Genetics of PFIC and Its Subtypes (2020)
Genetics of PFIC and Its Subtypes (2020)
Dr. Richard Thompson, Emily Ventura
Dr. Richard Thompson 00:05
Okay. Hello, everyone. Welcome to the second half of the PFIC Network Educational Webinar series. Joining us today is Dr. Richard Thompson. We’re gonna be talking about the genetics of PFIC. Before we get started, we’re just gonna go over a few housekeeping slides and a few introductions here. So you can roll this forward, Carrie. We want to give a special thanks to some of our sponsors. The PFIC Network is supported by generous grants from both Albireo and Mirum Pharmaceuticals. We also have a capacity building grant from Global Genes and we’re proud members of the Global Genes Rare Foundation Alliance. A few disclaimers before we start
These sessions are set up for educational and informational purposes only. So, any medical advice please consult your doctors for but you can absolutely use these points as talking points for discussions with your physicians. Zoom is not a HIPAA compliance platform. HIPAA is the Health Information Privacy Act. So if anybody does ask a question, please keep all patient identifiers out as Zoom will not be able to be compliant with those privacy policies.
And last but not least, we are recording these sessions so that we can make them available on our website for future future educational purposes. Before we get started, I just want to give everyone a brief background on the PFIC Network. My name is Emily Ventura. I’m the executive director and co founder of the organization. Our mission is rooted in four pillars: education, support, advocacy, and research. Our leadership is all PFIC patients and parents. So we’re governed by parents from all over the world, from Australia to the United States to Canada.
We have representation all across the board. We consult closely with our Medical Advisory Board who is also made up of clinicians from different parts of the world. And they help us guide in our decision making and prioritizing for you know how we move forward with the network and how we best advise patients with you know PFIC specific questions.
Emily Ventura 02:27
A brief history: pfic.org was actually founded in 2002. A network of physicians and parents, patients was subtly formed. Over the 15 years, a patient community was coming together and starting to ask some questions. PFIC was becoming a little bit better known. In 2018, myself and a few other parents took over the organization and we formed a charity called the PFIC Network. Our initial focus was to bring the community together and to raise awareness.
We did that with such events such as our Family Conference and our first PFIC Awareness Day. Moving forward into the future, we’ve been focusing on bringing public education to the forefront with our website and this educational webinar series. We have a patient registry, and we just launched our second successful PFIC Awareness Day. So in the future, we’re going to be working on building our global outreach programs with our global Patient Parent Advisory Board, and other programs to support those.
We’re going to move into a presentation. The question and answer session will be towards the end. If you do have any questions, please feel free to use the chat feature located at the bottom of your screen. And we can do a live q&a in that form. So I’m going to move on into our presentation. I’m going to introduce everyone to Dr. Richard Thompson from King’s College at King’s College of London who’s going to take it further. Thanks for joining us today, Dr. Thompson.
Dr. Richard Thompson 04:05
Thanks, Emily. Hope you can hear me. So I’m delighted to have the opportunity to talk to you. And I know that many of you are experts, genuine experts on these, this disease because you live with patients, yourselves and which I don’t. So I can’t tell you everything about these diseases. But I can tell you some things that we’ve learned over the years that we’ve been studying them and caring for patients. And really the focus of my work has been looking at the genetics of these diseases and using that information to unravel what’s causing the disease and therefore how we can think about it between them. And I think we have to understand them in detail before we can start treating them properly.
So I do work with many of the companies who are involved in this area, and some of whom you’ll have heard of on there, some of whom you won’t have heard of, but maybe coming into the field in the near future, I hope. So when I was talking to Emily, the other day, I was mulling over what I would talk about. And I think I said to her that I wasn’t going to talk about this. But in the end, I decided it will probably might be a good idea.
And because it’s the sort of thing that I’m sure has crossed your mind, and is quite important to families, and this is the concept of what we mean by a recessive disease and the dominant disease and other variants like that. And I think this is quite important to understand. I’ll explain why I’m starting here in a second.
So the basic concept, which has been around for a long time, and we talked about it as a Mendelian, after Mendel, idea that we have these recessive and dominant conditions, and I came up with this graph, to try and portray that. And the horizontal axis is the amount of functional protein that an individual has. So a completely normal person will be at the right hand side with 100% of the functional protein, whichever it was. And somebody who’s got both copies of a gene completely damaged so that they don’t work well, they’re completely the left hand side of the graph.
And then the vertical axis is supposed to represent the degree of disease or degree of freedom from disease. So if you’re up at the top, then you haven’t gotten disease. And if you’re at the bottom you have. So obviously, if you’ve the bottom left hand corner, if you’ve got no protein, then you’ve got disease. If you’ve got two normal copies of a gene, you’re up at the top right hand corner, two normal copies and you are disease free.
And I’d want a line in the middle for 50% of function and so that could be somebody who’s got one damage copy of the gene and one working copy, so they’ve got 50% of the ideal amount of function. And if that gene was behaving as a recessive, you can see the line in the top graph, the person at the 50% level is functionally normal. So that’s really, the whole concept of a recessive is somebody who’s got one normal copy should be completely normal.
On the other hand, at the bottom, we’ve got somebody who’s got the line is 50%, but they’ve got the disease. So we’re saying that everyone who’s got one copy missing, has the disease. So that’s the concept of recessive and dominant. But I’ve rather arbitrarily drawn where those lines are, because the truth is, that line at the top, it may be that if you’ve just got slightly less than 50%, you’ve got the disease, or it could be that you could be right across, almost at the left hand side. And so you can actually have no disease at all until you get down to 10%, or something like that.
And for most of these recessive conditions, the PFICs, the cystic fibrosis and things like that, most of these conditions, we don’t even think about that most of the time. Because we just think, if you’ve got one good copy, you’re fine. If you’ve got two bad copies, you’re not. But it is actually very important to understand exactly where that curve comes, because there are actually plenty of people out there who lie in that zone between zero and 50%. They may be around 25%, for instance.
And likewise, in the dominant, is it does it make a difference whether you’ve got a slightly wobbly copy or do you have to have one copy that is not working at all, to have the disease? And that the more you look into this, in different diseases, the more you realize that actually, there’s no such thing as a straightforward recessive or a straightforward, dominant.
They’re all more complicated than that. And I’m sorry if that’s just puts a spanner in the works because it does. It’s gonna make life more complicated because these diseases that we’re talking about, are not simple recessives or dominants and some of them in particular, are far more complicated. And let me show you a couple of examples. So the disease, which I suspect you all know something about, even if there’s not present in your family is BSEP, the bile salt export pump. And I think the true curve for BSEP is approximately like that. Which means that if you have got one good copy and one completely abnormal, one good copy and one completely non functional copy, you are somewhere in the middle and you really shouldn’t have any disease at all.
But what we know in BSEP is there is a common polymorphism, so a very common variant in the population, which actually reduces the function to about 50%. So if you’ve got two copies of that variants, which actually about a third of the population have. A third of the population have got two copies of that common polymorphism, they’re already in the middle here. But they’re fine. But actually, they’re not completely fine. They’ve got a three fold increased risk of getting cholestasis of pregnancy.
So they’re very near to the top. They certainly haven’t got PFIC. But they have got an increased risk of pregnancy induced cholestasis, because they’ve got two copies of this common variants, which a third of the population have got two copies of that. So this line isn’t quite at the top, there is a small risk. But it generally is only a small risk if you’re pregnant, or you take certain medications.
