Precision Medicine for Genetic Disease: from Prevention to Treatment


Event Details

  • Date:

 

Although individually rare, in aggregate, clinically recognized monogenic disorders compose a substantial fraction of known human diseases and are commonly associated with high morbidity, mortality, and economic burden. Over the past 25 years, with the completion of the draft human genome sequence and advances in technologies such as high-throughput next generation sequencing (NGS) have led to many novel genes and variants that are causal for genetic diseases to be identified rapidly, which enables more “personalized” or “precision” interventions for these disorders to improve patient outcomes. This webinar will review current status and challenges of making accurate molecular diagnosis, cover recent NGS-based prevention approaches across an individual’s lifespan, and summarize established therapies as well as new strategies for treating genetic disease at different levels.

Speaker:
Jun Liao, Ph.D., FACMG, Laboratory Director and Assistant Professor, Columbia University Medical Center

TRANSCRIPT:

John:

We would like you to welcome you to the Sanguine Speakers Series webinar precision medicine for genetic disease, from prevention to treatment. Today’s webinar is presented by Dr. Jun Liao, the laboratory director and assistant professor at Columbia University Medical Center. Now I will hand you over to Dr. Liao.

Dr. Jun Liao:

Thank you, John, for your kind introduction. So today, like you can see, my title, I’m going to talk about the precision medicine for genetic disease. I will cover from prevention to treatment. So yeah, this is all of today’s talk. First I will try to answer the question, why we think prevention medicine is also important for genetic disease. Then I will talk from diagnosis prevention to treatment of the genetic disease, and last I will use two very common genetic disorders. One is cystic fibrosis, one is spinal muscular atrophy, as an example to show how the prevention medicine can be practiced in prevention to the treatment of this kind of disease.

Dr. Jun Liao:

So first, why genetic disease need prevention medicine. First I want to make clear about the definition of a genetic disease, because in the broad term, probably every human disease has some genetic factor. However, the genetic disorders I discuss here, I more emphasize on the more narrow term, which is monogenic, or someone call it Mendelian disease. So this kind of disease, we normally have caused by the very rare alleles, but their [inaudible 00:01:52] is much larger, so normally it causes very dramatic effect to the human health. So although individually, this disorder probably is rare, but collectively, actually it’s not so rare.

Dr. Jun Liao:

So for clinically recognized monogenic disease, actually we can find in 0.4% of [inaudible 00:02:17], but if you include all the congenital anomalies, it could be up to 8%. Also, over the entire lifetime it’s estimated that prevalence of monogenic disease is about 2%. So, so far I think about 4000 known human genes can cause monogenic disorders. Traditionally, this kind of genetic disease gene was found by phenotype treatment strategy, which is we normally have to classify the phenotype, and then group the patients together as one kind of global patients with similar phenotype. Then we normally do the position of [inaudible 00:03:10]. It’s very time consuming and effort. That’s before the sequencing error.

Dr. Jun Liao:

And then normally you have to use Sanger sequencing or other genotyping methods to first narrow down the gene location by third position cloning, and then to the Sanger sequencing, to find out the mutation which caused the disease. But nowadays, started I think 20 years ago with the completion of the human genome project and the development of next-gen sequencing technology, I think currently you can see the gene discovered is much more accelerated, as shown in this curve. Also, nowadays you can see by this blue bar here, the majority of the new gene to associate with human disease is found by the NGS technology.

Dr. Jun Liao:

So this has really changed our strategy from the phenotype treatment to the genotype treatment, because we can just sequence the patient cohort, and then find what possible novel gene could cause human disease. [inaudible 00:04:26] for this strategy is, some disease have variable phenotypes, so by the tradition method, you probably cannot classify them into the same category of disease, but for the genotyping treatment, we can easily find the similar mutations, or mutations in similar genes. Also another advantage is, a lot of these human diseases is caused by novel dominant variants, which is difficult for the traditional method to find the disease gene, but for the next-gen sequencing, we can just sequence the family tree, including the [inaudible 00:05:05], mother and father, and we can easily detect this novel dominant variants.

