaffected siblings. However, whether these epigenetic changes are actually responsible for the higher disease risk is not clear.
On the path toward investigating the link between epigenetics and health, Mihai Niculescu moved from Romania, where he had earned his M.D., to the United States. There, he entered the Ph.D. program in nutritional biochemistry at the University of North Carolina (UNC) at Chapel Hill. His dissertation focused on choline, a nutrient that donates methyl groups required for methylation reactions and causes epigenetic changes related to fetal brain development and liver function. "It was a natural shift for me to think about how DNA is chemically changed by adding methyl groups to its molecules," he says. "After graduation, I shifted my area of interest toward the role that maternal nutrition has in this chemical modification of DNA in the fetus."
Now, as a nutrition and epigenetics expert at UNC, Niculescu studies the effects of maternal obesity and omega-3 fatty acids on the epigenetic regulation of fetal and postnatal development. His research has shown that diet can produce powerful epigenetic changes in both mothers and their offspring, and that these epigenetic changes have important, long-term effects on metabolism in toddlers.
Niculescu envisions using his research findings to establish personalized nutrition guidelines based on an individual's unique genetic and epigenetic makeup, and his goal is to use epigenetics as a tool for obesity prevention. "The child doesn’t have any choice about how he or she will look or his or her brain development or memory abilities, so this has very profound ethical implications. What's the responsibility of the parents even before conception and after conception regarding the health status of the child?"
Such epigenetic effects may even persist in subsequent generations, although this issue is debated. "We don’t know yet whether the epigenetic changes that we see in the offspring or the child are carried throughout multiple generations," says Niculescu. "It's very difficult if not impossible to follow-up several generations of humans."
Transgenerational epigenetic inheritance is "quite hard to explain, given that we know that most epigenetic marks are erased during meiosis in germ cell development," says Richard Saffery, an epigenetics expert who studies complex diseases in children at the Murdoch Children's Research Institute in Australia. "The evidence is quite compelling in animals that there is this transgenerational effect, and if that's true, that has a lot of implications. It used to be that you are what your mother ate, and it could be that you are what your grandmother ate," says Saffery. But epidemiological studies in humans are circumstantial, so "there is nothing as yet convincing in humans," he adds.
Asking for a Brain Biopsy
One major challenge in studying epigenetic changes related to nutrition in humans is that samples are often restricted to blood, which consists of multiple cell types that can have dramatically different DNA methylation profiles for a given gene. As a result, any change in DNA methylation could simply reflect the heterogeneity in the cell types.
"You can't just go and ask someone for a brain biopsy, so there is this nagging doubt in the field as to whether or not what you're measuring in blood or in a skin biopsy is relevant to the target tissue that you're interested in," says Saffery. "That's a challenge that's a lot harder to overcome, and probably that will need to be looked at quite carefully in the future."
Another challenge in interpreting epigenetics data comes in the form of copy number variations. Genes with multiple copies could result in false positives for changes in DNA methylation when microarray-based methods or pyrosequencing is used (4). "If I detect changes in DNA methylation, this doesn't mean necessarily that these changes are happening in a copy that is functional," explains Niculescu, adding that whole-genome sequencing could overcome this problem.
Ultimately, Niculescu hopes the future will bring widely available technology that will streamline the unbiased detection of a range of epigenetic changes, not just cytosine methylation. Although recent technology is capable of detecting other epigenetic modifications, it is often not commercially available, so "each lab is setting up its own method," he says.
Beyond technological progress, Saffery anticipates the future will bring more answers to the many open questions that remain about how diet-induced epigenetic changes affect behavior and disease in humans, and how to use this information to develop novel interventions. "It should be a very interesting period. I liken it to when we first started sequencing the human genome. We had very little knowledge about where it would take us. Certainly it has taken us a long way, but it's nowhere near as far as we thought," he says. "Who knows where we'll be in 10 years from now."
- Kucharski, R., J. Maleszka, S. Foret, and R. Maleszka. 2008. Nutritional control of reproductive status in honeybees via DNA methylation. Science 319(5871):1827-1830.
- Lyko, F., S. Foret, R. Kucharski, S. Wolf, C. Falckenhayn, and R. Maleszka. 2010. The honey bee epigenomes: Differential methylation of brain DNA in queens and workers. PLoS Biol 8(11):e1000506+.
- Foret, S., R. Kucharski, M. Pellegrini, S. Feng, S. E. Jacobsen, G. E. Robinson, and R. Maleszka. 2012. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proceedings of the National Academy of Sciences (March).
- Niculescu, M.D. 2012. Challenges in nutrition-related DNA methylation studies. BioMol Concepts DOI: 10.1515/bmc-2011-0052.