Podcast – The Epigenetic Equation

Voice Over:

The Dementia Researcher podcast, talking careers, research, conference highlights, and so much more.

Dr Fiona Mclean:

Hello and welcome to the Dementia Researcher podcast. Today we're diving into a fascinating area of research, epigenetics research, and its role in Alzheimer's disease. We've got an incredible lineup of experts joining us to help unpack this complex but highly promising field, so stay tuned. I'm Dr. Fiona McLean, and it's great to be back guest-hosting the show. Our guests today are Dr. Josh Harvey, Dr. Sarah Marzi, Dr. Alexi Nott, and Dr. Sam Washer, each of whom brings a unique perspective and expertise in epigenetics and dementia research. Everyone say hello.

Dr Sarah Marzi:

Hello.

Dr Sam Washer:

Hello.

Dr Fiona Mclean:

We're going to do a proper introduction to everybody, so let's start with you, Josh.

Dr Josh Harvey:

My name is Josh Harvey. I'm a postdoctoral researcher at the University of Exeter in the dementia genomics team, which is under sort of the wider umbrella of the complex diseases epigenomics group. I finished my PhD about a year ago, and that was focused on an epigenetic modification called DNA methylation, specifically looking at a field of neurogenetic disease called the Lewy body diseases, and specifically looking at dementia within them. That included both sort of profiling the postmortem brains of people who passed away with this condition, as well as looking in the blood and testing whether the epigenetic profiles that we saw there potentially inform about individual level risk for cognitive impairment within Parkinson's disease. Now I'm starting a postdoc that's kind of just getting off the ground, where we're looking at epigenetics in relation to early onset for Alzheimer's disease with sort of a particular focus on an epigenetic mechanism set called microRNAs.

Dr Fiona Mclean:

Amazing. Thank you so much for that. Sarah, how about you go next?

Dr Sarah Marzi:

Hi everyone, I'm Sarah. I'm a senior lecturer at King's College London and a group leader within the UK Dementia Research Institute here, and I work on epigenetics across a number of neurodegenerative diseases including Alzheimer's, Parkinson's, and ALS. My research group is sort of 50/50 computational and experimental, and we use epigenetics to understand the cellular mechanisms of environmental risk factors and genetic risk factors, and how they make cells vulnerable and predispose them to neurodegenerative diseases.

Dr Fiona Mclean:

Fantastic. Next up we have Sam.

Dr Sam Washer:

Hi, so I'm Sam. I'm a postdoctoral research fellow at the Wellcome Trust Sanger Institute in Cambridge. I'm working in the cellular and gene editing research and development team, so I'm running CRISPR screens in a variety of different IPSC or stem cell models of Alzheimer's and Parkinson's disease. Looking at sort of linking how functional genetics can play a role in both understanding dementia and Alzheimer's, but also being sort of the next generation of therapies, hopefully. I'm looking at sort of how we can link the genetics and the epigenetics that we find to actually what is happening in the cells themselves, and how we can use these hopefully as a next generation of therapies.

Dr Fiona Mclean:

Amazing, thank you so much for that, and last but certainly not least, Alexi.

Dr Alexi Nott:

I'm Alexi. I'm a lecturer in the Department of Brain Sciences at Imperial. I am also a group leader within the UK Dementia Research Institute, and my research is ... Where I came from was looking at epigenetics in the context of genetic risk, was one of the studies, that showed that there's a genetic association of Alzheimer's disease with microglia. We're now trying to expand that to rarer cell types and hopefully cell states, and also to look at how this changes with ageing, so across the lifespan. The other thing we're interested in is looking at the context of epigenetics in disease states there, to try and understand the molecular mechanisms or the drivers that are driving gene expression changes in disease. We're mainly focused on Alzheimer's disease, but we do some work on Parkinson's disease collaborating with Sarah.

Dr Fiona Mclean:

Amazing. Thank you so much for that. We chose to focus on epigenetics today because it's an area that's generating a lot of buzz in the scientific community, and it has the potential to revolutionise how we understand diseases like Alzheimer's disease, but also Parkinson's disease and other neurodegenerative diseases as well, where traditional genetic approaches haven't given us the full picture. Today, that's what we're going to do. We're going to learn from our experts about this area. For those in our audience who might not be familiar with epigenetics, could one of you explain what it is and how it differs from traditional genetics? How about you, Sarah? You look like you're ready to go with that answer.

Dr Sarah Marzi:

All right, well, so traditional genetics is interested in the sequence of your genome. Every human has a unique genome, and even though the majority of our genome is the same between individuals and it sort of encodes that we are a human, that we have two arms, that we have two legs, and that we develop an amazing brain, there are millions of locations in the genome where the DNA sequence can vary. This is traditional genetics, and there's been a lot of research into finding sequence variants associated with diseases and quantifying how much of a disease is caused by genetics, so how heritable a disease is. Epigenetics is like a regulatory layer that acts on top of the genetic information, and that controls and orchestrates whether genes are expressed, how much of them is expressed, in what context they're expressed. These are biochemical modifications to the DNA and the proteins and RNAs around them that control gene expression. Now, the cool thing is that even though in our body, basically every single cell in our body has exactly the same DNA, and yet we have hundreds of different types of highly specialised cells that do very different things, and they produce very different proteins, and all of that is regulated and orchestrated by these epigenetic modifications.

Dr Fiona Mclean:

That was a really, really good explanation. I mean, in my head, so I'm not an expert in epigenetics at all, but I do some genomics. In my head, it's kind of like you have this DNA template, and that's kind of fixed, that's inherited from your parents, but then the epigenetic, it's kind of things that can change throughout your life. It can switch on at certain moments in your life, say, through development, or be switched off, and I guess that's where the environment comes in as well. Your own environment, and how that can influence it. It's really cool. I'm trying to think back to when I first heard about epigenetics. How long has it been around as a topic, do you think?

