Ten Years in the Making: Transgenerational Epigenetic Study Leads to Journal Co-Publications for Honors Undergraduate and Alumna
By Phyllis Shier, WSU Honors College, peshier@wsu.edu
A ten-year study in WSU’s Skinner Laboratory provided bookend undergraduate research experiences for two Honors College students, one recently, at the study’s culmination, and one at its inception.
Sarah De Santos knew WSU might be right for her when she was invited to join its National Institutes of Health program Motivating Innovation and Research Achievement (MIRA). MIRA offers unparalleled undergraduate research opportunities for Honors College students from underrepresented groups majoring in biomedical science and engineering fields. A Genetics and Cell Biology major in the pre-medicine track, Sarah dreamed of becoming a pediatrician since she was five. But, as college approached, she began to dream even bigger. “I wanted to find a way to be a little more proactive and thought, ‘maybe I’ll involve myself in research,’” she said.
MIRA offers financial support for up to four years of tuition and an initial summer bridge program. It introduces students to lab rotations and summer research opportunities and provides the opportunity to attend a national scientific meeting. While the two labs she toured initially weren’t in her area of interest (i.e., genetics or epigenetics), De Santos reached out to WSU Eastlick Distinguished Professor of Biological Science, Michael Skinner by e-mail. Skinner is the founding director of the Center for Reproductive Biology.
“He replied very quickly,” she said. She visited the Skinner Laboratory a few days later. “After that meeting, he basically said ‘Just send me your resume and consider yourself a part of our lab.’”
Wrapping up a decade of research
Now a sophomore, Sarah’s undergraduate research in the Skinner Lab led to her first co-authored research publication in the latest issue of
Environmental Epigenetics. The paper, Multiple generation distinct toxicant exposures induce epigenetic transgenerational inheritance of enhanced pathology and obesity, chronicles the ten-year study that culminated a year and a half into her lab experience. The study examined three
successive generations of gestating year-old female rodents, strategically injecting them with environmental pesticides and jet fuel during fetal sex determination, followed by three generations with no exposure. The final “F5” generation determined the transgenerational phenotype for pathology and disease using “Deep Learning” artificial intelligence-based histopathology analysis. Results showed “compounded disease impacts in obesity and metabolic parameters,” while other pathologies increased only minimally, leveling out by the transgenerational F5 generation.
“While there was a slight increase with other diseases, like kidney disease, ovarian disease, different cysts, obesity was the one disease that you could basically track a substantial increase in as the generations progressed,” De Santos said. The study is novel in its transgenerational approach. “We bred them out pretty far and we saw how, not the first or second generation after exposure, but their descendants in subsequent generations showed an increase in obesity and epigenetic markers for that,” she said.
Sarah worked with first co-author, Eric Nilsson on histology and pathology. “Eric really helped me understand not only how to do certain tasks within the lab but also the reasoning behind them,” she said. She took tissue cuts of reproductive organs, preserving them in various rinses so slides could be created, and worked with the Deep Learning AI analysis program checking for abnormalities detected and correcting for variables identified that weren’t necessary for the study. “I was learning while helping it learn as well,” Sarah said. Even with the learning curve she noted great benefit in using the AI. “Using the Deep Learning system, we were able to speed up our analysis process; instead of it taking weeks or months, it only took one or two weeks.” She also helped with slide quality control, looking for cut off specimens or out of focus images, and helped with statistical data generation.
“For a first experience I thought it was pretty incredible that I was able to tag along at the tail end of this project and learn all about what we were doing and assist significantly,” she said. “I was very happy about that.”
De Santos credits Professor Skinner for having an impact on her overall journey as a student. “Coming into college I was very focused on just the MD track…nothing else mattered,” she said. Having previously shadowed doctors, she’d seen the clinical side of medicine. Discussions with Professor Skinner helped her realize how conducting research would allow her to help pediatric patients both in “…identifying problems and potentially designing solutions as well,” she said.
“That helped me get a better understanding of what Dr. Skinner calls preventative medicine… instead of, as a physician, just reacting to a problem, we identify the problem and are already researching solutions for it,” she said.
Outside her interests in science and medicine, Sarah loves learning in general—something that’s supported in her honors education. She took a poetry course with Honors College Professor Colin Criss and discovered an interest in poetry. She joined Palouse Review, the WSU Honors College biannual arts and academics journal and was surprised to find a strong science contingent within the group.
“Honors gives you the opportunity to kind of branch out a bit—maybe do something you’re not really comfortable with or used to, but, once you kind of take a chance, it’s really rewarding,” she said. “With science, you’re focusing on facts and data…it’s still creative but a different sort of creativity from poetry, so I appreciated that,” she said.
An honors English course with Professor Bryan Fry expanded her knowledge on literary and historical research.
“That was a very interesting class for me because whenever I hear research, I think scientific paper… and here’s this professor my freshman year saying ‘let’s go into the archives; let’s go to maps; let’s delve into these different first-person and second-person accounts… His class was very much about research but literary research and historical research.” Sarah’s project focused on early discrimination and exclusionary laws towards Asians, specifically Chinese, Filipino, Japanese, and Korean immigrants. The project was of specific interest to her as her father and grandmother immigrated to San Francisco in the 1970’s from Manilla. While the Chinese Exclusionary Act was no longer in place, that change only occurred three decades earlier. “So, it was very interesting to see that contrast of my experience and my parent’s experience versus the experience of those who had to deal with such laws before they were finally done away with,” she said.
