As mentioned before we used the grid-computing site Folding@Home. They specialize their research in Huntington's Disease, ALS Lough Gehrig's Disease, Alzheimers, and Parkinson's Disease. Since the beginning of semester we have accumulated over 11,010 points, 22 work units, and a rank of 309,375 out of 1,543,542. We made it into the top 20% of grid-computing donors. This was definitely a meaningful project because we were able to contribute, even if on a small scale, to a collaborative effort to advance science and medicine. Reading the article, conducting and interview, and doing background research also contributed to our understanding of Huntington's Disease as well as how evolution has played a part.
We thank you for those who took the time to read our blog. We hope that through our research efforts you were able to learn new things about this disease as well as some of its misconceptions.
Patrick, Justin, Lee, and Brian
Sunday, May 1, 2011
Friday, April 22, 2011
Huntington's Article Questions
1. The PNAS paper entitled “Potent inhibition of huntingtin aggregation and cytotoxicity by a disulfide bond-free single-domain intracellular antibody” (Colby et al. 2004) describes a potential treatment that uses “intrabodies” (intracellular antibodies) to bind the toxic fragment of the huntingtin protein and inactivate it or prevent its misfolding. Could this treatment be modeled using grid-computing? The intrabody would have to be introduced using gene therapy. How would this work?
Yes. First they would need to isolate the huntintin protein and determine its 3-demensional shape and its sequence of amino acids. Then through a series of trial and error they would be able to use grid-computing to try and figure out what sequences would potenitally bind the huntingtin protien. The antibody would need to be able to be recognized by the bodies immune system for degredation. A potential mechanism for correcting the overexpression of the huntintin protein would be to use a gene therapy by way of intrabodies. To successfully administor these intrabodies the intrabody would need to be sequenced and placed into a vessel would have a target in the basal ganglia and also be able to pass through the blood-brain barrier. If this was able to be accomplished the intrabody gene would need to be inserted into the host DNA and expressed. If the gene was able to be expressed then it could recognize and bind the huntingtin protein to then undergo regulation.
2. In an evolutionary sense, why is it informative to study Huntington’s and its implications in mice?
Its important to study the evolutionary aspect of huntingtons disease because we can better understand how a disease comes about due to a mutation. It is also beneficial to know how the disease can be spread to offspring or other individuals through generations. In Huntington’s Disease we know that the disease is autosomal dominant which basically means that the inheritance of one allele can result in the disease. This combined with a late onset is why the disease has not felt the effects natural selection. Selection can only act on phenotypes it can see. Typically an individual with HD would most likely have reproduced before the onset of noticeable symptoms and the disease can proliferate.
It’s important to understand its implications in mice because they are a commonly used because of their genetic and physiological similarities to humans. In addition they can be used for manipulation to test treatments or other effects of potential therapies. They reproduce quickly and in high number. In addition they are relatively easy to manage in a research lab.
3. Apply Darwin’s four postulates to the traditional view of neuron selection.
Within an individual’s brain tissues, variation is present in the genetic makeup of neurons—or more accurately, the genes that code for neuronal products vary. These genetic differences underlie both phenotypic and behavioral variation of the neuron. Within the somatic line, as neurons undergo mitotic division, they pass on their genetic makeup to daughter neurons (including any mutations they have accrued). This results in one kind of cell that produces multiple genotypes, a process termed genetic mosaicism.
Because neurons vary and that variation is heritable, there exists a potential difference in neuronal performance. In short, some neurons are better at doing their job than others, and these differences can result in differential fitness between cells within an individual’s brain tissues. For example, a line of neurons that has acquired a mutation that leads to cell death will have a lower reproductive success than other healthy neurons. Theoretically, the “adapted” neurons would then become more numerous and shift the population of cells towards its own genotype. Important to neuron selection is the concept that neurons exhibit genetic variation, that variation is inherited (mitosis), neurons experience differential reproductive success, which together results in the evolution of cell populations within brain tissue.
4. Now add the selective pressure of MSH3 and instability and describe how this violates the assumptions we have made in class about “important” mutations.
Huntington’s disease is caused by a mutant allele that possesses an excess triplet repeat sequence of CAG. A threshold of 36> CAG repeats has been correlated with the onset of the disease. As the CAG repeats are translated, they create excess glutamine, which accumulate and cause the improper folding of the Huntington protein (a protein required by all cells). Mutant proteins then sequester important proteosomes required for cell function. This in turn results in neuronal cell death, specifically in the striatum.