Dr. Jun Liao:

So when we talk about precision medicine, normally people probably first think of targeted cancer treatment and maybe think about pharmacogenomics or some complex disorders. But actually I will argue here, actually genetic disease is a really great area for us to practice the precision medicine. One reason is locus heterogenetics, which means a lot of genetic disease, exactly the same disease could be caused by different genes. One example is heterotopic cardiomyopathy, actually it’s caused by more than 50 genes. Another disease, [inaudible 00:06:00], like I show here, actually can be caused by around 100 different genes.

Dr. Jun Liao:

Another reason is, also maybe even two individuals have the disease mutation in the same gene, but even within the same gene, it could have a lot of different mutations or variants that could cause the disease. One example is CFTR, that’s the disease gene to cause cystic fibrosis. We already found more than 2000 disease causing variants in this gene, and a lot of this variant actually is very rare, or it’s [inaudible 00:06:41], so probably just one individual carry this mutation in the whole world, so that obviously needs an individualized treatment. Next, also because genetic are environmental modifiers, so even the different individual could have different severity of the phenotype.

Dr. Jun Liao:

Normally in genetics, we call it penetrance and expressivity. So it could have a variable expressivity or incomplete penetrance, so that also need individualized treatment for different phenotypes. Last I will say, I’ll give that the basic research in the genetic disorder, because normally the genetic impact is very strong in these genetic disorders, so it’s very easy to find out some various treatment biological pathway, which is important even for the common disease. One good example is familial hypercholesterolemia. This is a genetic disorder caused by a gene called LDL receptor gene, and normally if you lost the function of this gene, could cause this disease. Later I think people found actually a region called [inaudible 00:08:10], actually can increase the expression of this LDL receptor. That’s why they can decrease the cholesterol level in the human blood.

Dr. Jun Liao:

This pathway found by this genetic disorder actually can help us to discover this new treatment drug, statins. Currently it’s very common drug to use to treat the patients with high cholesterol. So, next I will talk about the genetic disease diagnosis. As you can see, first before we can go ahead for treatment or prevention, we first need to make a diagnosis for genetic disease. Historically, I think the very basic, the first whole genome past in the history I think is this chromosome [inaudible 00:09:13]. Basically, if you look at this picture, you’re seeing the whole human genome. But the resolution is so low, so probably the only thing we can see is we can count the chromosome number. So we can tell the genetic disease caused by the gain or loss of chromosomes, for example trisomy 21 we know cause Downs syndrome, or monosomy X, cause of Turner syndrome.

Dr. Jun Liao:

The later development of new technology, we have this tool called microarray. You probably know, the microarray detect large division or duplications in the genome, normally from several hundred kb to several mb. So this one actually have a better resolution, but still only a small portion of genetic disorders can be detected by microarray. So microdivision, microduplication syndrome, you’ve probably heard of for example DiGeorge syndrome, or Prader-Willi syndrome, Angelman syndrome. That’s all caused by deletions. The last, I think with the development of next-gen sequencing technology, eventually we can have the best resolution to look at the human genome, which getting to the single base pair level.

Dr. Jun Liao:

However, the challenge for this, I will talk about in detail later, is although they can dramatically increase our detection rate for genetic disorder, at the same time also in many variants we don’t know how to do it. That’s also a challenge for that, but still with application of the NGS technology in the diagnosis field, you can see, right now we can get relatively good diagnosis rate for genetic disease. Like this shows, in general the diagnosis rate is from 30%, for example for development or delay, to the highest category, Rhizopathy, you can get 70% of the diagnosis rate. The questions is, again, why we still cannot get near 100% diagnosis rate. Why is there a lot of patients we cannot get answer for what kind of genetic disease they’ve got?

Dr. Jun Liao:

So we have several [inaudible 00:11:42] challenge, or the reason for that. So first is technical limitations. Currently the short read [inaudible 00:11:49] next-gen sequencing, still kind of difficult to find variants in for example non-coding regions, or some structural variant like balanced translocation, and also some disease caused by the repeat expansion, or some genes have a pseudo gene. It’s all challenge for current NGS technology. Second, like I mentioned earlier, only around 4000 genes we know cause disease, but in the whole human genome, we have over 20,000. So about 80% of genes which we still don’t know what’s their function. So still a lot of new genes needs to be discovered.#

Dr. Jun Liao:

Last, like I mentioned, this next-gen sequencing will give us a large amount of new variants. A lot of these new variants we don’t know what’s their clinical impact. Normally we call these variants of uncertain significance. So we don’t know how to do with it, we don’t know what’s their functional impact to the disease. Also, sometimes you run the genetic test in different labs, and even for the same variant, it could report as a different category. One lab could call it variant of uncertain significance, but other lab could call it likely benign or benign. So they still have [inaudible 00:13:25] of consistency in the diagnosis field.