Now, if you’ve got one damaging variant, one copy that does nothing at all, but the other copy has this common variant, and it’s which again, is you know, a third of the population, you’ve got two copies. So if you’ve got one good copy but it’s got the common variant, which reduces it, and your other copy is damaged, then these people are hovering around here, around 25%. So traditionally, they’ve only been described as having one abnormal copy, but they’ve got this other variant on the other copy. And they’re hanging around here and these are the people who get drug induced cholestasis.
They haven’t got PFIC, but they’re at risk of drug induced cholestasis, because they’ve got about a 25% of the ideal BSEP function. They haven’t got PFIC. They’re not gonna get progressive liver disease, but they could get episodes of cholestasis. So BSEP is almost a recessive. There, even if you’re a 25%, though there is a little bit of a risk, I mean at 50% here. There’s a little bit of a risk of getting drug induced cholestasis, cholestasis of pregnancy. If you’re 25%, then you’re when you’re about the risk of going down the curve and getting disease. So BSEP we understand quite well and it behaves fairly like a recessive but not straightforward. MDR3 deficiency, I believe has a completely different curve.
So what this means is, again, if you’re got completely normal function, you’ve got no disease. If you’ve got no protein, you’ve got very severe disease and severe early onset MDR3 deficiency is actually quite rare. But there’s a lot more people of various positions on this curve. And I have drawn this intentionally. And actually, I think I would should redraw this curve slightly and make it a little bit lower, if anything, such that the people here who’ve got one normal copy, and one completely non functional copy and they’ve only got 50% of the ideal amount of protein, they don’t present as children with PFIC either. But they do have a very definite risk of developing cholangiopathy, that’s damage to the bile ducts. But it might take decades and so these people do need following up.
And unfortunately, these are of course, the parents of children with severe….. excuse me…..severe MDR3 deficiency. So I think if one of the parents or both of them have a severe mutation, which causes no protein, then they are at somewhere on this position here. They haven’t got PFIC, which is what you’d have to have to be over here, but they have got risk of cholangiopathy.
Dr. Richard Thompson 14:53
Now these are the sort of the PFIC genes. These are the two that where we’ve got enough information to really understand or begin to understand the shapes of these curves. But, so really, this one is all about how much residual function you’ve got. Whereas with BSEP, there’s been a much more steep curve here, because there’s a critical point and if you’re below that level, you’ve got a problem. If you’re above that level, you’re okay. So there’s a threshold effect here, which is not the case with MDR3. It is much more of a continuous variable and it depends how much functional protein you’ve got left. So this makes life complicated.
Now, if any of you have had testing done, you’re very likely to have had variants found. And they will be classified according to the American College of Medical Genetics classification, and they comes in five categories, and they’re across the top there. If they are benign, and likely benign, they very often don’t appear on the reports, so you won’t see those very often. But what you will see is these things are variants of “uncertain significance”, “likely pathogenic parents’, and “pathogenic parents”. Now, these actually, rather annoyingly, don’t tell you how damaging they are. All they tell you is the likelihood that they’re damaging at all. But it’s really based on a traditional Mendelian model, so really, they have to be quite damaging, for them to be registered on this classification system.
But in truth, any variant we find, we can actually give us a degree of damage, and the likelihood of it being damaging in the first place. So we’re actually already into at least two dimensions, when we’re trying to work out how damaging a variant is. And, again, that’s for one variant. And of course, all these genes, most of us have got two copies of every gene and so we have to take into account the consequences on both copies, when we’re trying to come up with a formula or a conclusion as to whether it’s likely to be causing a problem.
So for each patient, when we’re thinking about a gene, and the variants in the gene, we really have to understand what the gene product, what the protein does. We have to understand what we might expect to happen if it’s not working properly. And then we have to think, Well, what might happen if it stopped working only partially, not when there’s a complete loss. And we have to think, as I’ve shown you with BSEP, is there a threshold, is there a point where above that you’re fine, and below that you’re not. MDR3 is an example where there isn’t a threshold. It is a continuous variable.
And then all the changes, changes that we’ve come across are the is the genotype, the two variants that we can see in that individual, do we think they are going to contribute to the phenotype, which is a silly word, but we use it all the time now, the phenotype is what the patient looks like. It’s the features the patient has, as opposed to the genotype, which we can characterize as the changes in the genes. The phenotype is the consequence in the patient. So when we’re writing reports, we have to try and come up with a report, which pulls all that information together and give something useful to the clinician looking after the patient and the family, of course.
But some variants, as I’ve already hinted at with BSEP at the beginning, some variants aren’t going to cause disease. But they may cause a predisposition like the cholestasis of pregnancy. Excuse me one second. They certainly don’t cause cholestasis of pregnancy, in the sense that even those people in the middle where I was pointing to, they probably only still got a 2% risk of cholestasis of pregnancy. But it’s still three times more than if they haven’t got those variants. So it’s a predisposition, but it’s not a cause. And then there’s another concept which we have to think about, which is it a could these variants be modifiers? And this is quite similar and this is where there’s another identified cause, whether it’s a infection, or structural problem, but could the variant we’re finding modify that. In theory, the variant may be making it less severe.
But in most cases, the question we’re trying to get our head around is, “Are these changes making it more severe?” So, in actual fact, it all comes back to contribution to phenotype. Is this…are these changes the entire explanation? Are they diagnostic? If so, how bad do we think it’s going to be? Or are they just causing a partial loss of function and a predisposition to a condition with a secondary hit required? Or are they contributing by modifying a pre existing disease? So unfortunately, most of my clinical colleagues, who don’t spend all the time thinking about genetics that way I do, get very frustrated by this because they usually, when they send a genetic test off they want a yes/no answer. Is this a diagnosis or not?
And what they get back very often doesn’t give them a clear cut answer. And I’m sure you’ve seen this. There’s lots of patients who come back with variants of uncertain significance. And very often, rather disappointingly, the report just says that and leaves everyone else in the lurch because the lab has found it and they sent it back. And then the clinician and the family have got to decide whether it’s of any relevance or not. But this is what we do in my lab is we try and provide as much information as we can as to whether it’s likely to be disease causing or not. Okay, so I think that’s enough lecture on some genetic concepts. At least it gets you into something of the headspace that I occupy when I’m thinking about this on a day to day basis.
Dr. Richard Thompson 21:40
So let’s go through a few diseases, some of which are probably well known, and some less well known. I put up here a table because I thought it will be useful. And I think there’s seven, of the seven most common and there’s the list is definitely not finished, diseases is on here. And if any of you have had heard me talk before, you will know that my preference is for the disease names across the top, so the deficiency of the protein in most cases. Of course, they’ve all got other names, and PFIC Type One and Two and Three are frequently used. But I there’s lots of reasons which I won’t go into today why I believe they’re confusing, but I think in general terms, to call something after the deficiency of the protein is more logical.
And as I’ve already hinted, and we’ve you know, many of you know, there are these variable phenotypes associated with all these genes. So they’re not all early onset severe disease. There’s a milder onset, later disease, which clearly is not PFIC Type 3, for instance. Equally BRIC, benign recurrent, intrahepatic cholestasis, is an even worse term, because that is generally used for patients with late onset disease, or episodic disease. But the truth is that just because something’s late onset doesn’t mean to say it’s not going to progress. And of course, the B of BRIC is benign. And if you could get labeled as a “benign” disease, then your expectation is that it’s not going to be progressed. But if that turns out not to be true, then I think you’ve been mislabeled.