Similar to other diseases that are the product of an excess triplet repeats, the sequence expands with every somatic and gametic division. Unlike ordinary mutations, this implies carriers of the mutant Huntington allele will not pass on the same allele they inherited—it will be expanded. Different from other mutations, the Huntington mutant continuously accrues new and predictable mutations. Neurons in different parts of the brain exhibit variable repeat lengths (genetically differentiated neuronal populations evolve). The CAG repeat grows with every division, somatic or gametic. This is known as instability.
One of the most compelling explanations for why this happens involves the role played by MSH3—a DNA mismatch repair gene. Under normal conditions, MSH3 replaces mismatched base pairs: it acts to eliminate mutations or increase fidelity during replication. However, because the mutant Huntington sequence causes a CAG hairpin loop to form, MSH3 binds to the CAG hairpin, undergoes a biochemical change, and promotes expansion, rather than correcting the mismatches. Usually a positive force, in the case of the mutant Huntington’s gene, MSH3 has become an accomplice in the perpetuation of this mutation. What makes the Huntington mutation different from other mutations concerns a kind of independence it experiences from selection. In the case of Huntington’s, genetic variability is largely dependent on specific chemical conditions—the presence of MSH3. Both of these factors differentiate it from other typical mutations.
5. Is Huntington’s Disease itself subject to selection? Why or why not?
It is more subject to artificial selection because if the disease is diagnosed before reproduction it decreases the fitness of the gene. In past the onset of symptoms was after reproduction would likely occur and the disease was already passed on to offspring. Natural selection can only act on phenotypes that it can see. If the onset is commonly after reproduction then natural selection would ineffective.
6. Why is it important to study protein folding/misfolding in Huntington’s, even though we know its cause (trinucleotide repeats)?
It is known that due to the trinucleotide repeats in the Huntington gene, an excess of Huntington protein builds up in the neurons of the Basal Ganglia, which proves to be detrimental to the normal functioning of those neurons. The more we can learn about the actual three dimensional shape and the folding/misfolding of the excess Huntington protein, a therapy could be developed that either alters the Huntington protein to a less toxic form or degrades excess amounts of the Huntington protein in the neurons that are affected by the mutated Huntington gene. In short, while a mutation in the Huntington gene is the actual source of the disease, methods could be developed to help "silence" the effects of the gene by regulating the amount of Huntington protein that is produced. So being able to understand the folding of the Huntington protein and the effects of misfolding it would go a long way in finding a possible cure or treatment for Huntington's disease.
Friday, February 25, 2011
An Experts Take on Huntington's Disease
On February 4th, 2010 the four of us met with Dr. Richard Dubinsky at The University of Kansas Medical Center to aid in a better understanding of what Huntington's Disease is. Dr. Dubinsky is well qualified to answer our questions about Huntington's Disease, and we were able to learn a lot from him.
To give a brief background, Dr. Dubinksy attended the University of Missouri Kansas City Medical School and graduated in 1982. He completed an internship in internal medicine at Baylor College of Medicine followed by a neurology residency at the Baylor College of Medicine. His areas of interest include movement disorders, specifically dystonia, myoclonus, Huntington's Disease, and Parkinson's Disease. He is actively involved in clinical research in Huntington's Disease, Parkinson's Disease, and dystonia.
What was extremely beneficial in interviewing Dr. Dubinsky was that we were able to gain better insight into what Huntington's Disease really is. He was able to clarify some of the misconceptions about the disease and go into more detail about what is currently being done to aid in HD treatment/prevention. He was able to confirm many of the things we were able to find with our prior research on the disease and explain in better detail some of the grey area we were still unsure about.
Unfortunately Brian wasn't with us when we took these pictures; so we just made him there anyway.
We asked Dr. Dubinsky is he had ever heard of grid-computing and he said he was unaware of it, but that it did make sense why it would be so critical for research.
Below are some of the questions addressed during our interview, which really helped us to understand the disease from a clinical and research perspective:
1. In your own words, how would you best describe what Huntington's Disease is?
There are three domains that are affected of people with Huntington’s disease: behavior, cognition, and motoric. The motor part is the chorea movements which are easy to recognize but seldom cause problems. People with Huntington’s disease will be clumsier, and as the disease progresses they will move less and become stiff and more prone to fall. This is really the least of our problems. The behavioral problems are really the main source of problems. They really run the whole gamut of psychiatric problems. Typically there will be problems with depression, anxiety, irritability, compulsive activity, and obsession thoughts. The cognition is interesting in that it is different from Alzheimer's. With Alzheimer's you don’t make memories. You forget that you forget. With Huntington's Disease it is more like having difficultly completing simple tasks, like doing things in the correct sequence. The social aspects are also typically more problematic. It is a very visible disease when there is onset, and it can be very noticeable.