Dr. Jun Liao:

So there’s some potential resolution in the horizon, and I think one is for technical part, besides the short read, whole exome sequencing. A lot of labs right now start to offer clinical whole genome sequencing. So for the whole genome sequencing, they can cover these non-coding regions. Also, some new technology, like for example this long read sequencing like PacBio or Nanopore, they can sequence a very long length, so that can also detect the structural variations and also some repeat regions. For the novel disease genes discovered, I think one of the efforts in the field is push the data sharing. So it’s a lot of websites or databases in the field for that purpose, like Matchmaker Exchange, ClinGen, [inaudible 00:14:26], gnomAD. It’s all very useful for the gene discovery and variant interpretations.

Dr. Jun Liao:

Last, I think in some research, we try to do some high throughput functions study to help us to interpret the functional impact of the variant we found by NGS. One good example is one of the recent papers published in 2018. This paper, actually they use gene aggregate method to make mutation for every possible nucleotide in the functional important domain, in the BRCA1 gene. This gene cause [inaudible 00:15:12] breast cancer, ovarian cancers. Then basically they try every possible mutation that could possible happen in humans, and then they use some high super functional in vitro assay to see how this mutation affected the functions. This kind of study is really helpful for the clinical interpretation for the variant we can find in the human.

Dr. Jun Liao:

Another thing about the variant interpretation is this guideline we published several years ago, by the American College of Medical Genetics and Genomics, and also Association for Molecular Pathology. They tried to standardize the variant classification, so they proposed that based on the evidence strands, they classify the variant into five categories. Pathogenic, likely pathogenic, unknown, likely benign or benign. Most labs currently, I think, follow this guideline, so currently we see more and more consistency between the report from different laboratories. Next I will move from the diagnosis to prevention.

Dr. Jun Liao:

One of the main points for prevention precision medicine is, we should shift our focus from reaction to the disease, to the prevention of the disease. So, because the best strategy to treat the disease actually is not to treat the genetic disorder after it happened, it should be prevented from happening. That’s why I think genetic disease prevention is really important for the precision medicine. Actually, genetic disease prevention can happen in multiple stages across lifespan. At earliest stage, for example in the pre-conception stage, I think that we can run the carrier screen, which finds out the potential carrier couple. Before or after pregnancy, we have some other methods such as PGD, prenatal testing and IPP can find the fetus or embryo which carry the genetic disorders.

Dr. Jun Liao:

Then after baby was born, we can have a newborn screen and we can prevent some genetic disease which is very easily treatable, from some supplement or from dietary restriction. That can prevent the onset of certain genetic disorders. Eventually, some genetic disorder is adult onset. For example, we have some predictive testing, like for example BRCA1, BRCA2 gene test for the woman with family history of early onset breast cancer or ovarian cancer. So, that’s all predictive testing. Also, when we run diagnosis test for the family, we also report, we call it secondary finding, which means some mutation which is not the reason for the original indication of diagnosis, irrelevant to original patient symptoms, but it could have some later onset disorder, like for example increased cancer risk or cardiomyopathy disorders. So for that one we also report to the families, so this also can prevent it from happening, if we have some proper medical intervention.

Dr. Jun Liao:

Here, the rest of the talk about this section, I will mostly focus on the carrier screen, because you can see one reason is, this is the first step of the prevention. So, obviously [inaudible 00:19:38] best impact to the prevention of the genetic disorders. Second, actually the carrier screen has become very popular recently. It’s probably one of the most commonly ordered test for genetic labs. That’s why I think that we should look a little bit more on this carrier screen. For tradition carrier screen, it’s only offered to certain ethnic groups or race, which have high incidence of certain genetic disorder because of the founder effect, or the carrier [inaudible 00:20:19] or some [inaudible 00:20:20] happened in certain cultures.

