DNA Isn't Destiny, So What Is?

David Faulkner: Welcome to Adverse Reactions. I'm David Faulkner.

Anne Chappelle: And I'm Anne Chappelle.

David Faulkner: I'm a toxicologist and a risk assessor. 

Anne Chappelle: I'm a toxicologist and was the first runner-up in the Doctor Toxicology Competition of 2003. 

David Faulkner: And on this show, we explore the stories behind the science. 

Anne Chappelle: This is where we talk to toxicology experts from around the country and around the globe that use the field of toxicology to advance public health and also to protect the environment.

In this episode of Adverse Reactions, "DNA Isn't Destiny. So What Is?”

Dana Dolinoy: That's, what's really exciting is the things that we're exposed to early on can reprogram the epigenome. And these reprograms can sometimes be beneficial, and sometimes they can be negative. 

David Faulkner: Featuring Dana Dolinoy. 

Dana Dolinoy: So fortunately, there is a great reprogramming process that happens post-fertilization. And so most of the acquired epigenetic marks in the previous generation are erased and reestablished in a specific manner. But of course, like many things in life, there are always exceptions.   

David Faulkner: We are joined today by Dr. Dana Dolinoy from the University of Michigan School of Public Health. Hello, and welcome to the program.

Dana Dolinoy: Hi, David. Hi, Anne. Thank you for having me today.

Anne Chappelle: We are really excited to explore your field of interest. And tell us a little bit more about epigenetics and what is it and what your typical day looks like? 

Dana Dolinoy: Well, epigenetics literally means in addition to, or above, the genome. And we all know that we have a genome, the collection of genes or the genetics in our body, but what we need is the instruction book that tells all those genes when to turn on, where to turn on, how much to turn on, how to react to various things that are thrown our way. And all of that is the job of the epigenome. So you can think of the epigenome as the instruction book for our genome.

David Faulkner: It's like the genome’s the recipe book, and the epigenome is sort of the rules for when you make the recipes?

Dana Dolinoy: That's a great analogy, David. The field of epigenetics is full of great metaphors and analogy. Um, another one is that of the computer. If our genome is the hardware, our epigenome is all the various different software programs that run the computer. So, with just a hard drive, you have a computer that has data, but you need the epigenetic software to come around and tell all that data what to do.

David Faulkner: Yeah, I think that makes a lot of sense. 

Anne Chappelle: It makes a lot of sense, but it's also pretty confusing, too, because you go through school thinking about DNA is the end all be all. We have to make sure of, you know, we have all these genetic toxicology studies to look for these permanent changes. And now you're telling me that it's all more flexible and malleable and uncontrollable.

Dana Dolinoy: Yeah, it is flexible and malleable and plastic, but that's what's really great about the epigenome, because we don't want the same sets of genes expressed when we're four years old as when we're 40 year old or 80 year old; you want different sets of genes expressed, and the epigenome can help do that.

The other really exciting thing about the epigenome is it's hopeful. Unlike the genome, which is static, not modifiable, we can't do a lot about the genome that we inherit. Because of the epigenome’s plasticity, we do have some idea about how we might manage the epigenome in a way that can better protect health, for example, from all of the chemicals that we're exposed to.

Anne Chappelle: So, do you consider yourself a toxicologist, a geneticist? 

Dana Dolinoy: I have been called all of the things that you just said. An epigeneticist would be, you know, sort of a relatively new term. The field of epigenetics is not that old. It's quite mature in the field of cancer, sort of, but we're still talking about decades rather than hundreds of years, which some sciences can attest to. You could call myself a molecular biologist, but a molecular biologist would mostly be only in the laboratory.

And earlier you asked me about what do I do in a typical day? Well, I can tell you, no one day looks the same. But people who are interested in epigenetics from the standpoint of toxicology and public health, we really are using this as a way to understand how environmental exposures impact health risk. And this is across the life course. That's what's really exciting is the things that we're exposed to early on can reprogram the epigenome. And these reprograms can sometimes be beneficial, and sometimes they can be negative. And so thinking about it only from a negative standpoint is also not correct. There can be things that happen to the epigenome that are beneficial and adaptive. And so it's really a complex system.