2. How does Huntington’s Disease affect the physiology of the Brain?
Huntington’s Disease really does not effect neurotransmission. With Huntington’s Disease you have a loss of cells. The basal ganglia in the middle of the brain have spiny neurons and each make about 100,000 connections, and you lose those interconnections. This is why you may have difficulty trying to put things together. We also think that the cortex may be thinning. There is one genotype, but there are many phenotypes.
3. Is the accumulation of the Huntingtin protein HTT in the basal ganglia what damages the nerve cells?
There are proteinatious clumps in the cytoplasm and the nucleus which can be stained to show the presence of the HTT protein, but they are being bound with ubiquinone. We don't believe the actual proteins are doing anything. It's the other things in the proteinatious clump that are binding up all of the proteosomes needed for the cell. There could be a toxic loss of function by sequestering normal functioning proteosomes.
Overall the interview was extremely interesting and eye-opening. After doing our own preliminary research about the disease, we thought we had a decent understanding of what Huntington's Disease was. What the interview gave us that research alone did not was that Huntington's Disease, although ultimately a terrible disease, isn't as bad as people might think. Patients with the disease lead very normal lives with the exception that they must adapt when their conditions change. Having a positive attitude is sometimes the best medicine, and this is what really hit home in our interview. We really appreciate Dr. Dubinsky taking the time out of his busy schedule to meet with us and answer our questions.
If anyone reading our blog is interested in learning more about the interview or something mentioned in the interview, leave us a comment and we can help to clarify and/or better explain it.
To give a brief background, Dr. Dubinksy attended the University of Missouri Kansas City Medical School and graduated in 1982. He completed an internship in internal medicine at Baylor College of Medicine followed by a neurology residency at the Baylor College of Medicine. His areas of interest include movement disorders, specifically dystonia, myoclonus, Huntington's Disease, and Parkinson's Disease. He is actively involved in clinical research in Huntington's Disease, Parkinson's Disease, and dystonia.
What was extremely beneficial in interviewing Dr. Dubinsky was that we were able to gain better insight into what Huntington's Disease really is. He was able to clarify some of the misconceptions about the disease and go into more detail about what is currently being done to aid in HD treatment/prevention. He was able to confirm many of the things we were able to find with our prior research on the disease and explain in better detail some of the grey area we were still unsure about.
Unfortunately Brian wasn't with us when we took these pictures; so we just made him there anyway.
We asked Dr. Dubinsky is he had ever heard of grid-computing and he said he was unaware of it, but that it did make sense why it would be so critical for research.
Below are some of the questions addressed during our interview, which really helped us to understand the disease from a clinical and research perspective:
1. In your own words, how would you best describe what Huntington's Disease is?
There are three domains that are affected of people with Huntington’s disease: behavior, cognition, and motoric. The motor part is the chorea movements which are easy to recognize but seldom cause problems. People with Huntington’s disease will be clumsier, and as the disease progresses they will move less and become stiff and more prone to fall. This is really the least of our problems. The behavioral problems are really the main source of problems. They really run the whole gamut of psychiatric problems. Typically there will be problems with depression, anxiety, irritability, compulsive activity, and obsession thoughts. The cognition is interesting in that it is different from Alzheimer's. With Alzheimer's you don’t make memories. You forget that you forget. With Huntington's Disease it is more like having difficultly completing simple tasks, like doing things in the correct sequence. The social aspects are also typically more problematic. It is a very visible disease when there is onset, and it can be very noticeable.
2. How does Huntington’s Disease affect the physiology of the Brain?
Huntington’s Disease really does not effect neurotransmission. With Huntington’s Disease you have a loss of cells. The basal ganglia in the middle of the brain have spiny neurons and each make about 100,000 connections, and you lose those interconnections. This is why you may have difficulty trying to put things together. We also think that the cortex may be thinning. There is one genotype, but there are many phenotypes.
3. Is the accumulation of the Huntingtin protein HTT in the basal ganglia what damages the nerve cells?
There are proteinatious clumps in the cytoplasm and the nucleus which can be stained to show the presence of the HTT protein, but they are being bound with ubiquinone. We don't believe the actual proteins are doing anything. It's the other things in the proteinatious clump that are binding up all of the proteosomes needed for the cell. There could be a toxic loss of function by sequestering normal functioning proteosomes.