Dr Josh Harvey:

I think we've all kind of seen a lot of the classical studies that have been done in epigenetics, so there's these things called Waddington landscapes, which often get used to represent them, where it's sort of this massive plane with sort of slopes and balls on them. Essentially, it's supposed to represent how sort of the epigenome could specify an individual cell's function, as sort of a representation. It was done back in the days where you'd include hand ink-drawn images in your papers, so I don't know if that dates it specifically enough.

Dr Sarah Marzi:

I think it's first half of the 20th century, when this guy called Conrad Waddington was the first one to coin the term epigenetics. However, back then we didn't even know the structure of the DNA yet, right, and certainly didn't know any of the biochemistry of epigenetics. However, he coined it as a concept, as Josh said, to represent this sort of cellular differentiation cascade, how you go from this sort of potent stem cell that can become anything, and you sort of roll down this landscape and you become ever more specialised. For example, an embryonic stem cell going into a hematopoietic stem cell and then a certain blood cell lineage. I guess the idea was that it can only go one way, so once you're a hematopoietic stem cell, you're not going to go back and become a neuronal stem cell or something like that. Back then, he didn't know what mechanisms were controlling this.

That's, I guess, sort of been worked on maybe since the eighties, nineties, as a more broad molecular concept, but I'd say in the context of diseases and understanding how epigenetic regulation might link genetics to disease or what happens to epigenetic patterns in a disease context, that's more recent. Cancer has probably been the first field where epigenetics has been widely studied, because you get really quite global, striking changes in the epigenomes, especially in the DNA methylome in cancer, so they were sort of the pioneers of disease-associated epigenetic research, and then maybe in neurodegenerative diseases since 2010 or so, roughly, is when the first studies came. Yeah.

Dr Fiona Mclean:

Yeah, I love the idea in science, it happens more often than I think we realise, where concepts are actually thought of decades before the actual scientific experiments that are proof of concept actually come to fruition. I think that's so cool and so exciting, that people are able to think of these things and almost imagine them up, and then they actually turn out to be real, and how the body or the cells do work is so, so cool. Now that we've talked a little bit about epigenetics and how it's different from traditional genetics, why is epigenetics such a crucial area of study when it comes to understanding dementia-related diseases such as Alzheimer's? Alexi, what do you think?

Dr Alexi Nott:

Why is it essential? That's a good question. I guess there's two sides of it. Part of it is, I mean, depending on the disease you're interested in and the genetic heritability of that disease, if the disease is very heritable, people have done these genome-wide dissociation studies where they try to identify DNA changes. They're normally common variants or common changes that occur in the DNA, but that might occur more commonly in the disease group than the control group. These are called risk variants, or changes to the DNA that are associated with increased risk for disease. The challenge with these studies, and it's great. A lot of these studies for Alzheimer's disease, for example, have identified thousands of changes that are associated with an increased risk of disease, but the challenge is, a lot of these DNA changes don't happen within the genes themselves, so they don't happen within the coding regions.

One of the problems is, it's hard to identify what is the impact of these DNA changes themselves, and also, as Sarah said at the beginning, these genetic studies are just looking at genomic DNA, which is effectively the same code in every single cell type. It doesn't give you any information regarding the cell types that will be impacted. By looking at the epigenome, so the idea is that if they're not directly affecting the genes, perhaps they're affecting these, what we could call epigenetic switches. They're called enhancers, that help to determine whether genes are switched on or off or how highly they're expressed, and are extremely cell type specific. The idea here is that by studying the epigenome of different cell types, we can try to begin to understand which cell types will be impacted. The other thing we can do, which is a little bit more complicated, is look at how the DNA is folded to try and link these enhancer or these epigenetic switches to the target genes, so that way, we can also look and try and understand the gene targets. That's one aspect, and there are other things you can do as well. I don't know if ... I mean, this is my main interest, but other people, there are many things you can do with epigenetics. I don't know if anyone wants to jump in.

Dr Fiona Mclean:

Absolutely. I think, so one thing we haven't actually touched on yet, and it got mentioned in our intros, is the types of epigenetic changes. For Sam, what are the different types of epigenetic changes that can happen? What's your favourite one?

Dr Sam Washer:

There's many different types of epigenetic changes you get. I think Sarah already touched on the DNA methylation, is one of them. This way, you get the addition of a methyl group on cytosine guanine dinucleotide. Usually this happens in gene promoters, which either turns on genes or turns off genes, dependent on if they're there or not. I mean, I did my PhD on it, so I'm very biassed. I think that's one of the coolest ones. Then you've also got the next level, so that's very much at the gene level, DNA level, bound to DNA. You've then also got histone modifications. Now, these are all about sort of, how does DNA itself wrap itself into a single cell? All your cells have got this meter's length of DNA wrapped up in them, and that's through histones. These are modifications where you get the wrapping of the DNA around these histone proteins, and then modified to open or close DNA to allow genes to be turned on or turned off. These are really cool.

Josh is also, he's mentioned he's looking at the long non-coding RNAs, so these are other ways where you're regulating gene expression through binding to RNA, turning it on, turning it off. I could go on. There's loads of them. I just think they're all really fun. I mean, I'm a functional geneticist. I think how all these things interact and how gene expression changes and what effect that has on the phenotype is just really important.

Dr Fiona Mclean:

It's super fascinating. You've mentioned something, long non-coding RNAs. Josh, do you want to tell us a little bit, since Sam says that you love them? Do you want tell us a little bit about what are they, and how do they fit into the picture of DNA and our genome as a whole?