David Faulkner: I like that. I like the optimism of the discipline. Things, things can be changed. Because it can feel like, oh no, this is, the body I got, gotta kind of deal with it. You know, especially as, as you get older and things don't work as well.

Dana Dolinoy: Yeah, I really wish that I could change the epigenome of my knee right now to be a little less stiff, for sure.

David Faulkner: Well, could that work, though?

Dana Dolinoy: Unfortunately, we don't have all of the tools at hand yet, David, to change our epigenome. 

David Faulkner: That's kind of cool, though. If you could somehow manipulate the epigenome, would it be a thing that you could even fix using epigenetic tools?   

Dana Dolinoy: That's a great question. I don't think we're quite there yet in terms of what one might call epigenetic therapy that can be broadly applied, but that's sort of the goal of precision environmental health is to figure out whether epigenome can be one of the tools in our handbag. So, for example, there are a number of approved drugs that can be used to treat certain end-stage cancers. And these are drugs that act on the epigenome. But they're global targets. So they either erase all the DNA methylation in the genome, and that's good at certain regions, but at other regions, you want to keep that DNA methylation. And so the field of epigenetic therapy is really looking towards targeted locus-specific approaches. 

And one of the really cool tools that we're working on right now is harnessing an endogenous RNA called piRNA to be used as an epigenetic editor. It'll only work one way. It can be used to induce DNA methylation. But if you can induce DNA methylation, which is associated with turning genes off in regions that you want those genes off, then this can be a pretty powerful tool in the future for therapy. 

The other thing that epigenetic editing can do is we can use it in the laboratory to sort of test epigenetic mechanisms. We can induce DNA methylation and figure out what that would do to a system similar to an environmental toxicant that would induce DNA methylation. 

Anne Chappelle: So you could do a lot of very interesting things and investigate a number of different projects. From a research standpoint, and your laboratory's standpoint, there's kind of these lofty, futuristic, that-would-be-really-cool-to-fix-my-knee. And then there is the basic understanding of how things work to further the science as a whole. So how do you balance those really cool, interesting diversions, managing a lab, managing really curious students?

Dana Dolinoy: Some of the most interesting projects have been brought to me by the students, including questions about whether the epigenetics of hyenas can change by their social rank or sled dogs in Alaska have different epigenomes because they have exposure to particulate matter when they're cooked up in their kennels.

And those are really exciting projects, and we like to pursue them when we can. But in general, I motivate the lab by two overarching opportunities and challenges that I see in the field of epigenetics. And the first is how, on a population level, can we identify the suite of chemicals and who they will affect? And in particular, in the field of epigenetics, this is challenging to do in humans. 

So, for example, let's say we're interested in whether lead exposure affects the epigenome in a way that leads to Alzheimer's disease. Well, I can pretty much guarantee you that I'm not going to have access to that brain tissue that I need to test the epigenetic marks like DNA methylation and histone modifications. So we have to rely on surrogate DNA, which is blood or saliva or a couple other things you could think of. But does blood represent the brain when we're thinking about the epigenome? And so that's why, in our laboratory, we take a variety of approaches that sort of span mouse to human, and a couple of different species in the middle, because in the mouse we can do things like well control genetics, we can well control the other environmental factors. And then we can ask explicitly, does this particular diet, does this particular endocrine active compound, affect the epigenome, and how does that affect long-term health? And at the same time, I can look in the mouse blood and I can look in the mouse brain and then I can compare, are they similar?

And in some cases, they are, but in many cases, they're not. And so this poses a great challenge for when we try to move epigenetics to the population level or what we call epigenetic epidemiology, because for there, we can't control all of those things I just told you about. We're dealing with diverse populations with diverse experiences. But there are a number of great tools that have been developed for population-based epigenetics. And certainly, we're identifying places in the epigenome which are susceptible to different environmental chemicals. 

