Alexander Disease Research Update
Discussion of recent publications from the research literature on Alexander Disease, hosted by Albee Messing from the University of Wisconsin-Madison.
Alexander Disease Research Update
Alexander Disease Research Update - Episode #14: whole exome/genome sequencing; more questions on the brainstem
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Albee Messing and Josh Bonkowsky discuss the following recent publication:
[02:13] Identification of a novel de novo pathogenic variant in GFAP in an Iranian family with Alexander disease by whole-exome sequencing.European Journal of Medical Research 27, 174 (2022) [full text]
[14:20] Questions from email regarding the brainstem in Alexander disease.
Send your questions and feedback to: axdrupodcast@waisman.wisc.edu
Help support research on Alexander Disease at the University of Wisconsin-Madison's Waisman Center:
Hello and welcome to Alexander Disease Research Update, episode number 14, recorded on November 8th, 2022. I'm Albi Messing from the Wastement Center at the University of Wisconsin. And with me today is Dr. Josh Bonkowski from the University of Utah. Josh, since this is your first time on the podcast, can you say a bit about your background and current position?
SPEAKER_00Albi, thanks so much for the chance to uh talk with you and with your audience. I am a professor of piatric neurology and I work at the University of Utah. And the children's hospital here is primary children's hospital. I'm the division chief for piatric neurology and also lead the Center for Personalized Medicine at the hospital. I grew up in Georgia back in my childhood days and went to college at Harvard. Then after Harvard, I decided I need to light out for California. So I went to the University of California in San Diego for my MD and PhD training. And then in 2000, moved to my residency training and fellowship training at the University of Utah and Primary Children's Hospital. And now I've been here almost 22 years and still doing good so far.
SPEAKER_01Thanks again for joining us. Before we get started, please send feedback to AXDRU podcast at Wastement. That's W-A-I-S-M-A-N.edu. Today, our topic will be a recent case report that provides a good example of how advances in DNA sequencing and genetic testing are changing clinical practice. In addition, we'll address a question that has been sent in about the brainstem and how that area of the brain fits in with Alexander disease being a leuko dystrophy.
Identification of a novel de novo pathogenic variant in GFAP in an Iranian family with Alexander disease by whole-exome sequencing
SPEAKER_01Let's begin with the publication. This is by Heshmatzad et al. and is entitled Identification of a Novel De novo pathogenic variant in GFAP in an Iranian family with Alexander Disease by Whole Exome Sequencing. And the goal of this study was essentially a case report, and then strangely a literature review on topics unrelated to the case. But nevertheless, let's talk about this young girl who presented at the age of two years. Her symptoms began at the age of one and included developmental delay and vomiting, and later included seizures and delays in both speech and motor abilities. MRIs done at the age of two showed abnormalities in her frontal and parietal lobes that suggested either oleuchodystrophy or hypoxic, ischemic, encephalopathy, which is due to a loss of blood supply or oxygen that is not genetic in origin. The physicians proceeded to do whole exome sequencing and found a variant in GFAP at position 73, which normally encodes a methionine, and this variant changes that to a valine. Now, there have been previous reports of methionine 73 changes for Alexander disease, actually, four of them changing to either isoleucine, lysine, arginine, or threonine. So by itself, finding another variant in methionine 73 isn't so surprising. But what I found most interesting about this report was their immediate use of whole exome sequencing for diagnosis. I think that brought up in my mind this general question of how clinical practice might be changing in really fundamental ways as a result of new techniques in DNA sequencing. I can divide the way Alexander disease has been diagnosed over the years into several distinct phases. Initially, it was based on pathology in the 1990s and 2000s. MRIs were increasingly used to provide diagnostic criteria. We then entered the phase of single gene sequencing once we realized that GFAP was a causative gene for nearly all patients. Then I think there was a somewhat brief period where people used candidate gene panels, just short lists of genes that they thought might be responsible. And then we're entering this new phase where increasingly we see that whole exome sequencing or even whole genome sequencing is being used. Certainly from the literature, it seems like it's in very common practice. And I couldn't think of anybody better to answer these questions for us than Josh Bonkowski. So, Josh, let me ask you a couple of questions about this. How common is it for clinicians to now use whole exome or whole genome sequencing in their initial diagnostic work?
