350 Hellman
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Kevin Folta: [00:00:00] Hello everybody. And welcome to this week's podcast. Now DNA is always thought of as this master blueprint containing all these instructions to the form and function of an organism. But what if specific parts of that blueprint were blocked by some sort of overlay that limited the ability to actually use it?

You know, something that kind of obvious skated the information or, or what if other parts of that information were even more excited? That may be that part of the blueprint would be built first or maybe being built better or something like that. This is really the issue of epigenetics and its modifications in our master blueprint of DNA affect how that blueprint is accessed by the mechanisms that control gene expression.

One of the many ways that access is dictated is by small modifications of DNA, little tiny chemical decorations that that cover different parts of a DNA molecule that are added [00:01:00] enzymatically or removed enzymatically. One of them is known as methylation. It's the addition of a methyl group, that little C H three little tiny molecular decoration.

It has profound effects on how DNA behaves and can ultimately play a role in everything from a proper development, even diseases like cancer and today's guest has studied how methylation correlates with different disease states and how they may even contribute. To the progression or the ultimate manifestation of different types of cancers.

So we're speaking with professor SOF Hellman, he's in the faculty of medicine at the Hebrew university of Jerusalem. So welcome to the podcast, Dr. 

Asaf Hellman: Hi. Hello, Kevin. 

Kevin Folta: Hello? Yeah. Well thank you for being here with us today. What I would, I talked a little bit about methylation in this introduction, [00:02:00] but could you please describe more precisely what it is, but how it was even discovered and what does it mean to, in terms of development in the.

Asaf Hellman: Yeah. So as you know, this the coalition as you call it is something that is really important, any help the gene or the factors that control the expression of all gene, basically to better understand what the sequence of the DNA and what the X. Actually have to do when they say given enhanced or poor Moto or any control agenda and how to interpret the exact meaning in term of gene expression.

I ever I was always aware and I give a lot of attention for the the inability relations [00:03:00] in the eighties, early eighties of the 402nd century and epigenetic in general, there is still a lot of confusion. And I would say misunderstanding though. Please. It's unclear exactly how we, as a cell chip may understand the meaning of the epigenetic code engender DNA mutation called.

Kevin Folta: Yeah. So you mentioned promoters and enhancers. And so the, the promoter is kind of the, can be thought of somewhat as an on-off switch for gene, the enhancer almost as a volume knob. And so changes in the methylation state could affect the ability to say activate a gene or maybe control its level of expression.

Asaf Hellman: Yeah, so for sure, then a [00:04:00] mutilation is ever very close talking with the ability of transcription factors to bind the target sequences, meaning promote or goal Adobe element, which we usually call it. How exactly is a Z talk to the binding of the facto. We not sure yet it might be a causative means that the mutilation caused the facto to bind or unwind.

The DNA may be the opposite. The facto tell the DNA visited should appeal and most, probably most. Karen has a zero in the genome. So when you're talking about DNA methylation, I would say, is that the two most important worlds dynamics in a [00:05:00] function? If you think about the dynamics, many people knows it.

Most of the DNA is completely mutilation. This is stable also, eh, All certainly in the bodies, all life, always bit elated, completely methylated, highly methylated this probably too, in order to shut down repetitive element, I was like elements, things that was there in the genome, and you will never want them to be exposed.

Zen them. It's common knowledge and we'll say, is it in gym pool or. When the promoter methylated, the gin would not express because the fact or the activate, or was it by this, from what those sequence cannot bind it's means that about half of our gin, I've never methylated those [00:06:00] because those are the housekeeping genes that should express anywhere in order tissue and Zane, about half of the gene.

some tissue and the issue. And the methylated tissue would not express this gene. However, when you come in to the what happened in the express issue, and especially when we're talking about the difference between people, we deal with the patient, if you want in the expression level, Of the, the open Pomo tools.

This is start to be complex because while most of the DNA is always methylate that in Zen, most of the promoter of the development blogger, methylation, What actually caused the, or [00:07:00] produce the difference in the expression live in between. And we all are there understands that this expression, Tim expression, living between the view, this actually what respond to most of the disease of the patient suffer of the common disease, of course, all type of disease of common disease, of course, in very world.

Those me a difference in the expression level of GNO due to the Moto due to the promoter epigenetic, not . Those are always completely unmethylated and the gym are able to express what really defined the actual expression level of the sequences we call has. And what we bring into the picture and being by yourself group is the ability to block these through the eye of the . And what we find is [00:08:00] actually very interesting and I would say different. And on the same time had the hero. Well, we all in the understand about manipulation when we wrote quality of the book. 