Dr Josh Harvey:

You hit the nail on the head. I do find them really interesting. I think they might be my favourite epigenetic mechanism. In sort of the classical view of how genes are expressed, you get your gene sort of region of the DNA, this is transcribed into forming RNA, and then that RNA goes on to code or is translated through to a functional protein. Non-coding RNAs are a really cool set of RNAs which don't function primarily through the protein that they encode. They function primarily as RNAs themselves, and there's a few different kind of ways they can kind of work. There's long non-coding RNAs, which is sort of larger RNA transcripts. There's a circular RNAs, which are kind of these massive circular structures of RNA which mop up tonnes of other gene transcribing RNA molecules. Then there's one which I find particularly interesting, which is microRNAs, which are these really tiny, only 22 nucleotides in length, usually, and they bind sort of quite specifically to a number of genes and kind of act to regulate their expression, usually sort of through a silencing method. They kind of bind to that RNA that will go on to form a protein and decrease its overall expression.

Dr Fiona Mclean:

I actually think that's such a good synopsis on ... What do you call them as a collective? All the sort of, long, circular, what would you call them? Just non-coding RNA?

Dr Josh Harvey:

Yeah, non-coding RNAs. Yeah.

Dr Fiona Mclean:

Non-coding RNAs. Cool. Thank you so much for that. It's a really good explanation. For me, I've noticed that that's an area that's really crept up in the last few years as being really popular and really interesting. I mean, some of you will know, I sit in a sort of cross-field. I sit in type two diabetes research and in Alzheimer's research, and in both those fields, it's a massive interest area that's on the rise. In terms of sort of the most exciting findings that are coming out of epigenetics, and Alexi, what are sort of the forefront exciting areas that are coming out in Alzheimer's in this area in the last sort of year or so?

Dr Alexi Nott:

Okay, so I guess some of the exciting studies that are coming out, I'm a little bit biassed again because this is an area that I'm involved in, but there were a number of studies that, on one angle, showed that in terms of epigenetics, that there is a genetic association of immune cells in Alzheimer's disease. This was kind of unexpected. In terms of, I guess, genetics in terms of familial Alzheimer's disease, you see genes such as APPs, amyloid processing protein, and two other genes, presenilin-1 and presenilin-2, that are important for processing amyloid, and amyloid is what makes the plaques in the brain in Alzheimer's disease. This has led to the whole amyloid hypothesis, which is very kind of protein-centric, but also was thought to be very kind of linked to neurons and why neurons might be dying in the brain.

I guess a lot of research focus at the beginning was focused on neurons as being the important cell type for Alzheimer's disease, and obviously it is important, because neurons are lost, neuronal connections are lost, and that's probably really what leads to loss of memory, but in terms of late onset Alzheimer's disease, which is the majority of people who get the disease, the genetics is actually pointing towards immune cells. The concept was made more concrete through the studies that looked at the epigenome of these cell types, because it's really, these genetic components are in the non-coding regions of the genome and that's where the epigenetics is important. I feel like it was a turning point in the field in terms of understanding the importance of the immune system, and thinking of Alzheimer's disease as a neuro-immune disorder, almost.

Dr Fiona Mclean:

Absolutely. I mean, there's a lot of excitement around Alzheimer's disease and a potential vaccine for Alzheimer's disease, and the links of the immune system cells, so it's quite interesting to see how these areas are actually sort of coming up at the same time. You don't need to defend not being a neuron fan, because I love endothelial cells.

Dr Alexi Nott:

[inaudible 00:19:12].

Dr Fiona Mclean:

Neurons are fine. I like a neuron. They look really pretty down the microscope, but I love the endothelial cells, and I think we had a discussion in one of our other podcasts on favourite cell types. Sarah, what's your favourite cell type again? I think we had a chat about it.

Dr Sarah Marzi:

Do I have a favourite? I mean, I also like microglia, to be honest. They are fascinating and they're epigenetically highly responsive, as you would sort of expect from an immune cell type, because maybe immune cells are particularly prone to be context dependent and to have a need to be activated and to sort of punctually and morphologically shift under inflammatory infection contexts.

Dr Fiona Mclean:

That's a really interesting point, actually. Yeah, are cell types that need to be more responsive and flexible to the environment, are they more epigenetics susceptible, if that makes sense? That kind of actually leads me onto my next question, Sarah, which is around how we hear a lot about how lifestyle factors like diet and stress and exercise might influence dementia and Alzheimer's risk. How do these environmental factors impact epigenetic changes?

Dr Sarah Marzi:

This is a million dollar cost, really, and I think we're in the early days of discovering the mechanisms underlying these associations. What seems to be quite clear from a number of different studies, both in model systems and in humans, is that a lot of environmental factors can have quite dramatic effects on the epigenome. One big example in humans is that smoking, cigarette smoking, is associated with very vast changes in DNA methylation, in particular, across a number of different cell types and tissues. In fact, so much so that if you look at the blood epigenome of a person, you can say whether they're a smoker or not, and probably also roughly how much they smoke, which is pretty fascinating. I'd say this is also true for other environmental factors, but it's harder to study. Smoking is easier to quantify than some other environmental exposures.

Diet is another one where it's kind of somewhat obvious that there are quite direct links to the epigenome. For example, some of the things that we consumed through our diet are required for epigenetic machinery to function. For example, if you want to methylate positions in the genome, then the enzymes that do this, the DNA methyltransferases, they need a methyl donor, so a molecule that gives them a methyl group which they can then add. A lot of that is actually taken up through the diet, for example, through folate and the folate metabolism. It's been shown that depending on what you eat, if you're heavily deficient in some of these nutrients, then you're going to have a global impact on the epigenome. For some other environmental factors, it's more subtle and it's very region specific, the changes that can happen.

I think a lot of epigenetic changes that we see a response to environments are probably evolutionarily adaptive. They're happening because they were meaningful in some contexts, but sometimes they become maladaptive under the environment that they're in. For example, if you get continuous extreme up-regulation of certain immune cells, like the microglia in your brain, that might predispose them to become kind of a bit more hyper-excitable, and in the long run that can be a bad thing for your brain, even though in general it's good to have immune cells in your brain, and they play a very protective and even homeostatic support role that is needed at baseline, even, but under certain conditions some of these protective factors can become maladaptive.