So for each of those diseases, which I call after the proteins across the top, on the third row, you’ll see the genes, which are in some cases are very similar to the proteins but other cases are entirely different and bear almost no relationship whatsoever. And I think most of you probably know that some of these are clearly BSEP is the main bile acid transporter. FIC 1 and MDR3 are lipid transporters. FXR is the main receptor, nuclear receptor, intracellular receptor of bile acids, and is fundamental to regulating bile acids in the body.
And after that, it gets a bit more complicated, and we’ll touch on a couple of the other ones in a minute. And the other super important area to you handles is the question of whether the gene is used outside the liver, and whether it’s just going to cause liver disease and most importantly, is liver transplantation, for instance, going to completely kill the disease. Because usually, if the gene is not used outside the liver, then replacing the liver is an extremely effective treatment. But if the gene is used outside the liver, then clearly life becomes more complicated. And I think I’m sure most of you know in FIC 1 deficiency, the gene is widely expressed and the liver is only one part of that.
And that is why most of us will try and avoid transplantation. Although sometimes we do and we now have some tricks up our sleeve, which I think are starting to improve the outcomes there. Obviously, the further you go to the right hand side, the numbers of patients that we’ve seen get smaller. But we have got some idea now, and certainly TJP2 and this new one on the right hand side, which I’ll talk about in a minute, are widely expressed. And in fact, MYO5B, of course, was first identified as an intestinal disease, not a liver disease at all.
Dr. Richard Thompson 25:49
Now, if any of you have heard me talk before, you’d have seen a picture and looks something like this, and this is because this is what is happening. The canalicular membrane in the liver, which is the interface between the liver cells on the left and the canalicular space, which is the very smallest branches of the biliary tree, on the right. So inside the cell on the left, outside the cell on the right, and this is the interface where bile really starts.
Now the most common feature of liver disease and almost always the reason why children present to us is because they have jaundice. Well, they have jaundice because they have accumulation of conjugated bilirubin. And MRP2 is the bilirubin transporter. And there are mutations in that, as you probably know, and if you have mutations in that you have got conjugated jaundice, but actually you haven’t got liver disease, because everything else is transported fine. That’s a very rare condition called Dubin Johnson Syndrome. But the fact that bilirubin transporter is completely separate from the bile acid transporter is super important.
Because, you know, we know, that you can have a major problem with bile acid transport without having jaundice. And so a lot of the babies that present with BSEP deficiency may be jaundiced early on, but the jaundice can go away completely and they’re left with a major problem in bile acid transport, even though bilirubin transport is maintained. So bile acids are key to most of these diseases, as you realize. They’re transported into bile, but they are detergents. They’re very powerful detergents, just exactly the same as the stuff you wash the dishes with. And in fact, you could use bile acids very effectively to wash the dishes.
So we don’t have, we can’t have bile acids floating around free inside cells, or even in the bile ducts. So we have to package them up. And we do that by putting them into these things called mixed micelles. And when they’re packaged out like that, the hydrophobic components, the bit that attracts fat is tucked away on the inside and the hydrophilic parts of the bile acids are on the outside, the water soluble bits. So as a package like that, that is a water soluble, and very little detergent activity.
And as you can see, that’s mainly bile acids. But there’s also a small amount of other lipids are required to package micelles up in that fashion. And the major other lipid that’s in there is phosphatidylcholine. And we need MDR3 to be working properly, to get phosphatidylcholine into bile. So if BSEP is not working, the bile acids are stuck over here on the left hand side, that’s very simple. If MDR3 is not working, the bile acids have been transported perfectly fine for a long time.
But you don’t make these, you just have lots of free bile acids, because this guy is not working. And this is the problem with MDR3 and the problem is downstream in the bile ducts, not a problem inside the cells, because of the damaging effects of these bile acids that are wandering around on their own. Down at the bottom is the FIC 1 protein which is a lipid transporter, but it’s not transporting lipids into bile, like the MDR three is. It’s actually just flipping lipids from the outer leaflet to the inner leaflet. As you can see, I’ve drawn here, every membrane of every cell is made of a lipid bilayer and that is the surface of every cell out. And the the mixture of lipids on the inner surface and the outer surface are quite different.
There’s actually quite a number of transporters that are responsible for making the two layers different and keeping them as they should be and FIC 1 is one of those. And really, you need FIC 1 working and doing this job properly, to get the lipids in the correct places here. In fact BSEP does not work properly if you haven’t got the correct composition of lipids in the membrane. So the cholestasis that’s called by FIC 1 deficiency is actually a reduction of the BSEP function because of the abnormal lipids in this membrane. There’s nothing wrong with the BSEP itself in patients with FIC 1 deficiency. It is just not working properly, because of the environment in which it finds itself. So for PFIC 1, 2 and 3, at least in the liver, all the action is described in that one picture.
Dr. Richard Thompson 31:11
Now, I hope some of you have seen this and or at least come across this concept. These are figures data taken from a paper we published earlier this year, as a result of the NAPPED Consortium, which I hope you realize is a network of pediatric hepatologists from around the world who are contributing historical, anonymized data from our centers into a central database. And it allows us to ask questions when we have got large numbers of patients. BSEP is the most common of these diseases and it’s the one where we’ve got the first useful information. And well, it’s allowed us to classify the BSEP deficiency into three groups.
Now, we started doing this a while ago, but now we’ve got enough numbers that we can get meaningful results from this. So BSEP 1 is the mildest of these three groups, and they’re still got two damaged copies of BSEP. But one of those damaged copies has to be one of these two variants here. Now E297G is the most common of the BSEP variants that cause PFIC and is widely spread across northern Europe and people of Northern European ancestry, including in America, obviously. Whereas D482G is slightly less common, and is really most prevalent in Eastern Europe, particularly in Poland. But we’ve seen it all the way down Eastern Europe, all the way down to the Mediterranean in fact. But so about a quarter of patients in some populations have at least one of the damaging variants is one of those two.
At the other end, BSEP 3 is easy to understand, because BSEP 3 are patients were both copies of BSEP are predicted to cause no function at all. So they will usually be what we call a truncating mutation or a nonsense mutation, one where we can be pretty confident that neither copy of BSEP is going to have any functional whatsoever. And that’s about 20% of BSEP in PFIC, causing PFIC in BSEP deficiency, they have this BSEP 3 type of genotype. So the BSEP 2, which is actually the biggest group in the middle, are ones where at least one of the variants is a missense change.
And a missense change is what’s left in the middle, which are where one amino acid is changed to another amino acid, which is what most changes are in genes. And so it means that at least one of the two changes in those individuals leaves the possibility of some function, some functional protein. We admit that it is quite possible that some of those patients who were currently labeling as BSEP 2 actually don’t have any functional protein.
But at the moment, we can’t tell them apart. We can’t subdivide BSEP 2 at the moment. But we can fairly easily recognize the BSEP 1 patients because they’ve got one of those two changes. We can very easily recognize the BSEP 3 patients because they have got two severe mutations, which are not predicted to cause any function. Now, if we look at what’s happened to patients historically, on the right hand side, this is the chances of surviving with their own liver.
In other words, being alive and not transplanted, at various ages. You can see that BSEP 3, there’s hardly any patients make it past 15 and on average, they only make it three and a half years with their own liver before they are transplanted. Whereas in the BSEP 2 group, on average, they make it to seven years with their own liver. But as you can see, there are still 30%, 18 years out with their own liver. But if you’re lucky enough, that your form of BSEP deficiency, one of the variants is one of those two, then your, the outcome is much better and nearly 60%, are alive with their own liver or it’s actually 20 years before 50% have required liver transplants, so they are definitely milder.
