7.9 Drugs that target the epigenetic machinery as chemotherapeutics

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En provenance du cours de The University of Melbourne

Epigenetic Control of Gene Expression

424 notes

The University of Melbourne

Epigenetic Control of Gene Expression

424 notes

While the human genome sequence has transformed our understanding of human biology, it isn’t just the sequence of your DNA that matters, but also how you use it! How are some genes activated and others are silenced? How is this controlled? The answer is epigenetics. Epigenetics has been a hot topic for research over the past decade as it has become clear that aberrant epigenetic control contributes to disease (particularly to cancer). Epigenetic alterations are heritable through cell division, and in some instances are able to behave similarly to mutations in terms of their stability. Importantly, unlike genetic mutations, epigenetic modifications are reversible and therefore have the potential to be manipulated therapeutically. It has also become clear in recent years that epigenetic modifications are sensitive to the environment (for example diet), which has sparked a large amount of public debate and research. This course will give an introduction to the fundamentals of epigenetic control. We will examine epigenetic phenomena that are manifestations of epigenetic control in several organisms, with a focus on mammals. We will examine the interplay between epigenetic control and the environment and finally the role of aberrant epigenetic control in disease. All necessary information will be covered in the lectures, and recommended and required readings will be provided. There are no additional required texts for this course. For those interested, additional information can be obtained in the following textbook. Epigenetics. Allis, Jenuwein, Reinberg and Caparros. Cold Spring Harbour Laboratory Press. ISBN-13: 978-0879697242 | Edition: 1

À partir de la leçon

Week 7 - Cancer Epigenetics

This week we’ll bring together much of what we’ve learned in previous weeks of the course, to understand how the epigenome is affected, and can also affect, cancer development and progression. We’ll then go on to discuss the potential therapeutic benefits that can come from using epigenetic biomarkers, and targeting epigenetic modifiers in cancer.

7.1 Overview of cancer epigenetics7:13

7.2 Hypermethylation of CpG islands in cancer16:40

7.3 Hypermethylation of sets of CpG islands in cancer11:59

7.4 Hypomethylation genome-wide in cancer12:04

7.5 Altered histone modifications in cancer11:55

7.6 Long range epigenetic alterations in cancer and alterations to nuclear architecture10:25

7.7 Altered expression on piRNAs and long noncoding RNAs in cancer9:35

7.8 Mutations in epigenetic modifiers in cancer9:41

7.9 Drugs that target the epigenetic machinery as chemotherapeutics17:05

7.10 Extension lecture: Aging - Part 114:07

7.11 Extension lecture: Aging - Part 223:04

Rencontrer les enseignants

Dr. Marnie Blewitt
Head, Molecular Medicine Laboratory
Walter and Eliza Hall Institute of Medical Research

So over the course of the last few lectures, we've spoken about these

epigenetic abnormalities and we've spoken a bit about how they can be used for

diagnostic purposes or they can be used prognostically.

But now, I want to focus this last lecture for this week on thinking about therapy.

So, actually, what's been happening

in the last few years is there's been a really intense push by pharmaceutical

companies to target the epigenetic machinery with small molecule inhibitors.

So that is small molecules, chemical molecules, that can come in and bind very

specifically to epigenetic modifiers and inhibit their function.

So, why would you want to target the epigenetic machinery?

Well, I've just told you that we can see alterations in the expression levels or

alterations in there are mutations in the epigenetic modifiers and that

epigenetic abnormalities are really a hallmark of cancer if you like, they

happen in every cancer. And so, if we could reverse these

epigenetic changes because the epigenetic abnormalities are indeed reversible

unlike the mutations, then potentially we could help treat cancer.

So there have been some areas of the epigenetic community, at least that, have

been relatively weary about being able to treat patients with drugs that disrupt

epigenetic machinery. And this is because we know epigenetic

control is critical for all cell types. So what happens if we disrupt, if we just

give a person a drug that's going to influence all of their tissues and say,

for example, inhibit DNA methylation in all of their tissues?

What will happen in terms of side effects?

What will happen in terms of downstream consequences?

So despite this initial wariness, clinical trials are still gone on for

some particular drugs and the thing is that the drugs often work.

So, sometimes, although we worry or we don't want to have too great an

influence, in terms of we don't want to have terrible side effects.

