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Thursday, October 28, 2010

All you need to know about the Usher Syndrome and Related Diseases Conference Part V: Screening and Diagnostics

by Mark Dunning

Well, it’s November and we are still summarizing the International Symposium on Usher Syndrome and Related Diseases that took place in May. That should be heartening for our readers. Obviously a lot happened at the conference.

A lot is happening in the real world, too, especially when it comes to diagnosing Usher syndrome and understanding the genetics. Now, if you or your family member have already been genetically tested and an Usher syndrome mutation has been identified, you might wonder why you care about the testing of others. I mean, besides the fact that you are a nice person.

I’ve said this a lot, but it always bears repeating: to find a cure is going to require the efforts of all Usher families. We need their natural histories, their genetic information, their experiences, and yes, their money (or at least the money they might help raise). Eventually we will also need Usher families to participate in clinical trials. In short, we want to find as many Usher syndrome families as possible.

That’s what makes the sessions on genetic screening so important. Like I wrote earlier, the good news is there is a lot going on.

A DNA based screening test for Usher syndrome
William Kimberling
University of Iowa Carver School of Medicine and Boys Town National Hospital

Dr. Kimberling has been working on an inexpensive screening test for Usher syndrome. The test looks for the most common mutations in all known Usher genes. The idea is that this test would be part of a tiered approach. A screen essentially tests one chromosome. But remember, Usher syndrome is autosomal recessive, so both chromosomes need to have a mutation for it to actually be Usher syndrome. The second tier is DNA sequencing to verify the first tier finding.

One interesting result of their testing so far is that more than 10% of children with severe to profound sensorineural hearing loss may have Usher. That’s much higher than was historically believed to be the case.

Why you care

Genetic testing is expensive. I speak all the time with adults who have been diagnosed with Usher but have never had it confirmed genetically because their insurance wouldn’t cover it. A screen like this would make the most basic testing more widely available at a low cost. Remember, finding everyone with Usher is a good thing for everyone with Usher.

In proof reading this post, Jennifer made another good point for why you care. Her words: “To me the big ‘why you care’ point is the impact of adjusting the prevalence upward so dramatically. For years we have been saying that Usher syndrome is rare, citing the prevalence of 1 in 25,000 Americans derived from several older studies. Extrapolating from the new Kimberling data gives us something closer to 1 in 6000, which is more common than a lot of higher profile genetic diseases. This could potentially give us a lot more leverage in funneling research dollars to Usher studies as well as enhance our general efforts to raise awareness about Usher syndrome in the social, educational, and clinical realms."

An excellent point.

Developing more comprehensive genetic screening strategies for congenital sensorineural hearing loss (SNHL)
Richard Smith
University of Iowa

All the states in the US and many other countries do a standard newborn hearing screen. As a result more than 4000 infants are diagnosed with severe to profound SNHL each year in the US. According to Dr. Smith, screening programs have focused on follow-up physiologic tests to determine how well a given child hears. Genetic testing has been used to confirm the diagnosis but Dr. Smith argued that we need to develop a more comprehensive strategy for using DNA testing as part of the screening process.

Why you care

This is a frustrating point for many of us. We already catch most kids with Usher through the newborn hearing screen (though Usher 3 kids may slip through with their progressive hearing loss). However, a lack of a strategy for including genetic screening as part of the newborn hearing protocol means a lot of these kids slip right through our fingers. We find them again later when they are late walkers or begin to have problems seeing at night. We shouldn’t lose them in the first place. Imagine pairing a low cost genetic screen with the newborn screen and you see where Drs. Smith and Kimberling are going with this.

Asper’s diagnostic tool for Usher syndrome
Ilona Lind
Bernhard Weber
Institute of Human Genetics, University of Regensburg, Germany
The OtoChip sequencing array for hearing loss and Usher syndrome
Heidi Rehm
Partners Healthcare Center for Personalized Genetic Medicine

I’m putting these three together because they are all genetic tests for Usher syndrome. What is kind of cool about the three is that they each are aimed toward a different diagnostic population. The Asper diagnostic tool is specific for Usher syndrome. So if a patient is suspected of having Usher, this test aims to confirm it. But say a patient has hearing loss or vision loss but it’s not clear if the cause is Usher or something else. That’s where the RetChip 1.0 and the OtoChip come in. RetChip 1.0 tests for a bunch of different genetic causes of RP including Usher syndrome. The OtoChip tests for a bunch of different genetic causes of hearing loss, including Usher.