Now we’ve been able to break this down, because we’ve got enough data on enough patients. And I’m sure as we get more data, we will be able to start picking apart the BSEP 2 category and give you a much more accurate prediction of how bad things are. But this comes back to my original slide about BSEP. So the BSEP 1s are ones which are probably hovering around 10%, something like that. So they’re not right at the left hand side and they have they’ve got some residual function.
The BSEP 3s are the ones which are definitely across the left hand side. They’ve got no function, and they’ve got severe disease. So this is new, and it’s useful. It gives us some idea of the severity. And it also correlates with what we published several years ago now is that the BSEP 3 group are exactly the same group that have the highest incidence of liver cancer.
And if you remember our our original, our paper from 2008, where we, you know, cohort of 120 patients. We lumped in for this analysis, what we would now call BSEP 1 and 2 together, and they had about a 10% chance of liver cancer before they had a transplant. Whereas BSEP 3 had about a 40% chance of liver cancer before they got a transplant. So it correlates again with this group BSEP 3, having the worst disease, the least likelihood of surviving without a transplant, but also the highest risk of cancer. So this makes really, it’s really important now for managing these patients. Because we know if you’re really a BSEP 3 patient, which luckily is only 20% of the patients with severe BSEP deficiency, that group are at the highest risk of liver cancer and they’re also the least likely to survive with their native liver.
And what I haven’t put on these slides is that we also know that those are the patients who are not going to respond to partial external biliary diversion and they’re not going to respond to the new drugs either, the current drugs that are in clinical trials at the moment. Maybe other drugs in the future, but the drugs that are available in clinical trials at the moment, BSEP 3 are not going to respond. They’re not going to respond to partial external biliary diversion either and the highest risk of cancer. So really, those are the patients who should be going through early transplantation.
And that’s very clear and that’s the way we should be managing these patients now. So it is now we can… it’s not just knowing you’ve got BSEP deficiency, it’s really important to know which sort you have and what the options are available, and what the risks are. I’m sure for the other diseases will have…come up with similar classifications in the near future. But obviously, this is the one which is the most advanced so far.
Dr. Richard Thompson 39:26
If you do have a partial external biliary diversion, we think… we’ve always thought that what we were trying to do was to offload bile acids, reduce the amount of circulating bile acids going around the enterohepatic circulation such that the amount of bile acids coming back to the liver, are dramatically less and therefore bile acids didn’t accumulate in the liver. The liver worked much better and the lack of accumulated bile acids meant that pruritus has improved as well. Now, despite the fact that’s what we always thought was happening, we’d never really had any data to prove that.
But these data are gained from the NAPPED cohort and they show, these two graphs, show basically the same thing, but in two slightly different ways. But if you look on the left hand side, what that shows if you split patients with BSEP deficiency, in fact, BSEPs 1 and 2, because BSEP 3 does not work for partial external biliary diversion. If you look at the patients who have got their serum bile acids below 102 micromoles per liter within the first year, after partial external biliary diversion, you can see that 15 years out, those patients have not required transplantation. If you fail to drop your serum bile acids below 102, as you can see, 15 years out, there’s 70% of the patients have required transplant.
On the right hand side is almost the same thing but it’s where there’s a 75% reduction in serum bile acids. And the reason we’ve done it that way is because that is much probably better, but fewer patients had serum bile acids measured prior to surgery and after surgery, so we could only have the 75% reduction whether it had been measured beforehand.
So the numbers are bigger on the left hand side, where we’re just relying on the level of bile acids after surgery. So this is important for two things. It’s clearly it’s important, because once we’ve done the surgery, we can see how successful it’s been. And not just in terms of pruritus, not just in terms of maybe an ultrasound scan, or measurements of the spleen size, but actually, if we can measure the serum bile acids, and we find that gone down below 102, or they’ve gone down by 75%, then we can be very reassured that this has been very successful, then the chances of that patient requiring a transplant in the next 15 years are actually very low.
Furthermore, and this is the only time I’m going to talk about those drug trials, really this evening, is that, as I think you realize the current drug trials, the Mirum study and the Albireo studies, are basically trying to reproduce the effects of partial external biliary diversion, like these patients had surgically, but they’re trying to reproduce that using a drug, by blocking uptake in the terminal ileum in the gut. And so it means that there’s there’s a very high likelihood that the same criteria are going to apply that if we can get the serum bile acids to drop, then we’re not just going to make the pruritus better.
By using those drugs, we will actually cause a major change in the natural history of the disease and keep those patients transplant free. Obviously that needs proving, but the data so far do suggest that is exactly reproducing the same results.
Dr. Richard Thompson 43:23
So let me just now pile on through a couple of other diseases quickly before I come to take your questions. So this is another picture of this canalicular membrane, and with the BSEP here, transporting bile acids into the lumen. MRP2 transporting organic acids like bilirubin into the lumen. MDR3 transporting phosphorylcholine into here so they can make those mixed micelles and FIC 1 transporting lipids into the inner leaflet.
So this area in the middle is the canaliculus. It’s trapped between two adjacent cells and it’s kept sealed by these structures, which are tight junctions. And so they form the barrier by gluing adjacent cells together. Because there’s no point in pumping all this stuff into here, if you can just leak back out again. And there are some extremely rare patients who’ve got mutations in these proteins, in particular Claudin 1, and they have a cholangiopathy. They have a form of sclerosing cholangitis. So they don’t have retention of bile salts, so they’re not having a form of intrahepatic cholestasis. They have leaked through here and inflammation, particularly around the bile ducts, and they have cholangiopathy. They are incredibly rare patients. Okay.
What was on my original table and some of you might know something about is patients who’ve got mutations in the so called tight junction proteins, and in particular TJP2, which we discovered a few years ago. This is not actually one of the…. not actually in the junction itself. It is inside the cell. But this is definitely responsible for anchoring some of these surface proteins. And in fact, the, on my table with the different diseases, the one on the very right hand side, USP53, is connected to TJP2. It sits in here, inside the cell, and is also responsible for anchoring surface proteins and some of the downstream consequences of that.
This is a electron micrograph. So this is an extremely high powered photograph of what, at the microscopic level, to show what this really looks like. And this space in the middle is the canaliculus. And rather than having a hollow space, like I showed it, it is essentially full of microvilli. So these are outgrowings from the cell and this obviously increases the surface area. So in actual fact, BSEP deficiency, MDR3 deficiency….sorry, BSEP protein, MDR3 protein, FIC 1 protein, most of them are actually sitting on the surface of these microvilli, which are extensions from the cell into this canalicular space.
And these are the tight junctions here, sealing two cells together. So this is one cell up at the top, this is one cell down here and these are the tight junctions sealing that on the side. And the claudins are the proteins in here. And the tight junction proteins, TJP2 is just inside the cell, here in this right there and so is USP53.
So MYO5B was called microvillus inclusion disease or microvillus atrophy and it’s these microvilli, the same things we’re talking about. And here you can see, this is not a canaliculus, like I showed you just now. This is actually inside a cell. This is a membrane bound vesicle covered in the microvilli. And this vesicles should be transported to the surface, and their microvilli would then become part of the microvilli in that canalicular space, but it’s got stuck inside the cell.