Kevin Folta: Okay. So it seems like it's the methylation state of these enhancers that can have profound effects and enhancers just for the audience that maybe doesn't know the molecular biology, the enhancers are these DNA sequences that may be located reasonably far from the gene itself.

Like the master control portion of the gene, at least in terms of the number of bases away, but it may be located very close. When DNA is organized and packaged into its ultimate form. So is that correct so far? 

Asaf Hellman: Yes. This is exactly what people think about enhanced actually very similar to Paul Moto. I was also at north next to the to the [00:09:00] transcribe portion of the gene.

They may reside within what we call it. The Palagi associated domain and they may come across with the pole motto probably two very short period of time. But when this interaction long distance that the promoter can see the full variety or spectrum of factors that you have to see in order to transcribe.

And then you get the village. Best of transcription for a very short period of time. And then nothing happened for how well again, and this has said. They're like all motto, but I'm not like four Moto because they bind on a kind of activate or in the base or the thing at the same time, they also bind [00:10:00] the polymers.

what we call enhanced in a. And he'll come there. Maybe the most, everything has piece of information whenever they become active.

the DNA of the enhanced CBOs methylated in the math-related edging on the same time. So when I say that the entire genome is pretty stable in terms of methylation and the motto is welding wholesale seems to be very diminished. So the mutilation of. Pieces of DNA is always a term. And when you look on the DNA, same tissue, same pill, cell cell type, you always catch the enhancement methylation in some in-between, I would say between zero methylation to a hundred percent methylation.

And in this term, [00:11:00] this 4% of the metronome really. The enhanced summit dealership is V really they named me cause it was a C. 

Kevin Folta: So, does it change the association with, I guess this is my, my question as someone who understands molecular biology, but maybe hasn't kept up on methylation. Does it affect purely the structural.

Recruitment of factors to the promoter where maybe an obvious skates, the access to the H G C T code because of changes in the physical structure of the helix, or is it really just recruiting other protein factors like histones or other repressors that limit the access to the proteins that say turn on transport.

Asaf Hellman: Yes, this possibilities still open. We know as a DNA methylation talk with the [00:12:00] ASM level of epigenetic and the state of coma in organization, would it be open or zone and with the ability, all these. The ability of facto two binds and targets. And we still don't know, as I say, there's DNA caused this effect or really Paul this effect or probably boss, but anyway, it's very close to this happiness and.

You know earlier at the time, people like to think about the hassle is a given and how said we buying the Gideon activate or the skipper and facto, and when widely eat, interact with the poor mode, we have the expression, but actually what happens? The thing has survived many active . [00:13:00] And if you'd like to be precise, the Dean met measure and actually talk with the balance between bound activity and repressed.

So all the bounced stability of this factor and this why we see a very tight, very close correlation between the level of material. Only in that, on the in-house side versus the expression level of the targeted gene. This is a very unique situation and they will see it in poor Moto. Always. Mid-to-late completely methylated.

It's Claus completely unmethylated open, but, but only sites that actually correlate closely correlate with the expression level of GMO. And, and what more you can define being housed. There is [00:14:00] positive or negative in half. So what records silence. So if the, the, these, these

It will affect negatively the expression level of the gym. If it's a buy more activity or you have more expression and you, you should take into account that most of the gym, it was several in-house in a silence like this. So if you really want to understand what the genome do it. You should know it's specific, eh, combination or network of enhancing and sound cell.

And the, the best way we find so far to describe to addict the expression level of gym is by looking at the DNA methylation level with, in the K and answer our silent cells at the actually [00:15:00] define its expression. 

Kevin Folta: Now. Very good. So if you're, but this is one other question I have is if you have methylation of an enhancer or a silencer, does that really affect say one target gene or since it can be far away, does it affect the entire set of genes in a certain neighborhood of the.

Asaf Hellman: Yes there no such good mapping of gene

In our methylation visit data, we estimate that the given gene ever an average of 2.2 site, many of the important gene of transcription factor itself and has science and Zen, I give him in the house cell may talk to several genes. [00:16:00] In each neighborhood neighbor with a mean median basis of DNA and the outset.

One day, you know, on this is what happened if you ever was in the same tab seven or sometimes 10 say, well, tell us of gene. And this gene are not necessarily working together. They are not. A common expression poor for each of these gym is free to express itself in different tissues, different level, different way.