David Faulkner: You're a faculty director of the Epigenomics Core at Michigan Medicine. Is that sort of a way of working towards these population-level questions? What is that all about? 

Dana Dolinoy: So at many academic institutions, including the University of Michigan, you have core facilities. And at Michigan, we're so fortunate to have an Epigenomics Core. And this is really important because epigenetic technology is rapidly advancing, and epigenetic technology needs to rely on the platforms that much of genomics rely on. And so these are either array-based platforms or next-generation sequencing platforms. So the Epigenetics Core is able to work with clients to conduct all of the upfront troubleshooting work that needs to be done to look at DNA methylation, histone modifications, the way the chromatin is assembled, and then pass these samples off to a DNA Sequencing Core that has all of the fun, very expensive tools to do that.

And that makes it easier for researchers to gain access to epigenetics. For example, if an epidemiologist is interested in looking at a birth cohort of individuals in Mexico City, for example, and whether lead exposure affects the epigenome in cognitive development and the children later in life, and they themselves don't have a laboratory, they can work with a core facility to run these hundreds of samples through in a much more efficient way. The core director, Claudia, loves a slide that she's prepared with all of the different species the core has ever worked on. And there's actually a bottlenose dolphin on that slide, if you can believe, along with those hyenas I mentioned earlier.

Anne Chappelle: So this raises potential ethical questions, doesn't it? Are you changing the genome or not? And are you consciously affecting it? I've heard a lot about CRISPR and should you edit the genome of someone, but I think that as alright, that's heritable. But this more subtle methylation status and changes, that's a little different.

Dana Dolinoy: Yeah, certainly the fact that environmental exposures, especially during pregnancy and perhaps during preconception in the egg and the sperm, that results in that pregnancy—it's a vulnerable time period—makes us take a pause and say, do we have some ethical responsibility for maintaining an epigenome with integrity, right, so that we don't pass on changes in DNA, methylation, or other marks to our offspring? So fortunately, there is a great reprogramming process that happens post-fertilization. And so most of the acquired epigenetic marks in the previous generation are erased and reestablished in a specific manner. 

But of course, like many things in life, there are always exceptions. And there are examples where you can see what's called multi- or transgenerational inheritance of environmental exposures. And so this is particularly problematic and troubling because could something that my great grandmother did be affecting my health, when I had no direct exposure to that? That's a really big problem, right? 

Anne Chappelle: That’s a lot of guilt, too. 

David Faulkner: But it also raises this question of culpability, in a way. Could you sue a, a parent for having lived irresponsibly before you were, you were born if chronic stress changes the epigenome? And I suspect that there's probably some evidence of this. Could you sue somebody for saying, you know, you put me in this position, and so now my kids have anxiety issues, and things like that?

Anne Chappelle: Yeah, I'm thinking of that with my own children: you grounded me, and now, that means that my knee hurts. I don't know. But maybe that's part of it.

Dana Dolinoy: Yeah, youboth are exactly right. Unfortunately, terrible things happen in the world. And there have been studies—I have not been involved in them—that have shown that events like the World Trade Center catastrophe have induced epigenetic changes in individuals later in life or even across generations.

This is also true for individuals whose parents and grandparents experienced the Holocaust. So it is a somewhat controversial field, but there is certain mounting evidence that has shown that these traumatic events can have lifelong impacts on individuals across the epigenome

Anne Chappelle: More mom guilt right there. 

Dana Dolinoy: Yes. And that's exactly right. And a lot of what we talked about directed at the mothers, although there are also epigenetic studies that look at preconception exposures to the dad and whether that is transmitted through the sperm. So like I said before, it should be erased and reestablished, but of course, there are always mistakes that can happen or always other things that can intervene in that reprogramming event. 

Fifteen years ago, when I started, you know, you would look at one gene at a time, and you'd publish a paper in a relatively high-impact journal on the effects on one gene at a time. But just like genetics, epigenetics has changed.