This is the problem with MYO5B is that it’s actually a transporter which moves these vesicles around inside the cell and gets them to the place they’re needed. And as I say, originally, this was described because of a problem with gut disease, but now we recognize it as a cause of liver disease as well. Long before I…. separate, a separate liver disease was established, the French described the fact that actually there was a problem with bile salts export pump deficiency. Secondary deficiency, because of course, BSEP is on these little microvilli here. And if those microvilli, the whole of this vesicle doesn’t get to the membrane, there’s not enough BSEP on the surface.
So the BSEP itself is perfectly normal but it’s not getting to the right place because these little vesicles are getting stuck inside the cell. And just very quickly, that’s what this is a this is what happens inside the cell. This is exactly …this cartoon is even better. And so this is a great big vesicle the top here, being pulled along an actin strand by MYO5B which is a the atypical myosin, which is dragging this cargo. And this cargo is the membrane containing those microvilli and BSEP and everything else, dragging it along an intracellular protein filaments of actin, dragging it up to the canalicular membrane where we need them. This is what goes wrong in MYO5B.
Dr. Richard Thompson 49:09
And lastly, because it’s the newest really of these, this is seven patients that we’ve described recently with variants in USP53. And so there was one family, there was a paper published from the Middle East with one family, with patients with mutations in USP53. Again, there’s a paper from China, with seven patients all with neonatal cholestasis which resolved.
But our seven patients here, as you can see in the middle, three months, two months, five months, seven years of onset here. But also the patient that had an onset at three months, it resolved but then recurred after nine months, 11 months, and then six years. As you can see a patient over here actually presented with cholestasis at 15 years, then again at 16 years and 18 years. So I think this series of ours really shows that USP53 is very variable phenotype.
And the one thing I can tell you is that this is not going to be simple to work out, genetically why that varies, because some of these patients, this patient here, and this patient, here, have got the same change on both copies, is predicted to cause no protein whatsoever. But this one had neonatal onset, and then several episodes and this one didn’t present until seven years of age.
And most importantly, because the original Chinese, the Chinese paper said that they all had early onset jaundice that went away, as you can see down the bottom here that several of these patients have got enlarged spleen, suggesting they’ve got chronic liver disease. And several of these, I haven’t got it on this picture, but several of them have got fibrosis and scarring in the liver, so they have actually got progressive liver disease. So this is not just a simple, transient cholestasis in babies, which is what was suggested by the Chinese paper.
Also, importantly, these patient, none of these patients have been described as having any problem with hearing, although some of them are still young. But there was…I can’t remember…. I think it was three or four of the Chinese patients had a failed hearing test, the neonatal hearing tests, suggesting they’ve got a problem with hearing. And the Middle Eastern patient…. I’m lying now the Chinese didn’t have that. Anyways, the Middle Eastern patients have got major hearing problems so that when this gene is expressed in the ear as well.
So we it’s critically important that these patients actually have follow up to check their hearing because we believe they are at significant risk of developing later onset hearing problems. And as I’ve already said, it’s associated with the tight junctions and this is actually in a normal bile duct and you can see the staining for USP53, the brown stain at the top here, but this is at the junctions between cells. There’s one cell there. There is another junction here between cells. And this is a normal this is what’s missing obviously in USP53.
Dr. Richard Thompson 52:32
So this is a gross simplification but um hopefully you realize if you come across patients with Alagille syndrome, they have got a problem with bile duct formation. I certainly haven’t talked about it but there’s a very rare patients with problems with actually synthesizing bile acids. There’s seven different types of that. There’s…. BSEP patients have problems with bile acid transport itself. FXR, which I haven’t talked about in detail today, have a problem with regulating bile salts both in the liver and the in the intestines. MDR3 is a problem with lipid transport into bile.
FIC 1 is definitely a problem with the membrane lipids and TJP2 may be having an effect on membrane lipids but I’m can’t possibly go into that today. Moving membrane and protein around definitely MYO5B, definitely ARC syndrome, which are not talked about, possibly TJP2 and USP53. And again, these problems it does look like having not having these proteins there means that the apical membrane is not formed properly in some cases. Claudins are the actually the tight junction proteins itself and are vanishingly rare, but tight junctions obviously are intimately associated with that. And then there’s a whole growing group of diseases now, which we call ciliopathies, which are cilia are, in the liver, regulatory organelles in bile ducts, which regulate bile flow.
And there’s now a growing number of conditions, whether the failure of normal cilial function, and they generally have inflamed biliary trees, they have sclerosing cholangitis and even some cases of biliary atresia now have variants in genes that encode proteins that form cilia. So we are starting to unravel the…biliary atresia is not a genetic disease, but there’s definitely genetic contributions to it. And the biggest genetic contribution we’ve found so far, are in these cilia, these regulatory, bile flow regulatory proteins.
So I hope that makes sense. I hope there was nothing there was too much of a surprise. I hope there was some things which were useful. And I’ll be extremely happy to take any questions.
Emily Ventura 55:06
Thank you so much, Dr. Thompson. It was very, very helpful. I actually have quite a few positive remarks, quite a few thank yous directly to you for making this information available. I know it’s very difficult topic to discuss, especially make in a way that is, you know, able to understand by all. So I think you did a really incredible job. Thank you for that. So I do have a few questions that we can roll into. First question, kind of more so about BRIC. So there’s a group of patients that have come together with some sort of, kind of hormonal link around BRIC, whether it’s pregnancy, puberty.
Dr. Richard Thompson 55:51
Emily Ventura 55:52
And so the main question is, per, is there any, do you have any access to research or thoughts around the hormonal link triggering BRIC episodes, or perhaps making any progressive disease worse.
Dr. Richard Thompson 56:09
So both of those things definitely happen. So there’s definitely patients who have got reduced BSEP function, for instance, who actually are coping, okay. They’ve not got accumulation of bile acids, but they only have a problem when they’re exposed to certain hormones in particular, and we know that progesterone is particularly bad. But it’s not exclusively progesterones.
And we know this, in some cases, it’s the the, the actual hormone that’s been transported into bile and once it’s been transported, then it actually reduces the BSEP function. So there’s definitely some patients where it’s been pinned down to that extent. Now, one of my colleagues at Kings is spends her entire life working on liver disease in pregnancy. And so they’ve got some explanations now, but they’re still working hard to get the rest. But there’s a completely separate question, which is absolutely no doubt at all, is that if you’ve got pre existing liver disease, then pregnancy can make it a lot worse.
And with MDR3 deficiency, I’ve seen a number of women now who had no symptoms, had were not known to…had never seen a doctor until they got pregnant, and when they got pregnant, they became very cholestatic and it’s clear they had actually progressively advanced liver disease. And these are women with MDR3 deficiency, and they’re somewhere in the middle there. Maybe they’ve got about a quarter of function, something like that. They haven’t got zero, but they’re worse than 50%, maybe about a quarter of MDR3 function, and they’ve had a slowly grumbling problem with the bile ducts, but no, no features.
They’ve never been jaundiced, never been itchy, until they got pregnant, and the pregnancy has unmasked it. And several of those patients have gone on to need liver transplant because they actually got progressive liver disease. This required transplantation. But they had no symptoms at all, until they were pregnant. Now, the vast majority of people that get cholestasis of pregnancy, do not have that. They’re gonna get better. There’s a risk to the baby, but there’s very little risk to the mother. But there is these other patients who genuinely have progressive disease, but it’s only unmasked and becomes clinically evident during pregnancy. So there’s all those possibilities with these genetic diseases, unfortunately.
Emily Ventura 58:40
Okay, in the same category, what about puberty, puberty, triggering BRIC episodes? Is that something that you’ve seen?