We know that the current options for drugs for cancer patients already give

them a horrible array of side effects. And so, it's not necessarily true that we

can predict what side effects might be just by thinking about a drug, rather you

need to try. And really, the primary aim is to get

patient survival, so while we want to minimize side effects, the primary aim is

patient survival. So if epigenetic drugs may in fact extend

the survival period, then they would still be a very good thing.

And then sometimes, it, at least for adult cancers, the long term consequences

of the use of these drugs is usually not considered.

This is considered for childhood tumors but the long term consequences of the

drug that you might give to somebody whose already quite elderly, so many

patients with myelodysplastic syndrome are in their 70s.

We don't necessary think so much or clinicians don't think so much about

these long term consequences but rather extending the lifespan and the quality of

life of these patients. So, to begin with these drugs have been

targeting the enzymatic epigenetic regulators.

So the ones with enzymatic function, that is that they actually lay down a

particular epigenetic mark, remove an epigenetic mark or the Swi/Snf type

class of chromatin remodellers, any of the chromatin remodellers

that have enzymatic function. They use ATP and bind ATP and use

ATP to move the nucleosomes around. All of these are enzymes.

And the reason these have been targeted first is that in terms of chemical

biology these are most easily targeted with small molecules.

They can find the active site of that particular enzyme and target that active site.

So if we come back to this picture again

of the various classes of enzymatic epigenetic regulators in this case, we

haven't got the ones that are binding to particular chromatin marks.

I'm just showing you a few of the drugs that are currently either in clinical

trial or FDA approved or the ones that are in pre-clinical trial for various

classes of drugs. There's no way I could fit all of them on

one slide and have you be able to read it, so I just have a select few here.

What you'll notice is that there are drugs against DNA methyltransferase, so

DNA methyltransferase inhibitors, histone deacetylase inhibitors, histone

methyltransferase inhibitors, histone acetyltransferase inhibitors, and

histone, sorry, I've made a mistake, they're histone demethylase inhibitors.

So we have broad classes of these drugs. We're targeting most of the enzymatic

epigenetic regulators, at least for the information that's out there at the moment.

There are just two classes where we don't

yet know of any drugs that are targeting this.

This doesn't mean that pharmaceutical companies aren't doing it, but at least

it's not public information at this stage.

So we don't necessarily know that they're targeting the DNA

demethylases the TET proteins or the chromatin remodelers.

I expect there will be but we haven't yet got the information in the public domain yet.

So what I'd like to point out is that,

say for example, EXH2, which I mentioned was mutated in several types of blood,

cell disorders and amplified in solid malignancies.

There's an EZH2 inhibitor that's currently in pre-clinical trials.

So that means, before it actually goes into a full-blown clinical trial, it's a

very effective EZH2 inhibitor called GSK126.

So this might be extremely useful in those cases, where you have gained a

function of EZH2 but less useful in the cases where you have a loss of function of EZH2.

We know there are many more in

development against others, and there's one in clinical trial against a histone

methyltransferase called Dot1-Like. There are those against histone

acetyltransferases, histone demethylases, that are in pre-clinical trials and many

in development. But at the moment, there are just four

drugs that are already FDA approved. So FDA approved means that it's the Food

and Drugs Administration authority that's in the US that's approved them for use

altough they're in use in other places around the world as well.

So these are the first sets of drugs that are supposed to be targeting the

epigenetic machinery. For the two that are DNA

methyltransferase inhibitors, decitabine and vidaza.

They're approved for use in myelodysplastic syndrome that has

progressed to cute myeloid leukemia or AML.

Whereas, the histone deacetylase inhibitors are approved for a cutaneous

T-cell lymphoma. So this is a very particular type of

lymphoma that is just, that occurs in the skin, where you can see the

build-up of the, the T-cells in the skin. Both of these of course are hematopoietic

malignancies, so malignancies of the blood.

So let's, think first of all about these DNA methyltransferase inhibitors.

So DNA methyltransferase inhibitors, I've mentioned one of them before in the past

when I was talking about X inactivation. And that was 5-azacytidine, which

inhibits DNA methyltransferase one. These drugs, Vidaza and decitabine and

also any of the other that are in pre-clinical trial are kind of very

similar to 5-Azacytidine. They've just had additional modifications

take place, so they're all nucleoside analogs.

So they get incorporated into the DNA upon replication, and then, when the DNA

methyltransferase comes along to bind it, the DNMT1 comes along to bind that

nucleotide to then copy the methylation to the daughter strand, that DNA

methyltransferase is bound irreversibly and it can no longer be released.