Dr. Jun Liao:

For that one, normally, like I mentioned, because the limitation of the screen method, normally we cannot even sequence the whole gene. So, normally it’s only limited to certain number of founder mutations in a single gene. So, that’s the kind of limitation for this traditional carrier screen. However, regardless of its limitation, it still has a huge impact in the public health. This is a tool, a good example for the traditional carrier screen. One is beta-thalassemia in Sardinia. Another is Tay-Saches disease carrier screen in the North American. So you can see that both carrier screens start same time, around 1970’s. Then you can see original, the incidence of these two diseases in these two populations is very high. But with the carrier screen offered in whole population, you can see they have a dramatically decrease of the disease incidence.

Dr. Jun Liao:

Actually, one of the good [inaudible 00:21:36] is this right curve here. This shows the incidence of Tay-Saches disease in a non-Jewish population. At that time they are not being offered Tay-Saches disease carrier screen, so you can see incidence is not changed. Actually, it didn’t show current data, but nowadays, actually the majority of the Tay-Saches patient is actually non-Jewish, although this Tay-Saches disease was originally considered as a Jewish specific genetic disease. So, the medical society, they have some common suggestion for some very common genetic disorders should be offered the carrier screen. As you can see from this table, that includes cystic fibrosis, spinal muscular atrophy, Fragile X disease, alpha thalassemia, beta thalassemia, sickle cell, and they also offer the Tay-Saches and other diseases in the Ashkenazi Jewish population, or the French-Canadian populations.

Dr. Jun Liao:

In recent years, actually they have another test offered more and more common in the carrier screen field, which is called expanded carrier screen. So compared with traditional carrier screen, the expanded carrier screen can simultaneously screen a large number of conditions at the same time. Also, normally they don’t pay attention to racial ethnic background, so they can screen any general populations. The reason why this new test emerged, for two reasons. One is advance of the molecular technology, majorly it’s next-gen sequencing. So, basically we can sequence a large amount of genes with the same cost. Even lower cost compared with the traditional carrier screen. Second, more and more individuals nowadays actually born in the family with multiple ethnic background. So it’s more difficult for nowadays people to define themselves as a single ethnicity.

Dr. Jun Liao:

That’s another reason it’s become more popular, this pan-ethnic carrier screen. One advantage obviously is it can increase the detection rate. So you can see here, if we use the disease incidence one in 100 adults, we need to test 18 conditions at the same time. We can detect 61% of carrier and 84% of [inaudible 00:24:36] at-risk couple. However, if we actually decrease the incidence cut-off to one in 500, then we need to test 91 conditions at the same time. However, that’s going to increase our detection rate to the 80.5% for the carrier and 95% for at risk couple. So obviously, more disease genes you’ve tested, the better the detection rate will be.

Dr. Jun Liao:

However, one of the carriers you can see is with more gene added into this expanded carrier screen. Eventually, this curve will reach a plateau. Which means if you add more and more rare genetic disorder, you’re not going to increase the detection rate any further, at least not [inaudible 00:25:36]. That’s why this has some potential issue, current expanded carrier screen-wise, because between the next-gen sequencing for a lot of genes, like I mentioned earlier, we are going to get a lot of variants we don’t know how to with. These variants of uncertain clinical significance, we don’t know how to interpret. Second, also because the more disease genes we test, eventually more than half of individuals will become a carrier for a certain disease. No one is perfect, we always have some genetic defects in our genome. So they will increase the genetic counseling effort burden to the limited number of the genetic counseling work [inaudible 00:26:30].

Dr. Jun Liao:

At last, as I mentioned, because currently it’s market driven, so a lot of companies just try to add more and more genes and conditions into their carrier screen panel, but eventually they will reach the plateau. Currently I think it needs some regulation in which you should be put into this carrier screen. Next I will move from the prevention tot he treatment. Eventually, if we have the patient with genetic disorder, then what’s the best treatment strategy? Traditionally you can we can treat this genetic disease at a different level, they have different strategies. Traditional treatment normally is at the lowest level, the most downstream level, which is I the phenotype level. So they basically just treat the phenotype of the patient. One of the examples is, for example if a patient have [inaudible 00:27:42], then they will give the transfusion.