Dr. Richard Thompson 58:47
It definitely happens. At least you see, even with those USP53, I think you can see that there’s sort of clustering around puberty as well. So obviously, we all know that there’s massive hormonal changes, and it’s not too surprising. But of course, the other thing that happens in puberty is you you actually have huge demands on your liver as well, because you are growing rapidly. So there’s two things, there’s the hormonal changes, but there’s also there’s a much greater demands on the liver.
So, you know, we’ve got patients with, we know about with end stage liver disease, and actually, they can’t go through puberty because they just their body is incapable. They cannot summon up the energy, if you like, to go through puberty. So it can unmask some of the milder ones, but it can be a big problem in patients with severe disease.
Emily Ventura 59:34
Okay. Okay, thank you. So next question. This is coming from a patient who has MDR3, but I think I can kind of apply to most patients. So she was diagnosed via liver biopsy. But wondering if that is a concrete diagnosis or if genetic testing is needed to solidify that diagnosis?
Dr. Richard Thompson 1:00:04
Hmm. Well, that’s particularly interesting, actually. Because if we go back, right to the beginning, as you, as I showed you that MDR3 deficiency is on this slope. And so there’s actually very few patients all the way across at the left hand side of that slope. And to have no MDR3 staining on a biopsy requires you to be right across at the left hand side. So the majority of patients with MDR3 deficiency that are on that slope actually have staining for MDR3. So I don’t know how what sort of test they’ve had, but if they’ve got a complete absence of staining, then that suggests that they have got quite a high degree of lack of MDR3.
Now, with all these stains, there is an important proviso. And I think, you know, in reference to the exact question, I would say, there’s one word of warning. Because what we know is that there’s, if you’ve got a badly damaged liver for various reasons, then sometimes these proteins are not in the right place, and don’t stain normally. So if we are staining for MDR3, or staining for BSEP, if we’re staining for that protein, and we always stain for a number of other proteins. And actually, the one that we always use as a control is the bilirubin transporter MRP2. So we would have to see MRP2 there, normally expressed, to be able to say that MDR3 was missing.
Because in a damaged liver MDR3 could be missing, and MRP2 was missing and then that wouldn’t tell you anything about MDR3 at all. It was just because of the degree of liver damage, and it may be a nonspecific effect. Which may be only temporary or it may be a permanent thing, but it’s a secondary consequence of something else. So a complete absence of MDR3 is useful. But you will definitely have a normal presence of MRP2 for instance, just as a control. But if you really want to know how bad things are, then I think genetics these days is giving us more information.
And as most people know, genetics is much more widely available now and certainly in in the US, is basically available free to most people. Not all over the world, I do admit. So I think the combination is still ideal to try and make a diagnosis because you can have and with BSEP as well, you can have dramatically abnormal BSEP staining, where there isn’t a BSEP mutation, there’s not BSEP disease, but there’s usually abnormal staining for other proteins as well.
Emily Ventura 1:03:01
Yeah, the topic of genetic testing seems to have changed a bit since you and I first met a few years ago.
Dr. Richard Thompson 1:03:06
Absolutely. Yeah, no, I’m pleased to say it has. It has become much more widely available. Thank goodness,
Emily Ventura 1:03:12
Do you think it’s gonna become the gold standard of diagnosis as time goes on?
Dr. Richard Thompson 1:03:16
It’s not perfect now. And as I’ve alluded to, right at the beginning, when I was describing how to interpret the results, it’s not perfect. It doesn’t always give us yes/no answers. But it’s, it’s… even that is improving rapidly. So I think the the answers you’ll get will improve dramatically in the next few years. At the moment, you know, we still do biopsy a lot of patients, because it gives us a lot of information. But you know, when we combine all that information with the patients and the genetics, then we are learning rapidly, such that in a few years time, we will be able to use the genetics alone, I hope, to give, you know, a really accurate idea.
So with BSEP, as you saw, we’re starting to get somewhere nearer to that, where we can start to make some predictions just on the genetics, but it’s not perfect. And for these other diseases, we’re a bit further behind still, just because of the numbers. But it is not far away where genetics will give us much better prediction of what really, we want to know, which is how quickly the disease is going to progress, what are the complications likely to be and what treatments are likely to work, which is clearly there’s what we really want to know.
Dr. Richard Thompson 1:03:30
Right. Well, that’s hopeful at least.
Dr. Richard Thompson 1:04:35
Yeah, yeah, yeah. We’ll get there. We’ll get there.
Emily Ventura 1:04:37
Yeah, yeah, it’s going well. Okay, so a few more questions, more related to kind of treatment within subtypes. For PFIC 1, based on what you’ve learned so far, is, you know, clinical trial or diversion treatment showing to be effective in PFIC 1 patients?
Dr. Richard Thompson 1:04:58
Okay, so biliary diversion, as you know is you know, has been shown to work quite well in BSEP and FIC 1, but it’s unfortunately, it’s only sort of about 50%. And it’s about… overall it is about between a third and 50% of BSEPS. And if you take out the BSEP 3s, it improves. In FIC 1, overall, it’s about 50%, that have had a good response to biliary diversion. Now, rather frustratingly, the Mirum study, the first ASBT inhibitor really didn’t show any response in FIC 1 deficiency.
I’m optimistic that the Albireo study is going to show a better response. But we have to understand why it is that biliary diversion seems to be better than the drugs so far. And that may be something to do with dose. Maybe we’re not using it the best we could, because clearly they should be having a very similar effect. Obviously, with FIC 1, as I’ve already said earlier, it’s a much more complicated disease. It’s not just the disease of the liver. And obviously, we are going to have to be much cleverer about how we try to improve the function in the gut, as well as improve the liver as well.
Because clearly, it’s possible that we will just, by putting all the bile acids into the intestine, we’re actually going to make diarrhea a lot worse, for instance. So I think it is a more complicated disease. And I’m pleased to say, I said to you the other day, I think there’s now people becoming even more interested in FIC 1 deficiency, in terms of drugs. And there are some, some definitely some possibilities, but they are several years away from clinical trials still, I’m afraid. But it is a more complicated disease. And we have to understand why the diversion works in some and not others, because that’s not explained genetically yet.
We’re further behind than the BSEPs in terms of understanding the response to treatment for FIC 1. It’s definitely not as simple as the BSEP genetics, which still not simple. But with FIC 1, we’ve haven’t found the correlation, at all, between why some people respond, and some don’t. The drugs are frustrating at the moment, but again, we need to understand that as well. We’ve still got tons to do.
Emily Ventura 1:07:27
You definitely have a lot of work on your plate. I’ll tell you that. So that’s a little bit different, though. So then the BSEP patients. And BSEP patients, it seems as though if diversion isn’t going to work, the medication isn’t going to work. But in PFIC 1, maybe that’s a little different?
Dr. Richard Thompson 1:07:45
Yes. It may not be that simple. Exactly. Yeah. Yeah. So I think we’ve got to we got to establish that. Absolutely.
Emily Ventura 1:07:54
Okay. So another question, what is the likely chance of having a pharmacological solution to correcting the BSEP protein?
Dr. Richard Thompson 1:08:06
Okay, so that’s a really, really good point. So, as some of you will know, definitely, there are now drugs, which increase the function and expression of the cystic fibrosis protein, for instance. And clearly, if we could do something similar for BSEP, for instance, which would be great. We could, if we, as I’ve shown you from my graphs, in fact, we don’t have to get 100% of function. We just get a few more percent of BSEP function, that might be enough.