Dr Fiona Mclean:

Just to sort of bring it back to a question we were talking earlier around genetics that are inherited versus epigenetics and environment, can you inherit epigenetic changes from your parents, or is that all sort of once you exist?

Dr Sarah Marzi:

Do you want me to take this? I actually ... I am sort of, I had a different AES in my scientific career during my postdoc years, where I worked on this question of trans-generational epigenetics, as they call it. It was very trendy at the time, but it was and still is quite controversial. This is the idea basically that an acquired change in an epigenome from the parents can be passed on through the germline to their offspring. For example, if your parent eats a terrible diet and is obese, and say, becomes glucose-resistant, do they pass the propensity, the epigenetic change associated with that, onto their child? It's a very difficult question and it's nearly a possible to study in humans because you can't do controlled experiments through multiple generations. What seems to be clear is that what happens as an embryo develops in utero is that there can be a lot of permanent effects, and sort of what's happening in development seems to shape the whole life, certainly into adulthood until the end of life.

If you're in utero and you're developing as an embryo and you're nutrient deficient, for example, that's going to have long-term consequences on your epigenome and on your long-term health and your metabolism, and the way you process food. There are a few studies of trans-generational epigenetic inheritance. It's been pretty well demonstrated in some species like plants, definitely Arabidopsis. There are some great experiments that show plants have this trans-generational epigenetic adaptation. If you think about it, it sort of makes sense, because plants can't really remove themselves from their environment, so maybe they need an additional adaptive mechanism that acts faster than evolution. There are a few studies on mice, but none of them have actually really been replicated very well, so not sure whether they do or not. I think this year, there was a pretty convincing one from nematodes, from C elegans, that showed trans-generational inheritance patterns, but it's very hard to say from a study like that whether this is something that happens in humans as well.

Dr Fiona Mclean:

Yeah, it's really ... I wonder if there's been twin studies of identical twins, and I guess epigenetics would be a way of explaining why identical twins maybe end up developing different diseases. Can be explained through epigenetics, because they start with the same sort of genetic baseline, so to say. Really fascinating stuff. A question for Sam now. What are some of the key challenges with studying epigenetics, and are there any new tools or technologies that are helping to sort of address these challenges in order to research epigenetics?

Dr Sam Washer:

I think one of the biggest challenges we always get asked when we're studying epigenetics is, is it actually causal or is it as a result of the disease? It's always trying to work out ... It's like the chicken and egg situation. Which came first? Was it the epigenetic change or was it the disease that then resulted in the epigenetic change? Trying to work out this causality and this direction of causality is going to be really important if we're going to be able to kind of study and work out what's actually going on. There've been some really good developments in the last couple of years. I mean, I'm a CRISPR nut, I'm a real fan on anything genetic editing or anything epigenetic editing, and there's been some real breakthroughs in the last couple of years on this side of things, for studying it. I was doing some work on, everyone's heard of CRISPR-Cas9, the molecular scissors that actually cut DNA, but there are actually lots of cool modifications that we can now do to this system where we can actually mutate the Cas9 so it no longer cuts DNA, but it can actually deliver other proteins to specific regions of the DNA themselves.

What we can do is we can now start to deliver these DNA methylation editors to specific sites within the DNA, so a gene promoter or a target site that we get from these studies, edit it in a way that we can either remove or add these changes, and actually physically see what is actually happening to gene expression changes in real time. We can do this. We can then work out, is it the epigenetic change which is giving us the result, or is it something different? Is it actually as a result of the disease? The other thing we can do is we can couple this also to the histone modifications as well, so we don't also get the methylation editors. You also get the histone modifiers, so these are ones where you can change histone accessibility. What we're able to do is we're able to do these sort of big, big screens where we can look at sort of activation and repression of different promoters, different genes, to see how these are regulated through those kind of mechanisms.

Hopefully, we're going to get to the point where we can actually also start looking. Now we've got prime editing, which is the next generation, where we can start looking at the genetic-epigenetic interaction. We can now start to mutate individual bases, so you're looking at the genetic interplay, and see how that affects the methylation and see how that affects gene expression, and then hopefully a phenotype. These are all really cool, novel, new techniques that are just sort of kicking up and going on. What would interest Josh is, actually, there are new methods now ... There's a new Cas found every week in bacteria. They're being published all the time. My favourite one at the moment is 7-11, which is used to target RNA. We could find a potential therapy where we could find a non-coding RNA or something like that, and then we could target these epigenetic editors to either destroy this RNA or activate it. It's a really cool kind of way that we could be looking at sort of how we can ... It's always, how and why does this cause the disease, and how can we actually change that progression? That's always the question. Well, it's on my mind, anyway.

Dr Josh Harvey:

I think it's something the field is really calling out for at the moment, is, we've had so many discovery studies now, we can really show clear reproducible signals in the epigenome beginning at a bulk level, so looking at an average methylation or histone modification profile across a tissue. Then, with Sarah and Alexi's work, kind of define that down to, okay, which cell types in the brain or in your tissues of interest are those actually happening? Sort of now, I think we're beginning to see the beginning of kind of the functional side and actually trying to un-tease that cause and effect, between the two.

Dr Fiona Mclean:

Sam and Josh, you've both kind of touched on the next question that was in my head, which was, how do we or how do you see the field of epigenetics being translated into therapeutics for, I mean, Alzheimer's, but all sorts of diseases? How do you see that working? Another tricky question maybe to add onto to it, around sort of, we're talking about gene editing, is, what are the ethical implications of those treatments? If you're going in and editing someone's genes, how do you see that? I would ask Josh first.

