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10x Genomics Blog

*“You are what you eat.”* Many of us heard this phrase growing up, and there is a core of truth to it: what we put in our gut shapes who we are. Dr. Aaron Burberry is proving this old adage truer than we knew. Driven by his breakthroughs in understanding how gut-brain interactions can help deconvolute complex CNS disorders such as amyotrophic lateral sclerosis (ALS), the field is beginning to rethink how the gut microbiome can influence the brain in health and disease.

![2022 ECIA winner, Aaron Burberry, PhD, Assistant Professor at Case Western Reserve University](https://cdn.10xgenomics.com/image/upload/dpr_2.0,e_sharpen,f_auto,q_auto/v1663794678/blog/image_17.png)

While the field of researchers was competitive, Dr. Burberry was selected by our panel of neuroscience experts as the winner of the [2022 Early Career Investigator Award](https://pages.10xgenomics.com/es-2022-06-challenge-ra_n-ecia-neuroscience-challenge_lp-1-nomination.html). Read on to see where his career started, where his findings have taken him, and where he’s planning on going next.

#### Your research interests focus on connections between the gut microbiome, brain health, and neurodegenerative disease. What sparked your interest?

I can take a little bit of a historical approach. In my graduate studies, I worked with Gabriel Nuñez, MD at the University of Michigan, studying innate immunity with genes that influence Crohn’s disease. So having a background in looking at the gut, the interaction of the immune system with the gut microbiome, I really took a turn in my postdoc studies working with Kevin Eggan, PhD, at Harvard University, who has a focus on neurodegenerative diseases, particularly amyotrophic lateral sclerosis (ALS) and psychiatric diseases.

I thought I was going to be studying something quite different from what I’d studied in grad school. But we actually ended up making this serendipitous discovery in mice that have a mutation that mimics the most common mutation in ALS patients. The mice developed this neuroinflammatory phenotype when reared in certain environments but, when we moved this mouse model to a different facility, many of the inflammatory phenotypes became muted. This was very confusing to us and everyone in the rest of the field, until we looked carefully at what components of the gut microbiome differed in mice between these different institutions.

We reached out to the \[research] community, we did sequencing, and ultimately found there were differences in which bacteria were present in these different facilities. Animal facilities where animals get sick look more similar to each other than other animal facilities where animals were protected. We did a lot of functional studies to show that it was the gut microbiota that changed how sick these animals got. This launched us on this route to try and understand how different gut communities influence the immune system to change brain health. It was kind of a serendipitous discovery, but we’re very excited and we think there’s lots of questions to be asked.

#### So what are your current research projects, and what tools do you find yourself using?

We’re trying to look at this problem from two angles. We want to know how differences in gut microbial communities might influence brain health—the bacteria and microorganisms within the gut and how changes in that community structure might sensitize people to neuroinflammation. We’re also interested in understanding how these genes, whose mutation sensitizes humans to neurodegenerative disease, might influence the immune system, and how those immune cells respond to different gut bacteria.

So we’ve generated different model systems in mice and human induced pluripotent stem cells (iPSCs), where we’re trying to do those with different exposures. We take different bacterial communities and expose them to common mouse or cellular models, or expose them to different immune cells, and see the interactions between the host genotype and the microbial molecules.

#### I have to admit, as much as I’ve thought about the gut-brain axis, I hadn’t considered the opposite—how the brain may influence the gut microbiome.

Well, as we age, there’s a lot of things—behaviors, changes in diet, stress levels, chronic inflammation, etc—that may act in myriad ways to change the gut, that can circle back to change the nervous system. I don’t think anyone understands all the ways that’s happening, and you want to know all the different cell types in these compartments and how they’re changing in response to that.

#### What tools do you typically use in your work, and what do you think the biggest hurdles are in pushing this research forward?

We want to take a multimodal approach to understanding changes at the single cell level. Certainly we want to do single cell sequencing of whole cells and nuclei depending on the ease of dissociation of the tissues to understand how these different cellular communities change in their structure. There’s this underlying question of whether there are many different cell types within a tissue, such as the gut or brain, that are going to change in their abundance in response to a stimuli; or whether there’s a relatively few number of cells that change their transcriptional state to accommodate the challenges and keep organismal homeostasis.

I think that’s one of the more powerful ways that 10x Genomics single cell sequencing technology can help us understand the complex biology that’s going on. I think that needs to be overlaid with other measures; obviously, dissociating tissues and doing flow cytometry and protein measures on the cell surface to identify different cellular states or identities. Also newer technologies like mass cytometry, where we’re not limited to the range of fluorophores that we can pack into a flow cytometry panel.

For limitations: there are challenges with tissue processing. When you get into complex tissues that have extracellular matrices such as the gut and brain, you have to enzymatically dissociate them, add inhibitors, do it at higher temperatures, and try to limit degradation of RNA and cell damage. It’s something we all struggle with and we need to keep in mind that we want this pristine state of the cells, but processing itself changes the transcriptome. We know things like microglia are incredibly sensitive to dissociation.