SPEAKER_00Yeah, Albi, that's it's a great discussion point. I think that the paper by uh Hesh Matad et al. uh, you know, illustrates uh how this has become you know routine clinical practice. And so I think I've lived through all the epochs of different types of testing they describe, ranging from pathology to MRI to single gene testing to this next generation sequencing. And it's a real revolution. We have moved where we can order whole genome sequencing on a patient in the hospital and have a result back in two to three days as a routine clinical practice. We're doing like two to three cases a week in the hospital of whole genome sequencing. And then on the outpatient side, the same thing is happening. It's slower than the outpatient side is because of insurance barriers, but we are getting whole exome or whole genome as routine clinical standard of care for a lot of our patients. And that's just a huge change.
SPEAKER_01Right. So obviously, the appeal of whole genome or whole exome sequencing is that it's unbiased in most respects, and you're not putting all your eggs in one basket as you would be if you were just sequencing GFAP. But there are a number of limitations of it too. So I wonder if you could discuss not only the strengths but the weaknesses. And in light of the fact that there are weaknesses, has the consent process changed the way you talk to people about whether this would be a worthwhile thing to do?
SPEAKER_00Yeah, I think that the things that we've seen are that for most patients, we're testing because of a disease condition. And so the risks of finding something that we don't intend are far outweighed by the need to make a diagnosis with someone who's facing a disease that could be progressive. And so there are risks of privacy and risks of you know parental, you know, who's the parent, or risks of finding some consanguinity in the past. But if you have a child who's experiencing a disease or a person who's experiencing a disease, that's much more important. And so I think that we as medical professionals have been we've been a little bit paternalistic in our concerns. I think that families and patients want answers. And so I think those needs outweigh our paternalistic concerns.
SPEAKER_01All right. Well, there are two limitations I want to ask you about specifically. One is we often see this phrase difficult to sequence. So when you talk about either of these methods, it's not really 100% coverage of the entire genome. There are certain areas that just aren't accessible. Roughly what percentage is that? And are we gradually developing ways to include those in the coverage as well?
SPEAKER_00That's a good point. That even with our best, for example, whole genome sequencing that we use clinically, we're maxing out our diagnostic rates around 40 to 50 percent, even with kids or families where it's gotta be genetic. There's like it seems like a genetic disorder, but we max out with diagnostic rates of 50%. And we can chip away with new technologies. So, for example, there's a new technology called long read sequencing, which maybe gives another 5 or 10% diagnostic rate. Adding in something called RNA-seq gets us another 5 or 10%. So it seems like through kind of technological improvements and kind of tricks of technology, we can maybe get up to the 70 to 80 percent. But there is a concern that there's some last piece of understanding that we're missing out on. Maybe it's something called methylation that we're missing out on, but there's probably one more technological hurdle to really achieve full diagnostic rates uh with genome sequencing.
SPEAKER_01So now my impression of this field is that the ability to do the sequencing has outstripped the ability to interpret the data. What I heard from some physicians several years ago that the real limitation at their institution was on the interpretation side. Has that changed in a fundamental way?
SPEAKER_00So the problem that's occurred is that we sometimes get results back where we don't understand whether this variant or genetic change is causing disease, or we're not even sure which variant we should be looking at. But that's becoming less and less less and less of a problem. And so it is still a concern, but practically speaking, no. It's not now we haven't solved the problem, but we know it's a problem and we know how to deal with it. So it's uh it's kind of a known risk.
SPEAKER_01GFAP is 432 amino acids long. With all this new sequencing data that we're getting, we're increasingly getting variants at different positions or different types of variants at a single position where the case for whether they're really causing disease isn't so clear. And so these fall into the category of variant of unknown significance or VUS. Are there well established ways of determining whether a variant is really disease-causing or not? Or if it is in this VUS category of using various experimental tools such as animal models, to try to figure out whether it might be disease-causing. I was going to bring up zebrafish.
SPEAKER_00No, I think the VUS problem, I think no one's got a great handle on how to deal with it. So I think that zebrafish, uh, it's turned out that they're slower than we wish. It takes, you know, it takes a half year to really pin down a variant. And you know, half year per variant, it's kind of slow. Like, and so if you have thousands, you know, really we have like thousands of variants where we don't know what's going on. So like you can't do a half year per variant, right? Um, and the same problems true in Drosophila, the same problem is true in in yeast. I think none of the bioinformatics approaches are very believable. I don't think we have a comprehensive strategy for VUSs that offers a clear solution at a cost and time limitation that we that's believable. I don't I don't think we're there. We don't have there's not a really a clear path forward at this point.