Dr Josh Harvey:

I think I'll give a slightly different perspective from Sam, and I'm keen to hear about some of the more CRISPR sides, but I think, at least from what I see in the field at the moment in terms of exciting stuff for potential translatabilities with some of that sort of microRNA work and some of those non-coding RNAs, if you think about how microRNA works, it's a short nucleotide sequence that binds to and inhibits the expression of another RNA molecule. We're actually already being sort of introduced to clinical trials in a very similar sort of domain with things like antisense oligonucleotides, which function quite similarly on a basic level. They are different and they do function differently. They're synthetically derived to do a similar kind of function, whereas a microRNA in sort of this biological context actually affects a number of different genes. Antisense oligonucleotides are already kind of going through to clinical trial and implementation.

If anyone went to AAC this year, there was a fantastic keynote speech from Timothy Miller who was showing some of the results from that, from I believe ALS and some sort of tau-specific isoform work there. You could viably kind of think about modulating an epigenetic signature on the non-coding level, in a similar way. It's targeting these RNA kind of classes in the cytoplasm in the same way that you would a coding transcript. You could potentially look at a modification on the regulatory level in a similar way by targeting some of these microRNAs or these longer non-coding RNAs. In other diseases as well, this is kind of beginning to be introduced. There are some microRNA targeting interference and antisense kind of trials which are going on. Not to my knowledge yet in sort of neurodegeneration and dementia, but watch this space and I think this might come into the field. I'll hand over to Sam.

Dr Sam Washer:

It's always a question I get asked whenever I talk about CRISPR, is the ethics of it, and I think we've got to be very careful with what we get into. I would just like to start by saying that we've had the first actual treatment for a genetic disease in the last year that's been approved by the US and the UK, which for sickle cell anaemia and beta thalassemia, and that's a breakthrough. This is technology that was 10 years old that is now actually going to be able to be a one and done treatment for these people. I think that if we can sort of do this in Alzheimer's, then that would be incredible. The stuff that Josh was talking about, these RNA inhibitors and these ASOs and stuff like that, these are still drugs you're probably going to be having to take for the rest of your life. Whereas, with the sort of genetic editing and stuff like that, it's a one and ... You go into hospital, you have some stem cells taken, you get them edited, put them back in, it's done.

Again, the issues around that is, at the moment, we still don't really understand DNA repair pathways. This is one of the things that we're really, for the genetic side anyway, we still don't know how the DNA repairs, and we also still have off-target effects with these sort of things. We've got to be really careful with our pre-screening, in our clinical aspects, so when we're doing the, growing the stem cells and that sort of thing, we've got to make sure that we're not creating any deleterious sort of mutations as sort of a by-product of our editing. I think the field's got a little bit more to go with this. I don't think we're going to be able to get there with Alzheimer's for a little bit with that, but I think with the epigenetics, what's really cool about that is you're not actually editing the genome, as such. You're not worrying about changing DNA that could potentially not be reversible, whereas with the epigenome, as we've been discussing, you can change it, it can go ... It's a very fluid state.

With these sort of drugs or anything that we're going to do with the therapies, we're actually hopefully going to be able to reverse these changes, if anything does happen that's wrong. Again, it could be that you're taking a drug for a long time. It depends on sort of when we're giving these drugs, as well, to the patients, because obviously we want to try and get people early on, and then that links into sort of diagnostic issues as well. How do we diagnose people a lot earlier to get these treatments in? Yeah, long-winded thing. Ethically, I think that we're not at the point yet where we can say we can do it for Alzheimer's, because then also we get into the concern around consent as well. Then we're getting into, if you're doing someone with late onset Alzheimer's, or it's quite late and they aren't able to give their consent on this sort of stuff, then that's obviously not what we want to be doing.

Dr Fiona Mclean:

Yeah, I think that's a challenge across a lot of clinical trials with diseases which have a cognitive component to them, because it's getting that consent, but also catching people early enough that the treatments have a chance to work. I think the field seems to have come to a relatively, a consensus that prevention is better than cure. Being able to capture the disease early and being able to treat people early and stop the damage that then leads to the cognitive impairment and the other symptoms we see is probably key. It's interesting that actually, it's probably the same in terms of any sort of epigenetic approach to treating the diseases. It actually comes down to that kind capturing the disease in an early state, to treat it. I guess, can epigenetics, do you think there's a place for it in diagnostic, then, as biomarkers? It was interesting, Sarah, you mentioned, I think it was the blood epigenome. Is that happening?

Dr Sarah Marzi:

There's a lot of work into that. My own work is mainly on the brain itself, and brain epigenetics I don't think is ever going to be a useful biomarker in the sense that you're not going to take a piece of brain and look at that. However, there might be changes that are correlated or that are happening throughout multiple cell types in the body that you can pick up in the blood already. One thing that's not been done yet but that I think has quite a lot of promise is cell-free DNA. Basically, when cells die, the DNA is discarded and a lot of it is mopped out by clean-up cells like the microglia or other macrophages, but some of it might enter your bloodstream.

One of the opportunities could be picking up some of that cell-free DNA that's swimming around in your blood, and because, as we've heard from Alexi before, the epigenomes of different cell types are super highly cell type specific, so you could be looking at, say, the DNA methylation of those little fragments of DNA, and potentially you could be saying, "This is coming from a glutamatergic neuron," or whatever. You could maybe even very specifically pinpoint the type of neuron, and you could be picking up neurodegeneration starting much earlier than you would develop the clinical symptoms. I mean, I'm sure this has been discussed in other podcasts, but one of the big challenges of treating Alzheimer's disease is that the clinical symptoms ... At the time point when you get forgetfulness in Alzheimer's disease, or other cognitive or personality-wise symptoms of disease, that happens so much later than the actual degeneration starts. By the time in Alzheimer's that you notice that anything is going wrong, you probably have had cells dying in your brain for a decade, at least. I do think there is potential. I think there are a number of real technical challenges that need to be overcome for that to become feasible and high throughput and everything, but it's super promising.