#### On that note, some of our recent technologies actually enable single cell sequencing, spatial transcriptomics, and multiplexed in situ analyses in FFPE tissues to minimize dissociation concerns.

Right; that’s great! And if you have the fixed tissue you can go into archival human samples, and many different tissue repositories.

#### So what do you think is your most important finding, or the one you’re most proud of?

I am really proud of our fearlessness to chase down these differences in the gut microbiota in this mouse model. I’d go to meetings and we’d talk about our findings, and how sick the mice would get in our facility, and I’d have—in some instances—heated discussions of what other researchers would find, and what we’d find, and I feel like this is a microcosm of many different scientific fields. People are trying their hardest, they have well-controlled experiments, and even when you try to do things exactly the same way as others you get differences.

One way to interpret that is ‘they’re wrong, I’m right’, but it’s also possible that everybody’s right and there’s different factors influencing how the biology is changing. We could’ve accepted we’re never going to come to a resolution, but we wanted to learn something from this. We profiled what the environmental factors were, went through functional experiments, and nailed the fact it was a gut bacterial community.

I feel like this is influencing a lot of other animal studies and there are examples you can point to. One is the *SOD1* transgenic mouse model in ALS: another group showed that if these mice are treated with antibiotics, their phenotype gets much more severe. It raises this idea of a super common transgenic model studied for decades and decades in various people’s hands, but it can also be influenced by the gut microbiota. How does that influence the interpretation of this body of literature?

It also raises this idea that the gut microbiome will interact with these genotypes in many different ways. Whatever your animal model, or your human organoid system, it’s going to change the outcome based on the genotype of those cells, so you need to be aware of that.

#### What does receiving this award mean to you, and your research moving forward? Do you have any plans on how you want to use it?

It’s certainly an incredible honor that your group values the research direction we’re pursuing, and that how we’re addressing these questions is worthy of investment. I’m very proud of that. We want to use this technology to profile the different model systems: we’re going to perform fecal transplantations with different gut microbial communities into conventionally housed mice, into germ-free mice, then profile the gut, peripheral immune system, and brains of those animals. We want to see how those gut communities are changing the transcriptional profiles of these different tissues. Hopefully this will lead to new biomarkers in how the gut-brain axis influences brain health.

#### How has the field of neurodegenerative disease changed in the last few years, and how do you see it evolving over the next few years?

Science is driven by technology, and we’re doing much better at developing human cell model systems to study neurodegenerative diseases. Five or eight years ago, we could use iPSCs to make limited repertoires of neurons. But, now that we know more about genes and transcription factors expressed in different cell populations, we’ve been able to use that knowledge to direct differentiation of human cells into a myriad of cells that we can mirror in a dish. So now we can make increasingly complex models of human neurodegenerative diseases.

This highlights another limitation to these technologies. You want it to mimic human disease as closely as possible and evaluate how good our cell or organismal models are, so we need that gold standard of, ‘what do the cells look like in a human?’ Single cell sequencing technology is spectacular for this. It gives us a view into all the different transcriptional states of different human tissues that we can use as a benchmark. What we’re finding is that, even though we can model many of these different neuronal and glial cell types, in many cases we’re not giving them the maturation signals they need to adopt the adult program.

#### You’ve had a great career so far, so do you have any advice for researchers who are looking to delve into neuroscience?

The field is really exploding: there’s neuronal biology, immune biology, and environmental interactions. There’s a lot of new questions and research opportunities to pursue. People who are new to research get in through many different ways, and our first experiences can frame what we think we might want to pursue in the future.

I would say to young people: don’t let that limit you. If you’re excited about science, about answering new questions, and understanding more about human and organismal biology, keep an open mind. Go read those Nature and Science papers that have nothing to do with what you’re studying right now and just dream. Dream about what questions might be interesting to you.

Then go see who the best groups in the world are and how they’re trying to address those questions. Read their papers. Send them an e-mail. There are a lot more opportunities out there than you might know. I really appreciate umbrella programs in general for those going into graduate school, because a lot of times we don’t know what avenue we’re going to pursue. Having exposure to hundreds of different faculty members can be really powerful.

#### To wrap things up: congratulations again for the award, and thank you so much for doing this interview. Is there something you’d like to shout out or really emphasize while we have you here?

We here at [Case Western Reserve University](https://case.edu/medicine/pathology/faculty/aaron-burberry) are doing some top-notch science and there’s great overlap between neurodegenerative disease researchers, immunologists, gut digestive health programs, and it’s a stellar research institution. If there’s anyone reading who is interested in joining graduate studies, they should definitely consider here!

*While nominations for our [ECIA award](https://pages.10xgenomics.com/es-2022-06-challenge-ra_n-ecia-neuroscience-challenge_lp-1-nomination.html) are closed until next year, we hope to see you at Society for Neuroscience later this year—and be sure to submit your poster for our  SfN 2022 poster contest!*

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