And we find my arms at each of this independent gene may whole, it's all network of it. Say two and a half seven to silence. Well, the next gene enabled gene may have a nozzle [00:17:00] network, all the enhancer and the science of given gene that was spread across the entire time. Z to interact reserve specific for Moto the, as a network of inhaler science cell use the same area or the DNA is there overlap with the first network, but they only talk with and this how different genes may contain or maintain independent expression, both.

Yeah, 

Kevin Folta: I see. So it's a lot more complex than we think. So when we talk about DNA, we can sequence a G, C and T. We can understand DNA sequence very easily through very well established protocols. How do you detect methane? 

Asaf Hellman: Well is not as easy as regular [00:18:00] DNS sequences, but not really complex. The most useful and common way is what we call by sulfite treatment.

We treat the DNA with chemical that make all seed to turn into teas, unless if they are methylated later, So following this treatment all non-manipulative, we'll see, we become teary and by sequence, and then compare with the original sequence of the DNA we can easily. Did you use what, which of these is was methylated?

Also as I made thought, for example, then you can get molecules. Sequencing is He said the difference between

So actually they seek Wales them as the few basic of the DNA for it. Like [00:19:00] they actually have this at the issue. So they, they met come on, easy, very stupid. And we have no problem usually level. 

Kevin Folta: Okay, well, this is an excellent. For now we'll talk about application on the other side of the brake.

So we've talked all about methylation, about its roles in either use in changing the ability to enhance or silence expression from a promoter by effecting a distal DNA sequence or an approximal DNA sequence. And now we'll talk about how this has roles and things like aging, diabetes, or cancer. This is the talking biotech podcast, and we'll be back in just a moment.

And now we're back on the talking biotech podcast. We're speaking with professor a soft helmet. He's the, he's in the faculty of medicine at Hebrew university of Jerusalem. [00:20:00] And we're talking about DNA methylation, mostly methylation of enhancers and how the methylation state of an enhancer. Enhanced gene expression or perhaps silence gene expression.

And it's the small molecule that's attached on to DNA to change the access to different genes by the factors that control gene expression. And all of this is great. We talked about, you know, the physical nature of this, how it works dynamically, but now the question. How do we apply what we've learned?

And this is where your laboratory has been. Just make some profound discoveries that really have been important in understanding the predictive nature of mat methylation. So one of the key key projects in your laboratory has been around diabetes and type two diabetes. And how a blood sample perhaps. We can examine the methylation state in, in blood.

And I guess we're talking about white blood cells because red blood cells are eat nucleate, but how do we [00:21:00] use, how do we, how can we use methylation to predict something about diabetes? 

Asaf Hellman: Yes. So once when the stands that the ability to trick the exact, the precise with the lesson level, At the cells, it really control expression level of the gene.

We came to a new point when we came, really measure very tinny of differences in the expression level of disease genes without even near. The ability to get the RNA, you know, and then Willy core is very unstable and it's hard to get, and you need biopsies of the two more. If it's diseased that you not true, each are the target tissue like type two diabetes, maybe, you know, or you think, you know, the target [00:22:00] tissue, but you are unable to biopsy this tissue.

In my people especially L a young and healthy people that you like to screen. So you'll come to a point when you suspect that the teeny difference in the expression level of prescription facto over decades of lifetime make some people to be. And a little bit of developing this. This is all the other diseases, something like a couple of hundred of common disease that we like to track this this way and being able to get all this information about the tendency of particularly individu are to little bit expressive.

Hi, higher or low well given genes using the DNA mutilation [00:23:00] market open for you a whole new world of, of possible markers and maybe also possible. To detect and maybe also to control to epigenetically control this expression. So in this field, we are only making first steps and we like to be very eh, cache, but it can only did it tells it, for example, when.

On the white blood cells of well think without diseases that seem to be depend or ever some crosstalk with the, with the the sings, a tip in, in, in white blood cells specifically. Type of white blood cell. We may see a little, very little but significant difference [00:24:00] between people all seem young people between those peoples, that in later life develop this particular disease or maybe protect for the development of this disease.

And and we can really click into dig this tendency by looking simply by looking on the methylation level of specific key enhancer or specific gene within specific Sipe type of white blood cell. I'm sure a soul is that I have to be a little bit Janet in weapons saying here, because it's also only first step, but we have Haiti.

They like what. 

Kevin Folta: No, that's okay to be cautious because I understand you're speaking like a scientist. You don't want to put the cart ahead of [00:25:00] the horse, but you know, and that's good, but at the same time, it's exciting for us to think about how this type of technology could apply. And so you're seeing changes in the methylation state.

