Research Update: March 2006

Over the past few months we have made significant new progress in evaluating “candidate genes” which may play a role in causing AHC. Candidate genes are those which are considered more likely to cause the disease for a variety of reasons including 1) location of the gene near a known place where a chromosome problem has occurred in a patient with AHC, or 2) the gene of interest has been found to cause similar symptoms, such as those seen in hemiplegic migraine, closely related to AHC, or 3) the gene seems to perform a function in the brain that, when disrupted, seems likely to cause such symptoms, or finally, 4) the gene is associated with similar symptoms in an animal model in which that particular gene has been disrupted in some way. We have continued to use this strategy as we move forward in evaluating promising gene candidates. I will highlight our progress in order to better help the committee assess our progress toward the outlined goals below. We are pleased with our progress, and I think that the speed and efficiency of evaluating new gene candidates in our laboratory and in collaboration with others has greatly increased over the past few months. Increasing interest in AHC on the scientific front is also a major goal, which will encourage additional investigators to become involved in research. Thus, presenting our ongoing work at meetings, such as the International Child Neurology Meeting to be held in June of this year, is another way in which we can help to keep this disease at the forefront and encourage others to participate in such research.

As mentioned in the previous report, we have established two important collaborations with other research laboraties, one at Harvard in Boston with Dr. James Gusella, and the other with Drs. Jen and Baloh at the University of California Los Angeles. We continue to work together with them, and taking advantage of resources at both of those institutions as well as at the University of Utah, to work together to better increase our chances of identifying a genetic cause of AHC as soon as possible.

Our work with the Gusella laboratory and Dr. Kim Hyung-Goo in Boston has focused on two major areas: 1) we have some indications that there may be a “position effect” of a specific chromosome abnormality rather than a direct disruption of a single gene. What this means is that instead of a simple error in the genetic message, the chromosome breakage may actually be interfering in a different way with the normal function of genes in the general area. 2) we continue to work to check every single gene in the region by more standard techniques to decode the message to look for any small errors that could be interfering with the function of one or more genes in the region. Thus, we have applied different approaches to move forward using the strengths of this particular laboratory.

As mentioned also in our last report, Drs. Jen and Baloh from UCLA have recently identified a new gene candidate, a glutamate transporter, which they determined to be causing the disorder in a single child in California. The symptoms in this child are very similar to that seen in AHC, and include episodes of alternating hemiplegia. This has given us an entirely new direction in evaluating a whole new group of gene candidates which could play a role in AHC. We continue to work together with our colleagues at UCLA to sequence gene candidates (decode the genetic map dictating how these genes are made into proteins) and also to use newer techniques to identify small and difficult to find changes in these gene candidates which could prove critically important.

As Dr. Reyna has indicated in a recent conversations with both the AHC Foundation President and Medical Liason, approximately two weeks ago the lab specialist who has been working closely with me for the past five years on this project unexpectedly moved. This provides us the opportunity to hire someone with experience in new areas we would like to pursue for the AHC project. We have been actively interviewing new candidates, and have tentatively identified a young scientist with excellent credentials to replace her. She has a PhD, and would bring a number of new skills to the project. We propose to dedicate 60% of her time to the AHC project. Our former laboratory specialist, Justine Johnson, was extremely organized, and we foresee no difficulty in continuing work uninterrupted.

Thus, we report the following progress, and continue to pursue the following goals.

Specific Aim 1. Genome wide linkage analysis and further characterization of resulting gene regions of interest in selected families with more than one affected child:

Simply put, genome wide linkage analysis is a method in which we utilize families with more than one affected individual to help us zero in on a particular area. Newer and better techniques are continually being identified to achieve this task, even using small families, because the tools to perform such work has become better and better in the last year or two. We are actively using a newer strategy, known as SNP analysis (or single nucleotide polymorphism analysis) that takes advantage of unique changes between individuals that occur throughout our genetic map to help identify subtle clues as to how those with AHC may be different than those without within families. Using this technique we are narrowing on focus on at least 3 different areas that could have critical genetic changes causative in AHC.

Specific Aim 2. Analysis of “gene candidates” which cause similar symptoms to those seen in AHC patients, or have an important function that has been implicated as possibly affected in these patients.

All three laboratories have been working on this effort. As a result, we have identified a calcium channel mutation in one of our families with two affected children with AHC. Neither parent seems to carry the mutation, leading us to assume the mutation could have newly occurred in either the eggs or sperm of one of the parents without he or she actually being affected by the disease. We are currently working on additional studies to better understand what this mutation is doing. In addition, we have redoubled our efforst in looking at this and other calcium channels as potential cause of AHC in other children within the database. If the PhD we mentioned above agrees to take the position, then we will have her focus her efforts on this front over the next few months, as it seems particularly promising.

In addition, we have been pursuing new directions with regard to regions within the genetic map holding genes in the following categories: the ATPases and glutamate transporters, using the families with more than one affected child to help us determine whether these additional candidate genes may be important to examine.

3) Cytogenetic analysis of AHC patients without a family history of the disease.

Cytogenetic analysis involves using techniques in which we isolate cells from the blood (we can use cells we’ve previously banked from our database) and then use a variety of chemicals to fix the chromosomes in place that hold all the genetic information in the cell together. We have used older techniques to screen patients in the past, but newer tools now provide improved power to identify very small missing pieces of chromosome. These small missing pieces are known as “microdeletions”. Disorders like Angelman syndrome, which has many symptoms in common with AHC, have been found to be due to such microdeletions, and we continue to try to use better and better techniques to help us find answers. To use an analogy: suppose you were to fly a plane over New York City, and instead of identifying entire missing buildings from the air, you could identify the equivalent of a broken window in one of the buildings….such techniques that dramatically improve our ability to detect changes among the 30,000 candidate genes are coming on line. So far, we have used high resolution karyotyping and fluorescent in-situ cytogenetic techniques to investigate a subgroup of AHC children. Tests performed in this screen include high resolution karyotype (to the 650 band level), and telomere FISH studies. We hope to use even higher resolution techniques in the months ahead to further explore this possibility.

Summary

I hope this above report outlines our progress for the committee in sufficient detail to assure them of our continued dedication and progress in trying to identify the genetic cause or causes or AHC. It increasingly appears from our data that more than one gene may be involved. So far, we and colleagues have identified mutations in 3 separate genes in association with AHC symptoms: ATP1A2, CACNA1A, and now the glutamate transporter SLC1A3. This represents considerable progress over the past three years as we approach the end of our current funding cycle, and provides new directions for identifying abnormalities in all AHC patients. Mutations in the SLC1A3 gene are directly responsible for our pursuit of a new therapeutic direction, since we can more specifically expand our focus to medications known to impact on glutamate related processes. We continue to be optimistic that with time, we will make progress in treating this disease by better understanding the genetics and biochemistry underlying symptoms in these children. I apologize for the previously highly technical report, and will make every effort to make our work more understandable in future reports.

AHCF Progress Report Swoboda Neurogenetics Laboratory

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