And actually, to have the… for these drugs that are in the current clinical trials now, the ASBT inhibitors, to get them to work, you still need a few percent of normal functional BSEP. The ones where there’s no BSEP, still doesn’t work, the BSEP 3s. But if you get what you need to get those drugs to work, you need a few percent of functioning BSEP. So actually, if we can get one of these little molecules like the like the ones that are being used for cystic fibrosis, we may only need to get a few percent of BSEP function in combination with one of these current drugs and we’d have a really good response. So it may be that what we don’t we don’t need to get a massive increase in BSEP expression.
We, if we can, using the current drugs that are in clinical trials now, all we need to do is to increase BSEP by a few percent and they will become responders. So that may well be the future is that we ended up using these drugs in combination. Which, you know, if it does the job, and the side effects are okay, then that’s what we’ll have to do.
Emily Ventura 1:10:00
Okay. Have you learned…….have you learned…..how do I want to ask this question? So for the, the BSEP group that has recurrence of disease post transplant
Dr. Richard Thompson 1:10:18
Emily Ventura 1:10:19
Have you learned which cohort kind of goes to that complication or is that still something that’s up in the air?
Dr. Richard Thompson 1:10:29
Okay, so in simple terms, if your immune system has not seen BSEP protein before transplant, then you’re at the highest risk of getting antibodies after transplant. So it comes that BSEP 3 group. Again, it’s bad news, because they are the ones which really can’t make protein. So they are the ones that are definitely the most likely to get antibodies after transplant. But hidden within BSEP 2, which is by far the biggest group, is this middle cohort.
Some of those people are actually able to make small amounts of protein. Many of those are not, which accounts for why they don’t all respond to treatment, because actually, some of them are just as bad as the BSEP 3s. It’s just that we’re not clever enough to work out which they are yet. So I’m sure it’s the ones that haven’t made protein before. Some of those are clearly the BSEP 3s, where they’ve not made any protein and ww guarantee that they have not made any protein. But some of the other ones are the hidden group in the middle, where they almost certainly weren’t making protein, but we were not able to predict it 100% genetically. Because the key obviously, is that you don’t…. if you haven’t made any piece of protein beforehand, then in your new liver, you will recognize this as a foreign protein.
But the truth is, in an intact liver that’s working normally, the immune system really doesn’t see BSEP because it’s on the far side of the liver cells. It is in the bile spaces, not being exposed to blood. And so in a really well functioning liver, BSEP is not being exposed to the immune system. So the the person who’s had the transplant doesn’t necessarily start making antibodies or other parts of the immune reaction against BSEP. So that’s what we’ve also seen is that it often takes something else to happen, some inflammation in the liver, a CMV infection, rejection, other factors that cause some damage, that then allows BSEP to be seen by the immune system, and then the body starts making the antibodies. And once they’ve made the antibodies, then the antibodies actually can go across the hepatocytes and get to BSEP.
But it’s recognizing BSEP in the first place is what they don’t necessarily do. And that’s why we’ve seen patients sometimes that have only had this problem several years out, but it is almost certainly where something else has caused some inflammation in the first place and made the BSEP exposed to the immune system. So in terms of causation is definitely is the patients that are really had no protein there before, but we’re not perfect to predicting which those patients are yet.
Emily Ventura 1:13:30
Dr. Richard Thompson 1:13:31
Again, we’re not clever enough…..yet.
Emily Ventura 1:13:32
I’m not going to go down that road, you’re fairly clever, but I’ll skip over it.
Dr. Richard Thompson 1:13:38
Only fairly. Not very by any means at all.
Emily Ventura 1:13:42
I have a few more questions on this topic. Are you able to stick around for about five or more minutes?
Dr. Richard Thompson 1:13:47
Of course, of course.
Emily Ventura 1:13:48
Thank you very much. So it’s, it’s all in relation to this current conversation. Let me just kind of read through this real quick. So okay, for kids…and I guess we just kind of talked about this… who had relapse of symptoms post transplant, if we could just increase BSEP by a few molecules, would the symptoms clear? You kind of
Dr. Richard Thompson 1:14:11
Oooh ooh, hang on. Say that again. I’m not sure I can see the questions here… the right questions.
Emily Ventura 1:14:18
Oh, yeah, so we’re down here. Would that be true for the kids that have had relapse of symptoms post transplant? If we could just increase BSEP by a few molecules?
Emily Ventura 1:14:26
Right. It is the body’s response to the BSEP that it did not have pre transplant.
Dr. Richard Thompson 1:14:26
No, no, no, no, no, no. Because the relapse post transplant is nothing to do with the amount of BSEP that’s there. It’s because there’s antibodies stuck on it. So the patients that have relapsed post transplant…. I hate the term relapse because it’s not relapse at all. Because there’s tons of BSEP protein there. There’s absolutely nothing wrong with the BSEP. It’s fully functional. There’s perfectly good amounts of it. It is just that it has got an antibody stuck on it, okay. So a small amount of increase in that is not going to make any difference. So, doubling the amount of BSEP may not make any difference at all. It is not the amount of BSEP. The BSEP is perfectly fine in terms of amount and function, but it’s got antibodies stuck on it, so no.
Dr. Richard Thompson 1:15:14
Correct. Absolutely, yeah.
Dr. Richard Thompson 1:15:17
So it’s not relapse…the mechanism there….of course, people call it a relapse. I understand why that is because the features, the symptoms and everything are so similar to what happened before. But the mechanism is completely different, so the treatments are going to be completely different.
Emily Ventura 1:15:34
Okay. Would a biopsy show if the body is making any of the BSEP protein, or is there any way to test how much BSEP a body is making? I know, you’re talking about these cohorts with genetic testing, is there another way?
Dr. Richard Thompson 1:15:49
So, I mean, obviously, we can do staining for BSEP protein. But it’s not, at the moment, those stains are not very quantitative. And even these BSEP 2s, even people that respond nicely to diversion and things, often have got very low levels of protein on when you stain them. So unfortunately, staining is just a sort of fairly crude test at the moment. Plus the fact that with these missense changes, that is where you change one amino acid in a protein to another, it’s possible that you’d have perfectly normal amounts of protein, but it doesn’t work properly.
So the staining has some correlation, but it is definitely not telling you the same thing. Because you can have a there are a few patients who’ve got perfectly normal stains, and no function at all because they’re making the protein, but it doesn’t work.
Emily Ventura 1:16:57
Dr. Richard Thompson 1:16:58
So genetics is complicated. The proteins are not perfect, either. At the moment, it’s really still helpful to have both. I was going to say, in a few years time, we’ll be able to predict better from the genetics, but at the moment, we learn from both unfortunately.
Emily Ventura 1:17:16
Dr. Richard Thompson 1:17:17
It’s not ideal.
Emily Ventura 1:17:19
That’s very helpful, though. I have one more question unless somebody anybody else has another one to ask in the meantime, but I think it’s a fantastic one to drive home on. What about gene therapy? Are we anywhere near gene therapy for PFIC?
Dr. Richard Thompson 1:17:35
So if you looked on my disclaimer slide, you will see a number of companies on there that are involved in gene therapy. The first thing to say the good news is the liver is actually a ideal organ to conduct gene therapy. So delivering new genes to the liver, whether it’s through viruses or not through viruses, to avoiding viruses, both ways around, we can deliver genes to the liver very effectively. In very simple terms, diseases where there’s a genetic disease in the liver divide into two types. There’s ones where you get progressive liver disease, which is most of the ones we’re interested in.