Why you care

Having multiple paths that lead to an Usher diagnosis is critical. As we just saw in the talk by Dr. Smith, we catch a lot of kids with the newborn hearing screen. They presumably would be candidates for the OtoChip test since they wouldn’t necessarily be demonstrating any vision problems yet. We also know that a lot of kids slip through our fingers at that point and don’t show up again until they start to have vision problems. The OtoChip would still be a viable test but they would also be caught if the RP was the focus and the RetChip 1.0 was used. Again, the more families we identify the better and these give us several ways to do so.

The utility of databases in diagnosis
Anne-Francoise Roux
Laboratoire de Genetique Moleculaire, CHU Montpellier, Montpellier, France

We’ve talked about Dr. Kimberling’s DNA screen that tests for common mutations. Tests like the OtoChip and others like it seek to find a specific mutation no matter how unique. This has led to a number of different variants being identified. Dr. Roux and her colleagues have created a database to store those mutations that is searchable for all researchers. These can then be folded in to the screens and the OtoChip-like tests so that they are more comprehensive and find more patients faster.

Why you care

Read that last line again. A database of all known mutations helps us to more quickly identify more people. That’s a good thing.

Lessons from the UK National Collaborative Usher study
Maria Bitner-Glindzicz
UCL Institute of Child Health, London, UK

One of the things we have long struggled with is connecting genotype (the genetic mutation) to phenotype (the physical changes caused by that mutation) in Usher syndrome. This study is an attempt to do that. They studied 190 families in the UK with Usher syndrome. They were able to identify 80% of them by sequencing known Usher genes. They also identified a number of new mutations in the process.

Why you care

This is exciting stuff. There have been very few comprehensive phenotype/genotype studies done on Usher syndrome. Being able to predict phenotype by genotype would be a great thing for all Usher patients. The question I hear most often is “what does the future hold for me or my family member?” This type of study can help us to be able to find the answers. It will be interesting to see the results. And remember the database talked about by Dr. Roux. This study identified 80% of the patients using known genes. That means 20% were unique. It takes a lot of work to identify those novel mutations. But if all newly discovered Usher mutations were put into a database that researchers around the world could easily reference, the next time a similar study is done those new mutations can be included.

OK, next post on the symposium should be the last. We should be finished just in time for the next symposium!

Wednesday, October 20, 2010

Usher Syndrome Working Group in Aalborg Denmark

by Mark Dunning

Thanks to Jennifer for carrying the blog while I procrastinated. I do have a partial excuse. I was in Denmark for a few days at the Usher Syndrome Working Group put on by Sense in conjunction with the Acquired Deaf Blindness Network conference.

This was my first trip to Denmark. In fact, if I were to list the places I never expected to visit Denmark would have been just above Romania on the list. Aalborg is the fourth largest city in Denmark which has about 6 million people in it. That’s about the size of my home state of Massachusetts. The fourth largest city in Massachusetts is Lowell which we in the area not so lovingly call Hole. Let’s say my expectations for Denmark were low.

Well, it was wonderful. Nice people, long history, beautiful architecture, and terrific pedestrian friendly outdoor shopping. It was chilly (as one might expect) and I couldn’t help but think of the holidays as I walked the streets even though it had just turned October. Most commute by bicycle even with the chill so on a Sunday morning with most sleeping in and only a few bikers around, Aalborg might be the quietest place on earth. An absolutely lovely city.

Aalborg Denmark
The conference was excellent, too. I had seen many of the presentations before. Bill Kimberling gave his omprehensive talk on the clinical and genetic aspects of Usher syndrome.  Claes Moller gave an interesting talk on hearing loss differences in siblings with Usher II and Moa Wahlqvist presented the same psychosocial findings that were presented in Spain. All were great and Moa in particular was a big hit, but like I said, it wasn’t new to me. What was new to me was the session on social-haptic communication. I know I won’t do it justice, but in short, where tactile sign communicates language, social-haptic communication is the use of touch to convey emotions and space. If you are deaf blind, you may not be able to see a smile or tell where in the room the speaker is standing. Social-haptic communication uses touch to convey that information. Very cool.

Probably most valuable, as is usually the case with these things, was the opportunity to network. I was able to connect with people from all over Europe (Bill and I were the only two people from the US) and from as far away as Australia (and I thought my flight was long). This networking is already paying dividends as we were able to at least start a global dialogue on the need for an Usher syndrome registry (a posting for another day) which I doubt gets started without the study groupUsher Working Group.

Thanks to the good folks at Sense for pulling it together. Marilyn Kilsby (who’s retiring) and Tamsin Wengraf (who is not) did a terrific job. It was well worth the trip and I look forward to doing it again in two years

Because I'm from just outside of Lowell and don't want the
chamber of commerce after me, here's a nice picture of the city.
Kind of like Aalborg, no?