Dr. Jun Liao:

Then if the patient have some congenital heart defect, they will have the surgery to fix the heart. So this is just in the phenotype level. I won’t go to the detail today. That’s not the focus of today. However, once we move to the more upstream, first we need to know better about the disease mechanism and [inaudible 00:28:11], and what mutation cause the disease. Then we really can treat them individualized right treatment. That go more into the precision treatment area. So that’s why the next level, we can treat the patient in the pathway level or protein level. This is several good examples. For the pathway level, some of the genetic [inaudible 00:28:40] affect the pathway.

Dr. Jun Liao:

Because of the genetic defect, this pathway cannot go through, then they have accumulation of the substrate. One of the pathway treatments is some substrate reduction, so then we can get rid of this substrate. Or we can maybe, we call it pathway inhibitor, like in number two here. We can inhibit these pathways to cause less rare disease phenotype. This is all in the pathway level. However, in the protein level we have also different strategies but this required. We know what kind of mutation, what effect of the mutation could cause the protein. For example, in number three here. This mutant protein actually cannot transport to, for example the cell membrane, where they can have proper function.

Dr. Jun Liao:

If you have some small molecular drug which can bind to this mutant protein, and they can help the transportation, then maybe you can restore the function of the protein. So this kind of small molecular drug’s called a corrector. So the number four is for another mutation. Although this mutant protein can transport to the cell membrane, they are now having a malfunction. So they have another type of drug called potentiator, so this one can bind the protein and increase their function. Last, some protein, maybe they have a stability issue, so maybe they get degraded too early. So some small molecular, we call it a stabilizer, which can bind to this protein and make it more stable. All these different treatments at the protein level, we need to know what kind of mutation it is. It’s a more individualized treatment and more into the precision medicine area.

Dr. Jun Liao:

Eventually, if we know better about this, we also can treat this in the RNA level. We can change the RNA expression and we can change the RNA splicing. One of the very important tools for the RNA treatment is called antisense oligonucleotides. This antisense oligonucleotide normally is about 15 to 30 base pairs and they target a certain sequence of the gene. Normally the backbone of this oligonucleotide is modified so it’s more stabile [inaudible 00:31:37]. So depending on your design and where they [inaudible 00:31:43] to the nMRA, they have a different function. For example, if you can just bind some important exome, then you can introduce RNA couplage, then you can degrade this nMRA. That’s a pretty basic function.

Dr. Jun Liao:

Sometimes you can design this antisense oligonucleotide to the translation start, aOG side. So when they bind to this side, they can inhibit the binding of the translation machinery into the starting code, so they can cause translation arrest. Also, some nMRA binding protein can bind to some certain non-coding area and cause some cellular toxic effect. If you use this antisense oligonucleotide to bind to this RNA domain, they can inhibit RNA binding protein to bind to this RNA, and can reduce the toxicity of this binding protein. Also, if you design the antisense oligonucleotide into the intron exon boundary, they can also change the splicing of the nMRA, so you can cause exon escaping, like for example here.

Dr. Jun Liao:

Also, if you design this antisense oligonucleotide into the [inaudible 00:33:20] or open reading frame, actually you can increase the gene expression for the downstream open reading frame, so you can increase the translation activities. So it’s a lot of usage for this antisense oligonucleotide. This actually are two good examples. I think both are FDA approved drugs, which use antisense oligonucleotides to treat the genetic disorder. One example is, they call Eteplirsen for the Duchenne muscular dystrophy. So this Duchenne muscular dystrophy is caused by loss of function mutation in this gene called DMD. So you can say they have a lot of [inaudible 00:34:09], a loss of function in mutation, for example [inaudible 00:34:12] here, in these genes.

Dr. Jun Liao:

So this antisense mRNA can actually bind to the intron exon boundary of this exon 51. Then they can make this RNA splicing actually escape this exon 51. So once they escape this exon, sometimes they can reinstall the open reading frame, because a lot of this other mutation cause the frame shift right? They cause a malfunction of protein which eventually degrade. However, this exon skipping of the 51, for about 13% of patients, they can reinstall the open reading frame. So the final result is you can get a shorter protein, but it’s in frame. So they still can kind of restore some function, compared with the loss of function mutation in here. So that’s one of the treatments for Duchenne muscular dystrophy.