David Faulkner: One of the themes this season is the state of toxicology. So what is the general state of epigenetic toxicology research today? Or what's the big stuff right now in epigenetics work?

Dana Dolinoy: So you will recall, several years ago now, there was the epigenome roadmap, and this was a really exciting time to be an epigeneticist because there were over 20 coordinated papers in Nature and Science published sort of in a single week that matched the human epigenome in 111 different cells and tissues.

And so this was a phenomenal set of data that was put out there publicly available. But what wasn't available in that data was the effects of any environmental exposures on the epigenome. And so one of the consortias that has been put up in the last few years by the National Institute of Environmental Health Sciences is a consortium called TaRGET II, which is beginning to tackle the issue of surrogate versus target tissue, using animal models. 

And so there's a consortia of about seven different laboratories that are conducting studies in a very similar way, but with different toxicants. And so there is a group in Baylor that's looking at TBT. There is a group at university of Pennsylvania that's looking at the endocrine active compound bisphenol A. There are two groups, one in Chicago and one at Johns Hopkins, that are looking at different types of particulate matter. And then at North Carolina State University, they are looking at dioxin. And here, at Michigan, we are lucky. We are looking at two things. We are looking at lead and the plasticizer DEHP, a phthalate plasticizer. 

And so all of these groups have been working together very closely for the past three years to generate a set of data that—some of it is now publicly available—that shows whether in utero exposures to these various different things I mentioned to can produce signatures in blood that are representative of the target tissue. And the target tissues that the consortia are first focusing on are liver and brain because of the huge effects of chemicals on the metabolic system and on neurological function. But all of these groups have collected tissues that will be very important for other questions as well, including the lung and the heart and you name it. It was a big production. And so this is really poised to help epigenetic epidemiology figure out how they can best design their studies when they're limited to looking at blood in humans.  

David Faulkner: Is this where the mice come in? The agouti mice? Because the agouti mice are famously a part of epigenetics research and, and there's some great pictures of these things online. First of all, what are these mice, and what did chubby mice have to do with chubby people? What is the connection there? 

Dana Dolinoy: The viable yellow agouti mice are how I accidentally became an epigeneticist. These mice are genetically identical, but they look very different. One sister would be brown and slender, and the second identical twin sister would be yellow. And when that sister grew up, the mouse would be obese.

And the thing that's really interesting about these two mice is that it's an epigenetic change at a single locus in the agouti protein that turns this gene on all the time, when it should only be on during a specific period of development. And so the fact that this gene loses its DNA methylation in the yellow mice, and it's on all the time, including in the brain, the yellow mice don't feel full after eating, and they continue to eat, and they develop adult-onset obesity.

David Faulkner: Interesting. 

Dana Dolinoy: It's from a spontaneous natural mutation that happened in the 1960s in the, in a colony of mice in the Oak Ridge National Laboratory. But what, what you see is that they're not only yellow or brown; there's a whole wave of mice in between that are mottled—sort of half-brown, half-yellow. And so it's a quite a variable phenotype, and the DNA methylation and the histone code of these mice can be correlated to their coat color. And so what these mice have been particularly important in the field of toxicoepigenetics is if you feed the mouse mother different things, you can shift the coat color distribution of these mice.

And so Randy Jirtle and Rob Waterland had shown that if you feed the mouse mother a diet that's really high in what things that we consider good, like folic acid and betaine and vitamin B12, these methyl donors, you could shift the population distribution towards the brown, slender mice. And so this was seen as a really good thing, right? 

And then I decided to join Duke University for my PhD. I was all set to start working in a laboratory group that looked at childhood lead poisoning and other chemicals, and environmental justice/health disparities issues. But the program decided that all new graduate students that year had to do rotations. And Rob and Randy's work happened to be on the cover of the Science section of the New York Times when I was told I needed to do a rotation.

So I emailed Dr. Jirtle and asked if he was accepting rotation students. And he emailed me immediately back and he said, I remember your application, but I thought there's no way you want to work with me; you want to work on environmental justice. And I said, yeah, but those mice are so cute. 