Dr Fiona Mclean:

I heard that Sam's going to fix all the technical stuff anyway, so ...

Dr Sam Washer:

I'm going to try. I'm going to just jump in with what Sarah was saying. I think with the diagnostic side of things, I think that the epigenetics is going to be used as part of a toolkit, along with everything else. I think we're going to see, we're going to get to a point where we've got loads of ... It's like you've got a load of overlapping Venn diagrams. I think we're going to have lots of different things. We're going to have the PET scans, we're going to have the blood work, we're going to have the DNA, we're going to have the epigenome, we're going to have environmental factors, we're going to have everything all linking together, to give us this mega diagnostic criteria. I never think the diagnostics just one field against another. It's not the epigeneticist against the geneticist, against the metabolic. It's always, we're all together, we're all pieces of the same puzzle trying to work out what's going on.

Dr Fiona Mclean:

Absolutely, couldn't agree more, and I think, I mean, from where I see it, from sort of the diabetes sort of field, is, I very much want to sort of be able to find people who are at risk and to stop them going down that route. Actually, you maybe don't have Alzheimer's yet and you wouldn't be diagnosed with Alzheimer's, but you would be found as a sort of high risk individual and then you can have interventions to stop you going down that route. That's kind of how I'd love to see it, and it's really interesting to see how epigenetics could actually play a role in that and help to sort of stop people before they head towards dementia.

Dr Josh Harvey:

Yeah, it's been an active bit of research for us as well. It's interesting you mentioned diabetes, as well, and Sam as well sort of mentioning it being used as a tool on top of other things. Sarah, you also mentioned that epigenetics is quite good at predicting certain things, but others, actually it's maybe a bit poor, and a lot of studies using epigenetics as a classifier and as a biomarker potentially is that on its own, at the moment. At least when you look at it in blood, it struggles to perform, but what we've been kind of doing in the group a bit is looking at whether we can use it as measures for proxy for other risk factors. That includes things like smoking, which we mentioned before, which you can calculate pretty accurately, but also things like diabetes, which you can also actually classify quite accurately from the blood methylome.

You can kind of use these to construct multiple methylation risk scores, and what we've kind of shown in some of our previous publications, one of my supervisors, Ehsan Pishva, published a paper on this very recently, is using these multiple risk scores, the kind of classical Alzheimer's risk factors as captured in the methylome, when added on top of things like CSF biomarkers and like the genetics, you do actually get an insight and a better, more specific classification of individuals at risk, both of cognitive decline and a kind of cross-sectional dementia diagnosis. Yeah, I think it's definitely a field with room to grow, and hopefully something that's used on top of other aspects.

Dr Fiona Mclean:

That sounds great, and if you're interested in diabetes, we should talk, because-

Dr Josh Harvey:

[inaudible 00:42:06].

Dr Fiona Mclean:

Well, I do love diabetes. It's my interest, it's my research interest, so absolutely. That's so fascinating. I guess, yeah, so we're talking about treatments and the ethical considerations, and I guess the public's understanding of genetics is already quite complex, although I feel it's getting a wee bit better, although that's maybe through stuff like ... You know when you send off your DNA and it tells you you're 33% cat or whatever? I feel like people are starting to grasp what your genome is a bit more, but how do you think the public can better understand epigenetics, and how can we improve public awareness in relation to epigenetics and the role that it can play in brain health overall? Alexi, I'm going to come to you first.

Dr Alexi Nott:

Yeah, that's an interesting question. I feel like doing things like what we're doing at the moment would help. Things like podcasts and public engagement would definitely help wider understanding. We did try one year here, Imperial has this great exhibition, really a festival, where it's completely open to all of the public, and there you kind of have to really think about how to communicate your science so that people can understand it, who are kids through to elderly people, people coming with their families. To be able to, one, explain what epigenetics is, and then also, like you said, explain the impact that could have on the disease and the possible benefits. I can't give you an answer, but we need to keep trying. I guess we need to do more, but a forum such as that would be a good place to do it, and I think podcasts is also a great forum, but maybe we could do a more lay version of this, what we're doing today.

Dr Fiona Mclean:

Everyone listening to this will obviously agree that podcasts are great. I think we should get in contact with the BBC and tell them to add it into Who Do You Think You Are, and be like, "You need to look at the epigenome, not just the records."

Dr Sam Washer:

On this, I was at a conference last year and one of the questions was, "How could we make genetics sexy to people? How could we make it better to the lay audience?" Because, they were saying that physics have got Brian Cox, maths have got Hannah Fry. There's no one out there who's being that person in the genetics field.

Dr Fiona Mclean:

Adam Rutherford.

Dr Josh Harvey:

That's who I was thinking as well.

Dr Fiona Mclean:

Is anyone just going away to Google Adam Rutherford?

Dr Josh Harvey:

I guess there's scales.

Dr Fiona Mclean:

Apparently he's the sexy guy in genetics. Wait, genetics or epigenetics?

Dr Sarah Marzi:

No epigenetics person.

Dr Fiona Mclean:

Well, all four of you could apply to be that person.

Dr Sarah Marzi:

How do I apply for this?

Dr Fiona Mclean:

I don't know who you apply to, but ... Oh, brilliant.

Dr Sarah Marzi:

I think the other thing that's quite important is that as you do publish studies, if they're interesting, they quite often do get dissected by the media and your universities will have media comms teams that help compose a press release. I do think that has an impact, because some of that really goes out into mainstream media and newspapers. Trying to explain it well and in simple terms, but also correctly, because I do see it get over-hyped and sort of make some slightly not so correct statements sometimes, at the time, because it sounds sexy or whatever and it sells well. That's a fine balance. I think as we see more epigenetics research, hopefully more of it will also make it into the mainstream media, and hopefully in a way that is educational and yet correct.