And this means that the action of these DNA methyltransferase inhibitors is

division dependent so you have to have the cell replicating.

So this means that cancer cells which are dividing much more rapidly than most

other cells in the body will be more severely affected because they're

replicating more. So these DNA methyltransferase inhibitors

were first used back in the 70s, I think. But at that time point, they were using

them with very high dosages and at very high doses they're just toxic really.

They don't have any specific effects, they're toxic, they have terrible side

effects and the patients become very ill. But they're not actually very good at

getting rid of cancer. And that's because you're not acting in

the range in which they cause DNA demethylation.

So instead, much more recently, they've been used at much lower doses.

And at these much lower doses, far, far, far lower doses, you actually do have a

very good anti-neoplastic effect, in other words, you are killing the tumor

cells. And that's because they seem to be

causing DNA methylation, at least in some cases.

So, the DNA methyltransferase inhibitors, although they are actually inducing

people who had taken them around the world, we still don't really know about

how much is specific about this DNA methyltransferase.

They probably hit all dividing cells to some extent, and so, we don't know what

the long term consequences would be on normal cells, because every, most cells

will divide at some point and if the demethylation transferase have been

taken, then they have the potential to be affected.

While I said this is that they've given it the range now that causes DNA

demethylation, we don't know that, that's their only mechanism of action.

Maybe that they're having an effect through other ways as well.

And at the moment, we're not really clear why it's only myelodysplastic syndrome

where they seem to be most effective. In fact, they're in clinical trial for a

very large number of other malignancies, including solid malignancies.

But it's possible that it's very effective or the reason they found it was

most effective in myelodysplastic syndrome is because, you remember, it

might be dependent on CpG island hypermethylation.

And we know that CpG island hypermethylation, heavy CpG island

hypermethylation, has a poor prognostic outcome for myelodysplastic syndrome.

What's interesting is that these myelodysplastic syndrome patients

tolerate these DNA methyltransferase inhibitors extremely well.

So these do tend to be older patients in their 70s.

They tend to be put onto this drug if they've already failed on other

chemotherapeutics, but they then respond extremely well to the DNA

methyltransferase inhibitors and have a far superior life expectancy.

But also, their quality of life is improved because their side effects don't

seem to be too severe. So this goes against all of those things

I think that we were wary about in the first place with the DMNT inhibitors.

So, for the histone deacetylase inhibitors, there are four different

classes of histone deacetylase inhibitors, and that's because there will

target different types of histone deacetylase. The two that are approved, are actually

pan histone deacetylase inhibitors. In other words, they target all four

classes of histone deacetylase. And at the moment, they profuse in this

particular cutaneous T-cell lymphoma. Although, some events suggest they are

effective in other lymphoid malignancies as well.

So with the histone deacetylase inhibitors they might be considered in

some way more dirty than those DNA methyltransferase inhibitors in terms of

their mode of action. And that's because they really show a set

of pleiotropic effects and that's because they don't only target the histone

deacetylases but also other protein deacetylation as well.

It can happen in the cytoplasm or the nucleus so it's not even necessarily a

nuclear restricted, but it also seems to inhibit the acetylation of other

transcription factors for example that are also important in gene expression.

The histone deacetylase inhibitors just like the DNA methyltransferase inhibitors

aren't selective for the cancer cells. So the precise mechanism action is

unknown for a couple of reasons, because we don't know which cells are really

affected, and we don't really know whether its working in the nucleus or the cytoplasm.

But you do see gene expression changes,

but as I said some of this may be explained by them actually working on,

inhibiting the deacetylation of transcription factors rather than the

histones themselves. At this point, the fact that we don't

really know their mechanism of action, again, isn't terribly important, because

again, they're very well-tolerated by the the patients who receive them for

cutaneous T-cell lymphoma and they are extremely effective for these patients.

At the moment, what's very interesting is thinking about how you could use two

different epigenetic drugs together. So we know that the way that epigenetic

works, if you think about maybe x inactivation as an example, is that you

have several layers of epigenetic marks all coming together to be able to bring

about epigenetic silencing, for example. So perhaps by just targeting one, maybe

with a histone deacetylase inhibitor, you won't have the most effective outcome.

