A Crash Course in Epigenetics

Diana Toledo, a PhD student in genetics at Dartmouth College, studies scleroderma, a rare autoimmune disease that causes tightening of the skin and joint pain. But to make headway she had to overcome an obstacle: she had a dataset that she didn’t know what to do with. “I was sitting on data, and I didn’t know how to analyze it,” she said.

Toledo’s data captures chemical changes to DNA that affect gene expression without changing the underlining genetic sequence—the study of which is known as epigenetics.  To make sense of this information, she joined several dozen likeminded researchers for a fastpaced introduction to the field through one of two summer boot camps organized by the Mailman School's Department of Environmental Health Sciences (EHS).

Epigenetics dates to the 1960s. In recent years, however, the field has experienced exponential growth, from 200 papers per year in the 1990s to more than 20,000 papers per year today. At the same time, new technologies allowed scientists to map DNA methylation—the most popular method of epigenetic study—across as many as 850,000 sites on the human genome simultaneously. The results serve as kind of “biological memory” for various exposures, including environmental toxins, that have shown to correlate with health outcomes from cardiovascular disease to schizophrenia.

“Epigenetics is opening a completely new world to researchers,” said Andrea Baccarelli, chair of EHS and a leading epigenetic scientist since the early 2000s. “It gives us powerful and precise methods to identify who is at risk and intervenes on those who need it the most. This is an important avenue for anyone doing health research going forward, particularly those interested in precision medicine and precision public health.”

Baccarelli, who also directs the Mailman School’s Laboratory of Environmental Precision Biosciences, led the sold-out boot camps, aided by two of the lab’s members—Kasey Brennan and Elena Colicino—along with researchers from Harvard Medical School, the Icahn School of Medicine at Mount Sinai, and the U.S. Environmental Protection Agency.

Boot camp attendees, ranging from doctoral students and faculty to people working in the private sector, were given a mix of seminars and hands-on practice analyzing data from Illumina, Inc.’s epigenome-wide methylation array. Along the way, participants learned about the design and execution of methylation studies, including sample collection and preparation, data handling, cleaning, and basic analysis using R, the statistical programming language. Participants were given the code they worked with—something Diana Toledo said would be “very helpful” to her scleroderma research.

Ashvinder Singh, an independent researcher from the Bay Area, sought out the two-day August training for a leg up on a field he hopes could provide the basis for his early-stage tech startup by allowing him to measure exposures like cigarette smoke and air pollution. “This is a one-of-a-kind boot camp,” he said. “It has given me a lot of perspective on how to do my own research. I made a really good decision.”