Dr. Jun Liao:

Another example to use this antisense oligonucleotide is this drug called Minomycin. This is for treatment of a hyperglycemic [inaudible 00:35:36]. This one is caused by the gene called APOB. So this APOB I think is actually important component for the LDL in the bloodstream. So antisense oligonucleotides can bind to the pre RNA of the APOB gene, and then they can introduce RSH and then they can have [inaudible 00:36:07] on this mRNA, which cause the decreased expression at the APOB gene, and eventually decrease LDL level in the bloodstream. So finally I think we can move to the highest level in the gene level.

Dr. Jun Liao:

So eventually, this is the final goal of the genetic disease treatment, because potentially they can treat a genetic disorder at the highest level, and have the potential to cure the genetic disease. So this one, for certain diseases we can do this by organ transplantation. For example bone marrow transplantation. Or currently, they use stem cells for transplantation. However, I think a more interesting development in this field is gene therapy and gene editing. So for gene therapy I think the basic concept is a very straightforward, just because a lot of genetic disorders are caused by loss of function in [inaudible 00:37:18] genes. So if you introduce a transgene into the human body, then they should restore the function.

Dr. Jun Liao:

However, I think the challenge is how to deliver this gene into the human body. You can say we have several different methods. I think the most commonly used method is this transfer vector, the original comes from virus. One of the most popular one is this lentivirus. So this lentivirus vector, I think advantage for this is relatively large, so you can put up to 8 kb DNA fragment, you can pack them into this virus vector. However, the disadvantage for this vector is, actually this vector could integrate into the chromosome. So potentially they could have some [inaudible 00:38:19] issue, cause mutogenesis.

Dr. Jun Liao:

Another type commonly used is called adeno-associated virus. This virus I think is relatively safe, because they have low frequency to integrate into the chromosome. So they are [inaudible 00:38:36], but the problem is they can only impact about 5 kb maximal of the DNA fragment into the vector. Also have two kind of delivery strategy for gene therapy. One is in vivo gene therapy, which is inject this virus vector, [inaudible 00:39:00] these genes, and inject into the human body. So this strategy, I think normally we use the adeno-associated virus. The major risk for this strategy is immuno response.

Dr. Jun Liao:

Another strategy we call ex vivo gene therapy. So this one, first we extract a cell from the patient or from a healthy individual, and then we culture them in the Petri dish, and the also inject, put it into the virus vector, [inaudible 00:39:43] this trans gene into this cultured cell. Then we deliver this genetically modified cell back into the human body. Normally, the lentivirus is used for this strategy more often. Obviously one of the risks is, you could have mutogenesis for this strategy. Also you need to have some cell. The cell part you use have to be easy to take out from human body and put it back in.

Dr. Jun Liao:

At last, I think the final is gene editing strategy. This is very popular nowadays. I’m sure you’ve heard about this, it’s a lot of publication about this gene editing. So the basic concept, I won’t go to the details because it’s a very popular topic here. But basically the idea is we use this nucleotide called the Cas9, and they can, with the help of this guided RNA, recognize specific targeted sequence, and this Cas9 nucleus can cut the DNA strand, create a double strand break. Then in the downstream, either this break can use the non-homologous end joint to join together again. But in this process, you will create insertion of divisions, so basically you’re going to knock out this gene.

Dr. Jun Liao:

Or if you provide some single strand DNA donor template, then they can based on this template they can, they’re called homologous directed repair. So they can repair this double strand break. During this process, they will introduce new DNA or new variant into this location, so this normally cause a locking. So basically for this strategy we could also have ex vivo or in vivo strategy. Currently they have several clinical trials. It’s still ongoing. Hopefully, in the near future, we can have more progress on this. But I think just the early days here, they have already one paper published from the first clinical trial. This is a paper published in The New England Journal of Medicine, and actually in this paper they only report two patients.

Dr. Jun Liao:

One patient have sickle cell disease. Another patient have beta thalassemia. So basically they used this CRISPR, Cas9 gene editing strategy. They made this protein just for both of these patients, because of the defects of the hemoglobin protein beta. So this hemoglobin beta is most expressed in adults. However, in the fetus stage, actually humans have another that kind of can replace the beta protein, called gamma protein. But this protein normally is not expressed in adults, so they used gene editing strategy and made this gamma protein expressed again. More than a year later, they found a high level of the gamma protein in the patient, and also they found this patient have transmutant independency, and also elimination of the episodes for the sickle cell patient.