What happened is I joined the laboratory as a rotation student. And Randy said, what do you want to look at? And I said, I want to look at genistein. And genistein is the phytoestrogen that's found in soy and soy products. And when we conducted a similar study with genistein, we saw the similar thing as the methyl donors: the coat color distribution of the mice shifted towards that brown, methylated, slender mouse. And that was also seen as a good thing. Right? Wow. What your mother eats during pregnancy, at least in this mouse, can affect your epigenome in a positive way. 

So by that time I was hooked. I decided to join the laboratory for my thesis studies. And the next thing we wanted to turn to was a toxicant. And we picked bisphenol A. BPA was very popular during this time as a potential endocrine-disrupting chemical, which had shown, you know, various results, depending on how much or too much or how little you gave.

But what we did is we fed the mouse mothers a diet moderately high in bisphenol A. And lo and behold, the coat color of the population of mice shifted towards the yellow, unmethylated, obese phenotype, which is bad, right, if you were that mouse. So, what were we going to do about it? So, Randy and I decided to conduct one more study, but this time the mice were exposed to bisphenol A but now given either genistein or a methyl donor diet, and lo and behold, a really good diet could counteract the effects of bisphenol A alone.

And so this was some of the first evidence that there was hope in the epigenome. You could use something like a nutritional intervention to counteract the effects of bisphenol A. So these mice are just so visually interesting that they became the poster children for toxicoepigenetics and sort of made their way around the globe and every different types of scientific publication. But what's not true in humans is we don't have an agouti gene that works in the same way.

Anne Chappelle: That's what I was going to ask. I was going to ask if you could just help me find that fat gene.

I guess when you look back at your career, you can kind of see how all of these things that you love to do are all woven into what you are doing now—social justice, the interest in the science, the ability to interact with lots of people. I mean, that is really fascinating to see where you are now, how it really validates all these really interesting things that you've been able to accomplish.

Dana Dolinoy: I can't imagine not being a scientist. It is such a blessing to be able to get up and work on something that you can be passionate about every day. The only drawback to being a scientist is that the questions are never done. They're never fully answered. There's always more to do. And so I find myself, how do you balance your time and your sort of emotional stress. 

I'm fortunate that I, you know, entered the field of epigenetics—especially environmental epigenetics—really early, when it was sort of just beginning. I get a lot of the people who have the really fun questions that take you down the road less traveled. They come to me because I have a background in epigenetics, but it's also really great because I get to learn from them, too.

David Faulkner: Do you have any advice for young people to get to where you are now? Do you have any advice for people entering the field as scientists or people with academic ambitions?

Dana Dolinoy: I really value mentorship, and there's not a one-size-fit-all mentorship arrangement. And so that's why, even though I told you the story about how the program making me do a rotation changed my trajectory, you really need to try out a couple of different research teams, couple of different research topics, to really understand what is going to be a long-term fit for you. 

There may be a topic that you know a hundred percent is the thing you want to work on forever, but the laboratory is not a really good fit for you. That's probably not a path that you want to take. But there may be the situation that happened to me: a topic I didn't know anything about, but it became a really nurturing environment. So I encourage everybody to be flexible and also to be a little bit persistent.

But I think it's particularly important to be persistent so that you can get access to the mentors that you would like. Just because someone doesn't respond to your email doesn't mean that they're not interested. It might mean that that email came on a day when there were 300 other emails that came into the inbox. So I always encourage people to check back in and not automatically assume that there's not interest from somebody that you might want to work with.  

Anne Chappelle: We have a couple of questions that we've been asking some of the guests just to get some off-the-cuff ideas and test your reactions. 

David Faulkner: What was the most significant adverse reaction in your life? 

Dana Dolinoy: You know, I could take the easy way out and tell you about how on the first day of my kids virtual school, this year I had, uh, I got appendicitis but still took a meeting with the dean. But I won't do that. 