Thursday, October 7, 2010

All you need to know about the Usher Syndrome and Related Diseases Conference Part IV: New Genes and Common Denominators

by Jennifer Phillips, Ph.D.

Here I am again to do some of the heavy scientific lifting required for a subset of the talks presented at the Valencia meeting. Last time I covered the presentations dealing with the molecular and cellular activity of Usher proteins--the factors known to cause clinical Usher syndrome in humans when altered by changes in genetic code. To briefly summarize, there is strong experimental evidence to suggest that at least some of the time these Usher proteins physically link together to form molecular complexes that carry out some cellular functions. There are a lot of different Usher proteins involved, so understanding just the activities of those proteins has been quite challenging.

In the next series of talks, the picture gets even more complex, as we learn about still more proteins, contributing to other disorders of vision and/or hearing. Some of these may be added to the list of known Usher proteins, while others are associated with vision and hearing disorders distinct from Usher syndrome, but also appear to have molecular relationships to Usher syndrome proteins. If this sounds complicated, well, it is. But fear not, dear readers. I’m here to guide you through this confounding thicket of information, and I will do my best go easy on the technobabble whenever possible, link you to backup resources when I just can’t help myself, and ferry you safely to the other side. Here we go:

Identification of a new Usher 3-like locus
Shzeena Dad, Kennedy Center, Glostrup, Denmark

This research described the discovery of a new gene causing Usher-like symptoms in a Dutch family. As the hearing loss is progressive in these family members, who also exhibit balance defects and retinal degeneration, the condition is is classified as most like Usher type 3. Two things convinced the researchers that it isn’t Usher type 3a: The genetic change that the affected family members share is not in or near the Ush3a gene, or indeed, in any of the other eight known Usher genes. Moreover, all affected members of this family were born with cataracts—defects in the lenses of their eyes, which has not been reported in other Usher cases (some Usher patients do develop cataracts later in life, but this is the only family we know of who are born with this problem).

Why you care
One of the endearing realities about biology is that, however complex things might initially appear, they usually turn out to be even more complex than that. Studying Usher syndrome is already a formidable challenge, made more so because we know, with absolute certainty, that we have not yet identified all the molecular players. Obviously this is important, because despite the amazing progress we’ve made in being able to screen for mutations in Usher genes, we can only screen for the things we know to look for. Thus, the more new gene information we can generate, the more complete our picture will be, enhancing screening efforts as well as our ongoing searches for therapies. Adding this new locus to the list gives us another target to aim for.

New strategies/technologies to identify new genes
Hanno Bolz, Institute of Human Genetics, University Hospital of Cologne, Germany
Center for Human Genetics, Bioscientia, Ingleheim, Germany

This speaker described a several new screening strategies that could help cast a wider net for known Usher genes as well as new players. On the species level, there is a huge amount of variability in the human genome, so in the noise of all those normal, background genetic variations, small changes in genes that lead to disease can be hard to pick up. Traditionally, the most successful way to reduce the signal to noise ratio was to conduct genetic testing on large families, thus reducing the background level of genetic variation and making the important, disease-causing changes easier to spot. Happily, new technologies have delivered success in looking for disease genes even in small gene pools. New ways of searching, with better resolution for picking up the small changes, different techniques for finding a broader variety of changes, and better, faster sequencing so that vast amounts of genetic information can be collected in a very short period of time, are all working to our advantage. For example: deleted information in a particular region of a chromosome can be difficult to spot with traditional DNA sequencing methods if you’re not specifically looking for it, but with a new technique called Comparative Genomic Hybridization such changes, and a number of other irregularities, can be detected without prior knowledge. This is useful not only for screening known Usher genes, but as a first step in changes in novel genes that might contribute to Usher syndrome as well.

In part III of the meeting summary, I explained how zebrafish are used as an animal model for Usher syndrome. In his talk, Dr. Bolz discussed a new way that zebrafish can contribute to the discovery of new Usher genes. Techniques that we use to disrupt gene function in zebrafish can be used to test whether a particular gene might be likely to contribute to Usher syndrome in humans. I humbly present one such example of this strategy here.

Why you care
In short, discovering new ways to examine the genes we know are involved in Usher syndrome as well as ways to identify new players is crucial to improving diagnosis and treatment.

Modifiers of ciliary diseases
Nicholas Katsanis, Duke University Medical Center, Durham, NC, USA

We’ve already discussed the putative role of the cilia in contributing to the symptoms of Usher syndrome. Cilia are important components in photoreceptors, hair cells of the inner ear, and many other cells of the body. Thus, it’s not surprising that defects in these structures underlie a number of human diseases. These conditions have an extremely wide range of associated symptoms, which sometimes include, but are by no means limited to, hearing and vision defects. However, as the source of all these problems can be traced to problems with the cilia in some or all cells, they are classified collectively as “Ciliopathies” (diseases of the cilia).