That that seemed to associate with the diabetic state that you don't know if they're causal or not, but they may be, but, but so is, are these tools that if someone were to go in today and and have their methylation state of a few key genes tested, could you really understand their potential predisposition to diabetes?

Asaf Hellman: Yeah. So as you probably know, when people generally think about, eh, type two diabetes, not the, the blood or the ability for blood will not miss a first tissue of, of, of the, with the sink about this. Because if it's [00:26:00] used to say. In Ms. Positions that okay. Type one diabetes in U2 to immunity tack of the, of the package inside the better cell, but in type two, they're resistant to insulin is the things that develop over years and, and seems that they can see like inflammation and general counting of white, not cell, maybe.

The issue we'll be doing all the same. Used to be sought as, since that happened. Where's the disease after the disease, before the disease. So we're really supplied to see is that looking in 17 years now, before the disease, they already show these Stinney difference in the methylation level. And indeed, as you suggest this Emmett dimension, like.

Come very close on next bite to [00:27:00] genetic variant to snips and all of the associated with the, with type two diabetes Jewess studies. But while the this very, and this snip not really, not really associated with the expression level of imaging and their prediction model of diabetes, risk of really, really weird.

The methylation side just next to these snoops are very strong effect on the expression level of particular genes. And also the predict the, the, the apparent addiction, where there might be much, much better or stronger. Zen the combination of ordinance need for, for example, type two diabetes. And this is actually makes sense because if you think about these, we all know, and LAN that, that different type of disease is the [00:28:00] outcome of the interaction between our genetic and the.

Environment. So we all know that if we become more fed and do less exercise, we are exposing to, to be, to develop the embedded and also Zen a mouse, the, the, the obese people, if they're what we call good genetics. So we not as a bogus into diabetes while some people. Even in underweight may develop diabetes.

So some interaction between genes and the environment, but what is the meaning? The molecular mechanisms behind this interaction, nobody know. And what we already know about materializations at any methylation site is actually an interrogator of clues from the genetic and from the environment. We know that about.[00:29:00] 

One serves of the variation between people affect the methylation level of nearby or even distant sites on the same time, what we eat or edge our stochastic experience, so on really affect methylation level. So if you think about. When the methylation of enhances what actually caused the expression level of the gym over the lifetime and this methylation site integrate the information form the genetic sequence from the DNA sequence and on the same time from the environment.

And what use out of this, the precisely the building, the individualist. Expression level of this disease gene, the chore. This ventilation might really [00:30:00] dig at the fact or at least the poor, the expression level of the gene. And by the way, if you think why this snip variation , it was solely intended for.

Maybe it's because the effect on the mutilation is on the school by the effect of the environment of motivation. So, yes, if you measure the association between a given variant in the given disease, you see some effect, but you will miss the effect of the environment. If you measure the motivation, you might measure them the same time.

Being tired of the disarm effect of the environment and the genetic of one particular individual over its disease gene. And this model, I would say the ones that we most like, and [00:31:00] it's the best express or discard what we actually see in the lab. 

Kevin Folta: Do you think that the environment. Affects our generic. Or do you feel that there are maybe specific environmental inputs that can change the methylation state of a gene?

Or is it just a general response to say stress? 

Asaf Hellman: Yeah. So talking about DNA methylation, we already knows that the, you have a diet and your age and your especial for many chemicals. In the environment may affect you are global and local DNA methylation level. Add on top of this, the stochastic event.

Whenever we replicate the DNA, we duplicate cell the mutilation, my shells, and do a correlate with incor, with relation with Tyshann. [00:32:00] And, and the extra, the, the value, the, the difference between individualism and they live in relation is at least hungered for, I would say, higher sales and the variance in Zelle, genetic sequences.

So for sure methylation C Or some of your entire in the experiment. And as I say the same time, it's also affected by the variant of ingenious sequences. The, the problem is to, to defile, to understand which. Wow. I'm out of this, of all these many, many difference or variation in DNA methylation level.

Talk about in house, of course, meditative effect or connect with given gene in a given disease. 

Kevin Folta: Well, what do we know [00:33:00] about the associations between methylation, state of enhancers and different cancers? 

Asaf Hellman: Yeah. So in castle ever to say, is it if you look at the same they canceled. We'll dive into genes that are common to several types of cancer.