I think I'll, I'll tell a little bit of a story that might be helpful for trainees out there. When I was a new, newly independent scientist and writing grants all the time to get that first grant and that can let you do the epigenetic magic that we wanted to do in the lab. So about a year after writing all of these grants, I found out that someone who I’d collaborated with on one of these grants had plagiarized the grant and had taken it and submitted it, which turned out to be over 10 of their own grants. And that was a really challenging time to figure out how to react. 

Anne Chappelle: Yeah. How big was your adverse reaction going to be?

Dana Dolinoy: I had an epigenetic range of reactions to this. I also happened to have been pregnant with my second son, who is, you know, now over 10 years old. So, so far so good. He's quite healthy. No reprogramming of the epigenome due to that stress so far. But that is where I would bring everybody back to having a variety of different types of mentors that they feel very comfortable talking through complex problems that can arise in science. 

Science is a really dynamic world. We have scientists that are in academia, scientists in government, scientists in industry. You can imagine that there are also conflicts that just arise in the natural course of going to professional meetings across these various different stakeholders. And so that's where I found that you have to rely on the network to understand when you need to speak up and when you should let something go. But plagiarism was not an area where I could let go. So we were able to speak up and work ourselves, work ourselves through that.

Anne Chappelle: That is a very good story. That is a fantastic, terrible adverse reaction.

Dana Dolinoy: You know, but I hardly ever think about it. I, I'm surprised that that that's what came up today. But you know, if I hadn't done anything about it, maybe I would think about it a lot more than I do now.

Anne Chappelle: So thank you again for your time, Dana. And it's been a pleasure to learn more about what you do and what drives what you do. And it will make me think twice about how I discipline and stress out my children so they don't blame me when I need my own care in whatever transitional home I end up in.

Dana Dolinoy: Yep. Everything in moderation, right, guys?

David Faulkner: Absolutely, absolutely.

Dana Dolinoy: Thank you, Anne. And thank you, David. And thanks to the Society of Toxicology for putting on the Adverse Reactions. This is a really fun podcast. 

Anne Chappelle: So, David, what did you learn today? 

David Faulkner: I learned that I need to be a lot more careful about how much I'm eating, what I'm eating, how much I'm sleeping, because otherwise my kids could hold me liable for it.

Anne Chappelle: My kids already have.

And now for the teaser: on the next episode of Adverse Reactions. 

David Faulkner: "Speak Softly and Carry a Big Dataset." 

Anne Chappelle: "The Exposome."

David Faulkner: We talked to Dr. Darryl Hood of the Ohio State University.

Darryl Hood: Although physiologically, we have mechanisms that govern adverse outcome pathways, they are exacerbated by place. The reason why we haven't sort of made any significant progress on dampening disparate health outcomes in America is because we've been looking at this from a skewed perspective.

 Anne Chappelle: Thank you, all, for joining us for this episode of Adverse Reactions, presented by the Society of Toxicology. 

David Faulkner: And thank you to Dave Leve at Ma3stro Studios. 

Anne Chappelle: That's Ma3stro with a three, not an E.

David Faulkner: Who created and produced all the music for Adverse Reactions, including the theme song, "Decompose." 

Anne Chappelle: The viewpoints and information presented in Adverse Reactions represent those of the participating individuals. Although the Society of Toxicology holds the copyright to this production, it has, 

David Faulkner: definitely,

Anne Chappelle: not vetted or reviewed the information presented herein,

David Faulkner: nor does presenting and distributing this podcast represent any proposal or endorsement of any position by the Society.

Anne Chappelle: You can find out more information about the show at AdverseReactionsPodcast.com,

David Faulkner: and more information about the Society of Toxicology on Facebook, Instagram, LinkedIn, and Twitter. 

Anne Chappelle: I'm Anne Chappelle.

David Faulkner: And I'm David Faulkner. Hopefully, at least half of you make it back for the next episode.

Anne Chappelle: This podcast was approved by Anne's mom.