But if you can target the epigenetic machinery twice, say with DNA

methyltransferase inhibitors and with histone deacetylase inhibitors, perhaps

both at much lower doses, you might have the optimal outcome both epigenetically

and in terms of side affects. So there are now many clinical trials

going on looking at these two being used together, but also in combination with

standard chemotherapeutics. So how, perhaps you can use standard

chemotherapeutics, which tend to be associated with terrible side effects and

lots of nausea. Maybe you can use them at much lower

doses with low doses of epigenetic drugs as well.

So, one of the recent developments, in terms of targeting the epigenetic

machinery is that now we're not just targeting, the pharmaceutical companies

aren't just targeting those enzymatic epigenetic regulators, but they've taken

a much broader look now. And so they're beginning to target just

protein-protein interactions. So let's say, for example, chromatin

proteins that bind to an acetylated histone mark or methylated histone

residue. In this case, the ones that have been

released are the ones that target bromodomain proteins, called

BET proteins. So these are called BRD2, 3 and 4.

So, remember bromodomains bind to acetylated histone tails as shown here.

And these BET domain inhibitors are again seem to be very effective.

So in this case, just like with the other two cases, we don't know a huge amount

about their mechanism. But what's interesting here is when you

treat cells with BET inhibitors, they don't have very many gene expression

changes, just a small set. And in particular, you seem to alter and

downregulate the expression of this potent oncogene, MYC.

So perhaps, they're having a very direct effect on MYC-, on MYC.

But in general, it seems like, maybe these BET inhibitors have a role by

altering transcriptional elongation. We still don't know how this might work

mechanistically, but it's possible that's how they have an effect in cancer.

So now, I want to turn to thinking just briefly about the future of targeting the

epigenetic machinery. Well, with every new publication that

comes out, there are new mutations being reported in the epigenetic machinery.

So, this is a very very active area of research for pharmaceutical companies,

and an active area of research on, in the basic end of science as well.

Asking what are these mutations doing, how are they altering the function of

these particular proteins? So, while there was early wariness about

target in the epigenetic machinery and there's still concern, it seems that

these drugs are surprisingly effective. And so, perhaps that early wariness is

going to dissipate with time. So what, what do we expect to see, how

will this change the future for cancer therapies?

Well, probably over time, we'll see that these recurrent mutations that are found,

maybe you'll have drugs targeting specifically that mutated form of the protein.

Now, if it only targets the mutated form

of the protein, it will be a syllable if you like.

It shouldn't affect the the neighboring cells because it will only affect that

mutated protein that's found in the cancer cell.

As I said, they're trying more combinatorial epigenetic drug

treatments, so putting multiple targets together and because we know this is how

epigenetics works normally. If we target multiple components of the

epigenetic machinery that go wrong in cancer, perhaps, you can have a more

effective outcome. And then combining these drugs with

standard chemotherapy. So while the approved drugs that are

being used are only being used at the moment in hematological malignancies,

they're being trialled in a much broader array of cancers.

And so solid cancers and these combinations of drugs and solid cancers

and hematologic malignancies. So probably in the coming years, they'll

be approved for all sorts of other cancers as well.

What's quite interesting is that cancer isn't the only case where we have epigenetic

abnormalities, it's not the only disease, it is the one that affects most people by far.

But maybe these drugs that are being

developed because of the high prevalence of cancer in a community may actually be

useful for other disorders as well, these disorders where we know epigenetic makeup

is altered. And so, indeed, now they are being

considered, these epigenetic drugs are being considered with other cases as well.

And perhaps the wariness that we should

keep those, the wariness that should remember about is that still these drugs

are going to be used throughout the system until every cell has the

potential to be effected by these drugs. So maybe still need to keep in mind that

younger patients, particularly those that have developing germ cells for example in

sensitive periods, we should remember about the sensitive

period so that one very large insult to the environment would be taking a drug

that inhibits the epigenetic machinery. So these sorts of things still need to be

considered, but it seems that the future is bright for targeting the epigenetic

machinery in cancer. So that brings us to the very end of this

7-week course. So congratulations to all of you that

made it all the way through the 7 weeks.

You've done very well to listen to me for that long.

And I hope that you've enjoyed the course.

Hopefully, you feel like you've come away with a better understanding of epigenetic control.

Maybe you'll be able to understand a

little bit about the epigenetics literature when reading scientific

articles, and hopefully, much more when you read something about epigenetic

control in the public press. Maybe you now understand that you are or

you are not what your grandmother ate and you understand a little bit about

epigenetic difference between twins. And I hope there's something you've taken

away that your excited about. Okay.

Thanks, bye.

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