And you look at the, you try to make the network of methylation related in and science. So that talk with the exposure limit of this gene. You find completely, maybe not completely different, but very similar network. So the same. Gene that expense in different tissue, different origin of guesses would control by a different set of enhanced set aside.

And this is [00:34:00] very interesting to note because it says that we can in this stand, what, what do you feel between different types of calcium in term of, of especially limit of, of, of diverging and And that's are things that we can say is that it's really understanding this network really help us to understand why different patient with the same type of cancer.

It was so long as the difference in the expression level of, of, of, of key driver gene, for example, the cyclin D one gene that really. The dividing it eight of sane and, and it's it say, for example, my mom women with breast cancer or Bish. And that, that would normally express [00:35:00] a cycling. The one might have sometime thousand four difference between the expression level of, of this particular gene, but they are all defined as having the same type subtype of breast cancer and get the same treatment and, and at the same Way to photo two to three, this disease.

And only if you look at the methylation of three or four key in hassle, you went to, to look at the, they, they, they, they, they in hassles, it really control this difference between the patients. So. Imagine we may in the stem, the the specific expression for file over, we'll say[00:36:00] 

and specifically understand what makes them to be actually different from each other. So we already in a given castle MSA in Buber stoma, we were able to describe something like 60, maybe 70 the expression level of each one of these gene based. We can predict it based on knowing the material nation level of.

Up to four key and hassle sites. And as I say, we still don't know what will happen if we Chan in with relation level of this, an asset, but we already enrolled that only way rocking on the methylation level of this false site in the genome. We can say and predict what would be the expression level of this very [00:37:00] important time.

Kevin Folta: So when you're talking about using this as a predicted. Tool. Is this something that you feel, and this may be speculation, of course, but is it something that you could maybe start serving somebody in their twenties or thirties or forties and asking questions about the methylation state of particular genes to maybe give them some sort of hints that maybe they should be more careful about, more be more frequent screenings or something like.

Asaf Hellman: Yeah. So this is something that we are trying to do with diabetes, not with cancer based on pretty strong, preliminary data. We have, we are not running like a national project in aisle that they look using a prospective cohort of the methylation level of

[00:38:00] People in Xero and it went is, or even earlier we are not skinny, something like a 700,000 multicolored enhance cell. And we are tying to develop more models that would detect the chance to develop diabetes you in life. And this project is would say we had the blues and we all did start to see some, for me seeing results.

Kevin Folta: Are those a methylation sites or patterns somewhat inherited or inherited at all? 

Asaf Hellman: Yeah. So this is another big problem. My surgical and they're available, they directly relate to this issue with epigenetic in general, in metalation particularly, is it generation level inherited [00:39:00] pets at some level?

Yes. If you're talking about with the veteran of Parent and painting Jim it's womb relations. It is not it is you in the beginning generation was ruthless fail. Whereas a small difference in enhancer, for example, made us made between generation. People, all of these, see these in any AME with barely any metal made the mice for sure.

Wong and for showing planets, but there was a way to in Uman was so far not real good. Every the house for this effect. Well, it might 

be 

Kevin Folta: well for me, this makes a lot of sense because we all know that we contain roughly the same genes, of course, different variants, things like that. But how [00:40:00] much does methylation and other types of epigenetic events?

Contribute to the gene expression events that give us differential predisposition to disease or other differences we see between individuals. 

Asaf Hellman: You need to understand that white, most of the is maybe stay better. And most of the promote or development. Mentholated, what really caused the difference in the expression of gene is contour.

So network of a science and use a DNA methylation that it's a very airport and precise. Using way too little kid is network and understand the real key. The grotto excited control, the small effect over the genius. We still don't know if the DNA's causative here or just a reporter. But this TME [00:41:00] difference in the ability to express a particular disease gene between individual.

He's probably what really makes the difference between individu are in the, in the bad disposition for, for four. I would say if it's all for cancer, if it's so for type two diabetes, Zen, it will probably be also too, too many hours are coming. Disease disease have in common. These are the basis control avail.

Save on test of disease digress. 

Kevin Folta: Well, very good. Well, professor Assad, Hellman, thank you very much for joining me today and talking about this very exciting way in which this regulatory mechanism could have important roles, both in prediction of the disease, but really a key part of personalized medicine.

So thank you [00:42:00] very much for joining me. And as always, thank you for listening to the talking biotech podcast. Remember to share and write reviews, do what you can to help promote this podcast and share with more people. I mentioned it all the time, but I got another email this week saying thank you for this resource.

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