Katsanis and colleagues have taken a systematic approach to studying factors classified as ‘ciliary genes’, using molecular screening techniques and animal models to characterize mutations in these genes and their potential disease causing effects.

Because a definitive link between the pathology of Usher syndrome and defects of the cilia is still being established, there is currently some debate about whether or not to include Usher syndrome on the official list of ciliopathies. The fact that many Usher proteins are known to colocalize in the region of the photoreceptor connecting cilium can be used to make a case for including Usher genes in this group. Another compelling argument for doing so is that we already know there is some level of molecular cross-talk between Usher proteins and other factors known to cause ciliary disease.

Why you care
The interactions between known Usher proteins is already pretty complex, but interactions also occur between Usher proteins and other, non-Usher proteins. Understanding more about how this works could enable us to identify new ciliary genes that may, in some circumstances, cause Usher syndrome, providing new targets for diagnosis through genetic screening and research for therapies.

The USH2A Interaction Partner NINL Associates With BBS6, Plays a Role in Establishing Planar Cell Polarity and Functions in Cilia Assembly
Erwin van Wijk, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

As much as I’d love to wax expansive on the particulars of this really exciting research, I’m starting to have that feeling I get at parties when I geek out over some neat bit of science in the news and chat excitedly about it for too long before it dawns on me that my conversational companion is surreptitiously making the ‘SAVE ME!’ sign to his or her partner across the room. So, let’s do a very rough sketch of the basics based on the informative title of this talk, and call it a day:

The USH2A Interaction partner NINL: USH2A is the gene behind Usher Syndrome Type 2A. It encodes a very large protein called either USH2A or Usherin. It’s a common biochemistry research tactic to use all or part of a known protein and find other proteins that can physically interact with it. These researchers used a portion of the Usherin protein as their ‘bait’ to fish through a solution containing many proteins to see what would stick to it. One of the proteins they discovered was an already characterized factor called NINL.

NINL associates with BBS6: As soon as the researchers determined that NINL interacted with Usher syndrome, they wanted to figure out what the effect of a mutation or other disruption of NINL might be. So, they depleted NINL in a young developing zebrafish (using the same technique of disrupting zebrafish gene function discussed above). These animals had developmental defects that were reminiscent of the defects seem when genes involved in Bardet-Biedl Syndrome (BBS) are disrupted in zebrafish. BBS has a number of genes associated with it, is officially classified as a ciliopathy, and has symptoms that include progressive retinal degeneration. The researchers continued to investigate the consequence of depleting NINL in tandem with members of the BBS gene family, and observed genetic interactions between NINL and many of the BBS genes. They then conducted the same type of protein interaction experiment as was used to identify NINL as an USH2A interaction partner, only this time they used NINL as the bait. Through this experiment, they were able to show a direct physical interaction between NINL and one of the BBS proteins, BBS6.

NINL plays a role in establishing planar cell polarity: In a nutshell, planar cell polarity refers to the organization of cells that make up a given tissue or organ. During development, the cells have to coordinate their growth and movement to form eyes, ears, kidneys, brains, etc. Determining which end of the cell is ‘up’ is an essential part of this organization, and it is known that the cilia of cells contribute to this organization. Thus, it is hardly surprising to note that mutations in genes known to be important for ciliary development or function can lead to disrupted cell polarity. This is true of the BBS genes, and in this study, the researchers noted disrupted cell polarity in zebrafish with reduced NINL gene function.

NINL functions in cilia assembly: The evidence from zebrafish, as well as what was already known about the localization of NINL protein, was suggestive that NINL might have some role in cilia formation or function. To establish this more directly, the researchers conducted an experiment with ciliated cells in culture dishes. They depleted NINL function in these cultured cells and observed a defect in cilia formation. This added data makes it even more likely that the problems seen in the zebrafish model are the result of poorly assembled cilia.

Why you care
Essentially, this is proof of principle for the approach that Hanno Bolz, Nicholas Katsanis and many others are advocating on a wider scale: Look for connections between known and potential contributors to Usher syndrome, or to cilia formation and function. Use genetic and biochemical tools to identify new molecular players, use model organisms to study the effects of disrupting these factors alone or in combination with other known contributors. Fill in the gaps and refine the definitions of these disorders by revealing how they relate to one another.

I see you giving the high sign to your spouse over there, so I’ll let you off the hook for today, and I thank you for indulging me. Next time, Mark will be back to conclude this meeting summary with some information about new genetic screening techniques for Usher syndrome. Until then, be well!