Dr Fiona Mclean:

I think it's so difficult, because there's currently no cure. I think the media love a headline, and I think we have seen that with the new treatments that are coming through for Alzheimer's. I've seen the headline, Cure for Alzheimer's, plastered across so many newspaper websites, and then you read into it. Because we sit in the field, we know that, okay, there are treatments that have come out. However, there are caveats, there's side effects and they're very difficult to deliver, and the impact of them can be minimal. Yeah, I think it's difficult to manage expectations with the media. I think that's such a challenge. I don't think the media are always going to take stories and hype them up, which, it can be good in some ways to keep momentum going and public awareness going, because I mean, I'm sure all of us have been funded by charity research at some point, and getting the public behind this type of research is so important to keep momentum going in these fields.

Finally, just to start wrapping this up, what do each of you sort of see as the future of epigenetic research in dementia and Alzheimer's disease? Even if you don't know it yet, what do you wish to happen? Let's start with Josh.

Dr Josh Harvey:

Yeah, I mean, we've already touched upon one of the ones I think I would've put here, which is sort of epigenetic classifiers and biomarkers. I think that is definitely a field ripe for development. I guess another one is, there's been huge leaps forward about understanding the cell specific nature of a number of different epigenetic marks, but I guess there's still a whole kind of dark matter of the epigenome, which, because of current profiling methods and technologies, can't really be looked into as easily. Current commercially available methods are able to characterise some things on a cell specific level, like chromatin accessibility, for example, but stuff like microRNA, which I keep harping on about, really struggles with these kind of commercially available cell specific methods. There's been, I feel like every week there's a new technology coming out in Nature Methods that kind of talks about developing new ways of looking at these marks on a single cell level. I think we're really going to start piecing together a cell specific profile and understanding on multiple epigenetic levels in relation to all of these kind of pathologies, which I'm quite excited to see.

Dr Fiona Mclean:

I know some people are tired of single cell, but I'm not. I love single cell work, and so yeah, looking at the epigenetics of single cells would be super cool too. Sam, what about you?

Dr Sam Washer:

I think it's going to be both the discovery, so the link between how the methylation or the epigenetic marker actually influences the gene expression, and more importantly, which gene they're actually influencing. We still don't really know. We sometimes assume that it's always the nearest one, because everyone seems to think that, my analogy for this is that DNA is like dried spaghetti, when actually it's like boiled spaghetti, because everything ... It's all touching everywhere else. You've got genes influencing genes further away, so until we can actually understand and identify these new targets which these epigenetic effects are implementing, how are we going to be able to develop the therapies? I think that discovery in the first place is going to be the kind of key thing that I'm looking forward to.

Dr Fiona Mclean:

I love that analogy. It's like boiled spaghetti, it's all mixed up. That's how I'm going to think of DNA from now on. Yeah, I actually guess I never thought. Yeah, can the targeting of epigenetics, can it be random? Can there just be methyl groups that just go wherever, or is it super targeted? That might be a naive question.

Dr Sam Washer:

No, so this is one of the biggest problems we've had with some of these early epigenetic editors, is actually, because like Alexi was saying at the beginning, a lot of these modifications and changes are actually in non-coding regions, and these are highly repetitive sequences. When we design our guide RNA sequences, usually these are 20 base pairs long, and the problem you have then is in these regions where you have these epigenetic modifiers, they're highly repetitive sequences. What you can see, when we did some experiments with these early epigenetic editors, is actually the off-target effects are massive. We need to kind of be working on these new techniques to kind of reduce that before we can kind of get anywhere with kind of working out what's happening within the cell anyway. Yeah, it's a great, great question.

Dr Fiona Mclean:

How cool are cells? They can just be like, "Yeah, I'm going to just do all this epigenetics and do a bunch of other things, and it's all good." Cells are so cool. Back to our original question. Yeah, Alexi, where do you see the epigenetic field going?

Dr Alexi Nott:

I guess what I have been thinking about a lot, and I still don't know how possible it is or where it will go exactly, is the translatability, right? This is what I get asked a lot. How can you translate these concepts and findings that will be beneficial to patients? I think epigenetics has a huge potential, because it is extremely cell type specific. We were talking about off-target effects of genetic approaches, because you're basically affecting the function of a given gene in every cell type, but with the epigenetic approaches, say one gene that could be expressed in all the cell types of the brain, but you know it's dysregulated specifically in immune cells or in neurons, and you really want to target it in just that one cell type, the epigenome provides you a tool to be able to do that. Because, normally these epigenetic switches, you think of it as like a switch of a light bulb, is normally extremely cell type specific. The biggest challenge there is, how do you control the switch, right? How do you switch it on and off? We were talking about tools and ways to do that, but that's not as easy as it sounds.

The other direction, so that's kind of taking a gene and a target approach. The other way I think epigenetics will be super useful is as a potential tool to deliver cargoes. The idea here is to use, say, enhanced AAVs or epigenetic guided AAVs, where you can try to better target specific cell types, but then you can also think of subtypes of cells. If you can think of, "I want to target immune cells that are activated in the context of disease," and these cells might also be kind of switching on specific epigenetic switches. Might be able to, you could use it as a tool to deliver a cargo to a specific subtype of a specific cell type, and it could be age associated, disease associated, all of these things. I think this is the future. How are we going to get there?

Dr Fiona Mclean:

Fingers crossed. Absolutely. Lastly, Sarah, where do you see? What's the one hope for the future of epigenetics?