De Santos is quick to confirm how much she values the access her Honors College and MIRA experiences have provided her.
“Before getting into the Honors College and the MIRA program… I was very much considering just going to a local college, dealing with that, because I knew medical school was going to be extremely expensive,” she said. “Being able to come to WSU, especially since I’m one of the few people in my extended family who’s actually been able to go to college—was very, very rewarding; I’m very grateful for that opportunity.”
The study from the start: An alumna’s perspective
“It’s been a minute,” WSU Honors College alumna Margaux McBirney said with a laugh, about her role as Environmental Epigenetics second co-author in the 10-year transgenerational epigenetics study in the Skinner Lab. “I think I started in his lab the first week of college, so right from the beginning!” she said.
Margaux began by exposing test subjects to environmental toxicants, but also learned the research background of the project she’d be participating in. This differed significantly from a traditional lab experience, McBirney said, where students may be inserted into the process without fully understanding the scope of the project.
“I really appreciated that model because it helped you start to develop this understanding of the basis of our experiment… and then you could start to contextualize. It provided this foundation to build upon.”
So, when Professor Skinner encouraged her to continue during the summer, she stayed, even though it deviated from her summer plans. “For context, during the school year I would be in the lab about 10 hours a week my first year; over the summer I was in the lab basically full time, so I think that’s really where things progressed.”
McBirney started working on histopathology analysis of tissues, helped to dissect animals, and helped to gear up for the paper on one of the biggest studies in the lab to-date. “It was absolutely worth doing it because…your rate of learning was so much higher,” she said.
One drawback of a long study meant significant data wouldn’t be available in time for her honors thesis, so Professor Skinner assigned Margaux to another study on the epigenetic effects of atrazine.
“That’s what was so amazing about Dr. Skinner and the Honors College is that they just worked in tandem so well,” she said. The atrazine study “paired beautifully,” with the timing of her thesis project. “Dr. Skinner and I reworked the plan to have me be more involved in that study and that ended with…another co-author publication and using that for my honors thesis.”
Margaux’s experience also included a summer in France via a connection the Skinner lab had there. She took an intensive French course onsite which helped with her honors language requirement. “That was a really fortunate opportunity as well—to go do that,” she said. An avid cycler, she got to see the Tour de France and do some cycling of her own.
McBirney progressed in the lab’s ten-year study to working with senior lab scientists on molecular techniques. “It was really an incredible experience where you got a whole lifecycle of these experiments; so often undergrads get a summer in a lab or a half a year… it was really amazing to have three and a half years of progressive experience,” she said.
“Ultimately, that’s really what got me my first job out of college, too, because that’s not so common,” she added.
McBirney’s first job at the Fred Hutchinson Cancer Institute in Seattle eventually transitioned into a lab management role. “I applied to a lot of jobs there,” she said of her start at the Hutch. “I think what really stood out to their HR recruiters was the depth of my experience and specifically this niche area, which is working with animals in research settings.”
McBirney is currently Lab Operations Manager at Talus Bio, a cancer therapeutics company in Seattle.
Positioning students for success
The Skinner Lab has mentored honors and traditional students for more than twenty years.
“Mike is a super advisor,” said Honors College Dean M. Grant Norton. “Over the years he has mentored fifteen or more honors students, integrating them into his research projects in ways that often lead to undergraduate research publications and even career opportunities; students are grateful for those opportunities and real-world connections,” Norton added.
Training the next generation of researchers is vital to the research mission of the university and students in the Skinner lab are an essential part of his lab’s workforce. “I’m in the university because I believe that environment facilitates research activity,” Professor Skinner said. “I’m really looking for students who have a career goal that we can help facilitate.”
That trait is something he finds consistently in honors students.
“Honors students are far more serious about their academic futures,” Skinner said, noting that a high percentage of them often “tend to gravitate” to his lab rather than him having to seek them out. Often, he said, they already know they want to go on to grad or medical school. “Those students are committed to go on in their careers and to do further education and so those are the ones that really fit the best in a research environment,” he said.
Honors students recognize the reciprocity the situation provides.
“What’s really special and unique about Dr. Skinner’s approach is that he enables the undergrads and gives you so much room to learn and try things,” McBirney said. “It’s worth noting because when you do give that ownership and guidance—of course, with oversight—it’s really impressive what undergrads, as a general term can do,” she added. “You learn you can start to really contribute, make decisions, and be an asset to the lab.”
“If you’re looking for someone…to work in your lab, if they have aspirations to go on to the more professional degrees and stay in science, that’s how you select the better students,” Skinner said.
Students like Margaux and Sarah, for example. “There’s two of them… one at the beginning and the other at the end with no overlap,” Skinner said.
“Margaux was in on the very beginning several years ago. She basically got this project started with some other senior people in the lab. It took us forever to get all the generations and all the pathology and everything else,” he said. “She was one of my more productive honors students in the sense that she co-authored four publications.”
“Sarah played a significant role in helping us finish up all of the pathology over the last year and a half…summarizing a lot of the data, putting things together,” Skinner said. Once he learned she was an honors student who wanted to do an MD and a potential PhD, he knew she’d be a good fit for his lab. “Finding those people early in their careers is not common.”