Dr. Jun Liao:

It looks like the preliminary data is very promising, so even only in two patients, they can publish this paper in The New England Journal of Medicine. I believe eventually we’re going to hear more about these clinical trials. Last I think I will go to some specific genetic disorder, which I think is used as an example for precision medicine. One is cystic fibrosis. So for cystic fibrosis I think it’s the most common autosomal recessive condition in U.S. Especially in the Caucasian population, the carrier frequency is very high, it’s one in 25. Obviously it’s a complex multisystem disease, and most [inaudible 00:44:28] pulmonary disease, but also some other organs get affected.

Dr. Jun Liao:

So the gene responsible for this disease is called CFTR. They encode cAMP regulated chloride channel protein, which is located in the apical membrane of the epithelial cells. Currently more than 2000 patients have been identified with this gene, and based on their functional impact, they have six different mutation classes. One of the most important mutations is this deletion of the phenylalanine in position 508. Normally we call it delta 508. It’s found in 30-80% of the patients, and this belongs to the class two, so they cause the major blocks in the protein maturation, based on which mutation you’ve got. You could have the very classic phenotype, or you can have a milder phenotype.

Dr. Jun Liao:

To prevent this cystic fibrosis, even started in 1997, it was actually already proposed to offer the cystic fibrosis carrier screen for certain populations. In 2001, ASMG and [inaudible 00:45:50], they have the guideline recommend this cystic fibrosis carrier screen offer to the non-Jewish Caucasian or Ashkenazi Jewish populations. In 2004, ASMG recommended this carrier screen most commonly with patients. They think it should be tested in the cystic fibrosis. Nowadays, I think with expanded carrier screen, almost every pregnant woman, or the woman who consider pregnancy, was offered the carrier screen for cystic fibrosis.

Dr. Jun Liao:

This is currently the most common mutations recommended by the ASMG, so all these mutations have allele frequency of more than 0.1% in general U.S. population. However, you can see one of the issues for the carrier screen of cystic fibrosis is, they have a given detection rate in the different ethnic groups. So in the Asian population or non-Hispanic white, the detection really is pretty good. However, the Asian population is less than 50% of the detection rate. The reason is, in the east Asian population, you can say the top three candidates or the most common mutation found in east Asia, is not even in these 23 mutations least recommended by the ASMG.

Dr. Jun Liao:

So for the southeast Asia, also top two is not there. So that’s why here, I think the NGS technology, compared with genotyping based technology, have an advantage. One, the study published in 2020, they suggest that compared with NGS technology, the genotyping technology test of only 23 most common mutations fail to detect probably 30% of at risk couple of cystic fibrosis. You can see the NGS technology can detect most of the mutations in the east Asian, or in the Hispanic populations. So for the treatment, I think one oft he very important treatments is this small molecular treatment, depending on the cause of the mutations.

Dr. Jun Liao:

Like I mentioned, for delta 508, the corrector plus potentiator is very useful to treat patients that carry these mutations. This is two papers published in 2017, I think. They combined these drugs together. Two of these three are corrector, and the last one is a potentiator. They found in combining these three drugs, you really can have a very good treatment outcome for any patient which at least carry a single allele for the delta 508. So this is FDA recommended treatment. You can say the last one is this combination of these three drugs for the patient with at least one delta 508 allele. This is really going to be helpful for the CF patient, because you can say more than 80% of patients could carry these delta 508 alleles.

Dr. Jun Liao:

I think the last maybe two minutes I will just briefly mention this spinal muscle atrophy. This one I think is also the second most common autosomal recessive disease, but it’s the leading cause of infant death. They have two genes, SMN1 and SMN2. SMN1 is major gene contributing to this disorder. Then they have a 100% functional protein, but SMN2, because of one of the mutations in exome 7, only 15% of the transcription can have a function protein. 80% of the protein, they don’t have the exome 7, and then they don’t have a function. Actually, they have a different types of the SMA. Although SMN2 don’t have the major function, but the copy number of SMN2 can modify the disease phenotype.