And there’s ones which don’t. And so the other ones that don’t are ones where they’re often where there’s a metabolic defect, where there’s an enzyme deficiency, and things like Crigler-Najjar, where they can’t conjugate bilirubin, or some of the urea cycles, some of these enzyme defects. So where there’s no damage to the liver, but the liver is not making a protein.
For instance, clotting factors like hemophilia, where the protein is made in the liver, but there’s no damage to the liver itself. Now, those conditions, where the liver is absolutely fine, and it’s not getting progressive liver disease, but the liver is not making a protein are very attractive to the companies developing gene therapy because they haven’t got to worry about the disease. They haven’t got to worry about the cell turnover and the remodeling of the liver and all that. They just need to be able to deliver protein and it will solve the problem.
But that’s okay, because that’s a testing ground and that is where these things will start. So unfortunately, the liver diseases that we’re really interested in are not going to be the first ones to get liver directed gene therapy. But we have to live with that because these things are only going to happen step by step. So but the liver is a great place to deliver genes to and it is happening and it’s happening on you know with different types of viruses.
The adeno associated viruses are…. many programs are working on that. There’s the lenti viruses, which are more like retroviruses like HIV, which have got other advantages. And there’s the nonviral companies. So the all three have got types, and there’s there’s dozens of people using the adenoviruses. Virtually all those companies have got programs delivering gene therapy to the liver. But PFIC is not going to be the top of anyone’s list, unfortunately, even the companies I’m heavily involved with. Clearly, I’m constantly pushing and pushing and pushing, because but I totally understand that we’ve got to get really good at delivering these genes to the liver.
And then we will tackle the far more complicated problem which we have, which is where you got a damaged liver, you’ve got liver that’s got fibrosis and scarring, you’ve got a liver that is making new cells all the time and the cells are dividing, and actually delivering effective gene therapy and really curing the disease in that context is going to be several orders of magnitude more complicated. So it will take a bit longer, but we are heading in that direction. And obviously, for patients, for instance, that have got no BSEP, let’s take the simple patients.
They’ve got two protein truncating mutations in BSEP. I’ve already said, I don’t know how many times these patients are the worst. They are 20% of the BSEP patients. They’ve got the highest risk of malignancy. They don’t respond to the current treatments. Even the chaperone molecules, like the cystic fibrosis molecules, are almost certainly got no chance of working in those. Those, so those patients have got a copy of BSEP which doesn’t work at all.
So really, we’re going to have to deliver a new copy of BSEP or we’re going to have to have gene correction where we put that gene back to the right, which is even further down the line. So that 20% of BSEP in particular are going to be obvious candidates for gene therapy. But we will get there. Gene therapy in the liver is happening. But it’s not happening for the diseases we want yet. But we have to do it step by step.
Emily Ventura 1:22:23
Dr. Richard Thompson 1:22:24
It’s a few years away, but we’ll get there.
Emily Ventura 1:22:27
I think we can live with that. I think knowing that it’s out there and that it’s a possibility someday is helpful.
Dr. Richard Thompson 1:22:35
Oh, yeah. I mean, I for ages, gene therapy seemed like it was five years away. And you know, for 20 years, it seemed like it was five years away, which clearly was bonkers, because it was always just around the corner. It is happening now, but not in these diseases yet.
Emily Ventura 1:22:52
We just got to keep these diseases as forefront as we can, so that when it’s available,
Dr. Richard Thompson 1:22:57
Don’t you worry. We’re push, push, push. But there’s logical reasons why it’s not the first line. You know it’s not just about because drug companies try and make money. Biologically, it is… these are much more difficult biologically to deliver effective gene therapy.
Emily Ventura 1:23:16
Right. Understood. Thank you for that. As we were, as we’re going through, there was one more question about the BSEP protein. So I’m going to ask it, I think it’ll it won’t take you too long to answer. Is there a way to tell if the BSEP protein is limited in quantity or just a misconfigured protein?
Dr. Richard Thompson 1:23:36
Well, in a patient with huge difficulty, but obviously, we’ve we’ve done a huge amount of work in the lab, trying to with individual variants, working out exactly what the mechanism is that causes the disease. So because the variants we discover are actually in DNA. DNA has to make a usable copy of RNA. RNA has to be heavily modified, processed, to make messenger RNA.
From messenger RNA, you have to make protein. Once the proteins made, the protein has to be then modified by a whole range of different enzymes, then the protein has to be taken to the cell surface and then it has to work normally. So there’s numerous points down that pathway where these mutations are actually causing disease.
So it is sometimes it’s about the amount of protein. Sometimes it’s about the amount of mature protein. Sometimes it’s about the actual function of the protein. And so we published a paper…. I can’t remember…. it’s 15 years ago, and we looked at 62 different mutations. And we characterized what the changes were and what we know in each of those mutations and which ones were the amount of protein, which ones were our mRNA processing etc.
And there’s very few genes that have actually had that level of study. Cystic Fibrosis has been studied like that, because there’s there’s mutations because it’s obviously seen as an important disease. In truth, we could, we could not get any funding to do that. I did all that work with money that was really supposed to be doing other projects, that we knew sort of stole money and did that. Because no one would fund us to do that.
They just said, “It’s, it’s sort of just navel gazing and who cares? They’ve got mutations and they’ve got disease. ” Well, we care, so we did that. But we looked at 62 gene mutations. It was a huge amount of work and I had a fantastic scientist and she took about four years to do it. But it’s a great publication, but it’s only 62 variants, and we’ve got hundreds of them now. But it gives us some insight into it, but we can’t…well at the moment, technologically, and well, more importantly, financially, to do a detailed analysis of every single mutation is totally prohibitive.
Emily Ventura 1:25:59
Okay well, that comment alone gives me and us some direction, I’ll just say that. Um, thank you so much. If you look at the panelist chat, you have a ton of a ton of thank yous. Everybody’s very grateful for your talk. We gained alot. And thanks so much for your dedication to PFIC and for taking the time out of your evening, on a weekend, to speak with us. We really, really, appreciate it.
Dr. Richard Thompson 1:26:25
In case in case people haven’t realized, I live and breathe this. I love it. And I’m determined to do as much as we possibly can to improve people’s quality of life. That’s, you know, and the only way we’re gonna do that is understand the biology and then try and fix it.
Emily Ventura 1:26:42
Well, we really appreciate it. And we’re very grateful that we have somebody like you working on our very rare disease. So thank you so much. For those listening, we have two more webinars in our educational series over the next month. We have a mental health talk coming up this Tuesday for coping strategies dealing with PFIC, things like the itch and sleeplessness and just dealing with a chronic liver condition.
And then there’s going to be a group from the Children’s Hospital Colorado presenting PFIC 101, which will be next month, December 8 at 7:30. So you can tune in for those. All of these are going to be made available on our website and on a YouTube channel. So you’ll be able to watch and rewatch so that we can really take this information in. But thanks again, Richard and to all the rest of the speakers. We’re really really appreciative. Hope you have a good evening.
Genetics of PFIC and Its Subtypes
2020 Educational Webinar Series
Dr. Richard Thompson is a Professor of Molecular Hepatology at the Institute for Liver Studies, Kings College London and Consultant Pediatric Hepatologist, at Kings College Hospital. He will discuss the complex topic of the genetics of PFIC, including the various subtypes and why they are each so unique. Dr. Thompson will also dive into some of the barriers behind genetic testing and why PFIC is so difficult to treat. He will then give us a quick look at what has been recently discovered in the genetics of PFIC.
This session is moderated by PFIC Network Executive Director and Co-founder, Emily Ventura, RN.