Dr Sarah Marzi:

Thanks for giving me the most challenging position, after everything intelligent has already been said. What I was thinking, and it sort of touches on aspects that have been mentioned by almost everyone here. My thing is, as I've mentioned also, what's mechanistic in the brain, what links the environment and the genetics to the disease, and how can we modify that? Maybe this is a little bit more immediate and not quite as outrageously in the future as what Alexi was describing, but one thing that we haven't talked about in terms of therapeutics is we might use the epigenetics not necessarily to find an epigenetic therapy and target an epigenetic mechanism, but it might tell us about a regulatory molecule that already exists, like a transcription factor, that might regulate, say, a whole number, 200 genes or whatever, 20 genes, a number of target genes and regions. Then we can start to target that transcription factor with whatever approaches, be it pharmacologically or with some other molecules. I think for some transcription factors, there are known pharmacological activators or repressors, and so once we identify those upstream regulators, there is actually a really feasible case for starting to target and think about delivery of those molecules as well.

Dr Fiona Mclean:

Amazing. Thank you so much for your answers. Well, as I had said at the start of the show, we chose to focus on epigenetics today because it's an area that's generating a lot of buzz in the scientific community. From what I have heard from you all today, epigenetics is essentially the study of how environmental and lifestyle factors can influence which genes are turned on or off without actually changing the DNA sequence itself. What's really exciting is that this field has the potential to revolutionise how we understand diseases like Alzheimer's disease, where traditional genetic approaches haven't given us the full picture. By looking at the epigenetic landscape, we might be able to identify new risk factors and develop more targeted treatments and maybe even find ways to prevent the disease altogether. It's an incredibly exciting time for this research, and we're so fortunate to have brilliant minds like our wonderful guests today working on this area of research.

One last question before we finish, and it's a fun one. If you could choose any historical figure, living or dead, to have their epigenome studied, who would it be and why? Let's go to Alexi first.

Dr Alexi Nott:

Let's go back to the first human. I've chosen Lucy, who's the first humanoid, because I thought her genome would be very different, so maybe from the epigenome, if we could get some cell type information, we could see what genes are switched on or off in particular cell types. I then took it a little step further and looked to see if they mapped the genome of Lucy, and apparently it's impossible from her fossilised bones, so that's a bit of a downer on that one.

Dr Fiona Mclean:

I was so excited for your Nature paper. I'm so sorry that that's not going to happen, though. That is a fantastic answer, and so good luck, Sarah. What do you think?

Dr Sarah Marzi:

Unlike Alexi, I did not look at the questions beforehand. No, I don't have any specific historic figure in mind, but what I would be really intrigued to look at is someone ... There are people who have a lot of protein pathology in their brain like aggregation of amyloid, but don't display any clinical symptoms. I think that is a super fascinating population where we really need to understand more about what's going on in different cell types in the brains. How are the different cell types interacting with those protein aggregates? Are the neurons just more protected through some gene regulatory mechanisms, or is it the other cells surrounding it? Pick someone with a high pathology, protein pathology load, and no clinical symptoms.

Dr Fiona Mclean:

I also think about those people quite a lot. I'm like, "What's going on? How are you doing it?" That's another really good answer. Josh, you next.

Dr Josh Harvey:

Yeah, my mind also sort of went to resilience when I saw this question, and sort of people who were aged and didn't necessarily have those cognitive symptoms, and the person I kind of chose as the case study for this, and I hope it's not insensitive or too soon, but it's the late queen. Older, not necessarily with those cognitive symptoms that we know of, and also a very unique, I guess, environment and genetic lineage to be looking from. Yeah. Not a massive royalist, but I thought as one person to case study for that, that's who came to mind.

Dr Fiona Mclean:

Actually, no, yeah. You should write a grant application. Say that you're going to get a sample from the queen and be like, "We just want to know what's going on there." She lived a good life. These have all been really well thought out. Yeah, I was also going to say an answer and I was just going to say Mozart. Why was he so good at piano? These seem a bit more relevant, so Sam, to end off, who would you like to look at the epigenome of?

Dr Sam Washer:

I've gone for Tim Peake, because I think it'd be really interesting to go down the interstellar rabbit-hole and sequence and have a look at people who have been on the ISS, and kind of see how that influences their ageing and their epigenetic profile. I think that would be really cool. Could this be why relativity ... Is it all down to their epigenome? Do they age quicker or slower because of these epigenetic markers? Think of it that way.

Dr Sarah Marzi:

There is a study. Have you heard of the NASA twin study?

Dr Fiona Mclean:

Oh yeah.

Dr Sam Washer:

I think I have heard of this one.

Dr Sarah Marzi:

Yes. Basically, they have these two identical twins. What were their names? The Kelly brothers. One of them went up to the ISS for a year or so, and then they profiled ... There was a whole team of people, but Chris Mason was leading, I think, the transcriptomic analysis of this, and they profiled telomeres, for example. They showed if you're out in space, your telomeres shorten faster than if you're on earth, so some indications of what's happening during ageing, and then obviously you're exposed to a lot more radiation if you're not within the atmosphere and on the surface of the earth.

Dr Fiona Mclean:

That is fascinating, though. Yeah. If you manage to get some spaceman DNA, Sam, you're going to get so many publications. Although, it seems like they might have already done it, which is kind of sad.

Dr Sam Washer:

That is quite sad. Oh, well. They need replication, though.

Dr Fiona Mclean:

Don't want that N of one. I love these answers. These have been so, so, so good. I'm afraid that's all we have time for today. If you can't get enough of this topic, please head to the Dementia Researcher website, where you will find a full transcript, biographies on our guests, blogs, and much, much more on the topic. I would just like to thank our incredible guests, Dr. Josh Harvey, Dr. Sarah Marzi, Dr. Alexi Nott, and Dr. Sam Washer. I'm Fiona McLean, and you've been listening to the Dementia Researcher Podcast. Everyone say bye.

Dr Sarah Marzi:

Bye.

Dr Sam Washer:

Bye.

Voice Over:

The Dementia Researcher Podcast, talking careers, research, conference highlights, and so much more.