Dr. Jun Liao:

You can say that if you have more SMN2 copies, actually you can see some milder phenotype in the patient. So for the carrier screen, I think one of the issues for SMA carrier screen is this called a silent carrier. So the silent carrier have two SMA genes in the same allele. So when we look at copy number of SMA, we thought they have as a normal individual, but actually they have another allele missing a copy number of SMN1. So this is called a silent allele. That’s because we cannot detect all the carriers in the SMA genes. For therapeutic, I think it’s two very promising. One is, again, use this antisense oligonucleotide. They can target axon 7 of SMN2.

Dr. Jun Liao:

Normally the SMN2 axon 7 cannot be spliced, but they can modify this and change the splicing, that make SMN2 produce a normal function of the protein. So, that’s one good strategy. Another is gene therapy. So they deliver this SMN1 gene into the patient, and then can also have improved outcome for the patients. I think that’s it, so I won’t go to the summary because of time, but I hope today’s talk, I can convince you that genetic disorder is really important field to practice precision medicine. I believe in the future, with better understanding of genetic disorder and more new methods about the precision medicine, we can hear more new therapy or new prevention methods for the genetic disorders. Thank you. So I think I can take questions here.

Dr. Jun Liao:

One of the questions, “Should we apply the personalized medicine approach for more common forms of the disease, once required scientifically?” That I think is a good question, because normally more common form of the disease is much more complicated, because it’s a lot of factors to contribute to it. I think first we need to understand better about the genetic mechanism, or maybe not only genetic, even come from the environment. Currently I found in the diagnosis field, one of the very popular tests called the polygenic score. So this is basically a measure on different polymorphism from the different genes in the different pathway, to try to calculate the risk for the disease, so I think that’s just the first step.

Dr. Jun Liao:

I think that eventually, with a better understanding, hopefully we can apply more personalized medicine to this common form of the disease. Another question is, “Have patients expressed concern with privacy of their genomic data?” Yes, I think that’s definitely a good concern currently, when we enroll a patient for their studies or for even the genetic test. However, I think normally we will provide very detailed informed concern, because we’re going to basically have the option for the patient, whether they want not only DNA, but the genomic information to be stored, or whether they want to contribute to the research. If they do not agree to store their genomic data, we will just within the limitation of the regulation requirement. After that we won’t store their data.

Dr. Jun Liao:

Also, all our database, everything follow the HIPAA rules, so data security is top of our concern. “Please address another privacy protection for subject giving DNA sample.” That’s kind of the same question as the previous one. Like I said, it’s different level. Even in the DNA level, normally we can [inaudible 00:55:30] the DNA [inaudible 00:55:31]. If they have not agreed we’ll keep their DNA, we will normally destroy the DNA after, I believe, six days, after the test was finished. For their genomic data, I already mentioned. So, “What’s some challenge within the personalized medicine approach? Any question [inaudible 00:55:59] practice implementation?”

Dr. Jun Liao:

That’s, I think, also very good question, because exactly mentioned, one of the challenges, I think that because all this, especially the treatment I think currently, all the treatment is very high cost, because it’s individualized. So normally it cannot practice in the large scale. I think that’s the most challenging one. I feel to address this, I’m not sure what’s the best solution for that, but I think one of them probably, like I mentioned earlier, maybe we should switch from the reaction to the prevention. So I still feel that prevention is better than the treatment when the disease already happened. In the prevention, you can have much lower cost effect compared with the treatment.

Dr. Jun Liao:

“Are there sequences that shift such as future genetics [inaudible 00:57:14] applied?” I’m not sure what this means. And, “When will precision medicine come to non-oncology application?” Yeah, it think that’s exactly the point of my talk today. I feel it’s still kind of ignored, this precision medicine, in the non-oncology. All of today’s progress are oncology. I think the oncology’s still the more hot topic for the precision medicine, but I hope with more and more realize this in the non-oncology genetic field, also with development of more new tests, hopefully we’re going to draw more attention to this field. So I think that’s probably the best conclusion for today’s talk. I think we’re already at the time, so thank you everyone.

John:

Thank you, Dr. Liao for an excellent presentation. And thank you for joining Sanguine for our S3 webinar on precision medicine for genetic disease, from prevention to treatment. For our list of upcoming webinars or to request patient samples, visit sanguinebio.com. Thank you again, and enjoy the rest of your day.