SPEAKER_01And there are a number of ethical issues that seem to have arisen as well. And I know that you've published on some aspects of this. Could you talk about what you think are the most important ethical issues?
SPEAKER_00As we use this technology more and more, we are realizing that we have issues of uh around kind of several ethical issues for for patients and how use this technology. So, one issue is uh making sure that everyone has equal access to this. So, so for example, if you come to see me in the hospital and I can do this test, can you afford to pay for it, or does your insurance refuse to pay for it? If you live in inner city Baltimore, is there someone who's gonna be able to give you this test? And is it fair that I can you know offer this to someone living in the suburbs, but I can't offer it to someone living in the inner city? So there's issues with cost and equity. Another issue is that we we have lots of information about people who live in the United States with this testing, and so that means that we can interpret the results well. But if you live in Africa or India or China, we have much less information about the genetic variants, and so maybe we can't understand those results as well. And so that's that's not fair if you come from uh an Asian background or an African background, we don't understand how to interpret the data as well. So these are challenges that we know about, but it doesn't mean that we we haven't solved the problem. Like we we know the problems are there, and there's there's efforts to try and make this better.
SPEAKER_01So, overall, what do you think the impact has been on the diagnostic odyssey?
SPEAKER_00I feel so I'll be a little controversial here. I feel like the diagnostic odyssey is over. So Odysseus has made it home, and now we're in this um what I would call like a post-diagnostics world where the problem is no longer diagnosis, the problem is we can make a diagnosis, what are we gonna do about it? So, really, we need to think about what we're gonna do with this information, how we're gonna try and um achieve treatment. I think we're in the treatment world now, the treatment odyssey world is where really where we're gonna be at for the next 10 to 20 years. And I think that's a whole nother uh set of problems.
Questions about brainstem
SPEAKER_01Now let's turn to some email. You can send your questions to axdrupodcast at wasteman.wisc.edu, and we'll try our best to address them in a future podcast. Please send any feedback about these podcasts to the same email. Here's the question from this past month. I was hoping you could discuss how Alexander disease is not just a white matter disease. My daughter had a very aggressive lesion in her brainstem. Let me begin by saying that overall brainstem damage is seen in almost all Alexander disease patients, and sometimes it's the predominant area of damage. Also, there is white matter in the brainstem as well as in other areas of the brain. It's just not as segregated from gray matter as it is in other areas such as cerebral cortex and spinal cord. The second issue we should think about is what are the bodily functions that are controlled by the brainstem? And this is such a highly conserved region of the central nervous system throughout evolution, and it really goes back to the beginning of vertebrate evolution. I think it's easier to understand how it might be essential for really fundamental bodily functions, such as control of breathing, control of heart function, and others. So when you have abnormalities in the brainstem, it can cause a number of different problems in neurological functioning. Josh, can you talk a little bit about the kinds of symptoms you've seen in Alexander disease patients who have brainstem pathology?
SPEAKER_00Yes, Albi, I think the brainstem is a very scary part of the nervous system because it is a very small and compact region, but it all the information coming into the brain has to pass through the brainstem, and all the information from the brain has to pass back out to the brainstem. So even a small problem can have huge consequences. And so, as you were pointing out, parts of the brainstem are in charge of breathing, in charge of your heart uh rhythms, in charge of swallowing. And so often one of the earliest kind of easy symptoms we look for for patients is if they're having problems swallowing, it's a marker for us that the brainstems not functioning correctly, which just makes makes us worried that we're on a on a that patients are experiencing brainstem problems, which are easy to see in the swallowing, but maybe indicates it also that breathing or heart problems could be the next things to happen. One challenging aspect, Albi, that you've kind of uh alluded to is that because it is a small region and we use MRI as a tool, that MRI has kind of a limit of resolution. And so it's difficult to assess problems in the brainstem because it's a small area, and the limits of MR technology just don't allow us great views of the brainstem often.
SPEAKER_01Thank you, Josh.
SPEAKER_00Cool, Abby. I'm glad you're doing this. I think it's uh it's a worthwhile thing.
SPEAKER_01That's all for today's episode of Alexander Disease Research Update. Thanks for listening, and thank you to Josh for joining me today. Our theme song was written by Charlie Allenson, special technical assistance from my daughters, Zoe and Rebecca, and from Clark Kellogg at the UW's Wastement Center. And thanks to our donors for these podcasts, the Barrent Riddle family. I'm Alby Messing. See you next time, and I'm not sure.