Image acquired from: http://www.nyctreatment.com/img/Basal-caudate,thala,puta,globus.jpg
Image acquired from: http://upload.wikimedia.org/wikipedia/commons/6/66/Proteasome.jpg
Proteasomes belong to a class of proteins called proteases and play an important role in the normal function of a cell. They are commonly found in the cytoplasm and nucleus and are primarily responsible for assisting in the degradation of damaged or unneeded proteins. They work by lysing the peptide bonds between amino acids, a process called proteolysis. In relation to Huntington's Disease it is a huge problem for the cell if these proteasomes are being used up because of the HTT protein over expression. A cell constantly regulates how much protein is present, and when too much builds up it can be detrimental to the cell.
4. If you wanted to be tested for Huntington’s Disease, how would you go about doing this?
It is about a four month process from start to finish. They come in first to see Dr. Dubinsky and myself for about an hour and a half visit to go over family history, personal medical history, and thorough neurological exam. Then they see a psychologist for two visits. Then they see a genetic counselor for one session and have their blood drawn. It’s about a three week wait for the results.
5. How does a geneticist test the blood to determine the presence of the Huntington allele?
The name of the gene is called IT15 gene. We all have this gene, but some have the expansion, and some don’t. They will either use western blot or PCR. They can look at the number of repeats and see if it is expanded. If they have one positive result they then use the other method just to be certain.
6. What does your research with Huntington’s Disease focus on?
Most of our research is through the Huntington’s study group. At the moment were are trying to obtain information for those participating in the group so it can be used to answer a lot of questions about the disease. In terms of treatment protocols we are using high doses of creatine going up to 60 grams a day, which will try to slow down the progression over three years. There is another treatment which is an antihistamine developed in Russia that may have cognitive benefits to improve cognition.
7. Is gene therapy a future treatment possibility for Huntington’s Disease?
What is really promising is the possible use of missense RNA and missense oligonucleotides where basically you custom-make RNA, which will bind to the transfer RNA for the mutant allele, which will inhibit transcription of the mutant allele. This is also called RNA interference.
This is a video we found that illustrates how RNA interference can be used for gene therapies:
What makes the use of RNA interference much better than doing a gene knockout is that with RNAi you can regulate the expression of a certain gene without deleting the gene completely. The problem with Huntington's Disease is not the expression of the HTT protein, but rather the over-expression of the protein. If we are one day able to slow down the translation so the Huntington's gene, so it doesn't get over-expressed, then it could be a very valuable treatment in the future.
8. Everyone has the Huntington's gene…What is the HTT protein used for normally? Would its complete inhibition cause any side effects?
The gene is transcribed in the basal ganglia. It is needed for life. It is found in the mitochondrial membranes and cell membrane. Also, the nucleus and cytoplasm. There is no difference in phenotype between homozygous for mutant alleles and only one mutant allele.
9. What are the most common types of treatments for symptoms?
For the cognition, not much has been proven to work. For the behavioral aspects, the usual medications used to treat those psychiatric disorders work quite well in relatively low doses. The chorea movements are really not that bothersome. It is when they are falling out of the chair when it gets to be bothersome. At that point, some medication can block enough dopamine to take the edge off. Some medications can slow down the chorea but at an enormous cost: a high risk of depression and suicide. So it’s not a common treatment. Simple things like cutting caffeine out of the diet can help a lot. Any sort of stimulant will increase the chorea. On the other hand, being stiff and not moving is more of a problem than moving all over the place.
10. Why should a doctor know about evolution?
From an evolutionary stand point it is interesting to see how a mutation spreads through a population and how it affects the population
If anyone reading our blog is interested in learning more about the interview or something mentioned in the interview, leave us a comment and we can help to clarify and/or better explain it.
Thursday, February 3, 2011
Introduction to Grid-Computing and Huntington's Disease
As technology continues to become more advanced and computing power increases exponentially, what once may have seemed to be a complicated task has now become easier and far less complex. A current issue that we face when it comes to analyzing data is that we are unable to build computers fast enough to interpret the data efficiently. However, a solution to this problem has been by the implementation of grid-computing. Grid-computing is rather new technology that uses the power of thousands of personal computers on a network to simultaneously divide and conquer large amounts of data to ultimately achieve a single, common goal. Individual computers are linked on a network using software called middleware, and they each work simultaneously until the work unit is complete. A well-known example that uses grid computing is the organization SETI (Search for Extraterrestrial Intelligence). This organization uses grid-computing to analyze data collected in search for signals from outer space.
The traditional method for analyzing vast amounts of data would have been to build a super computer. Super computers have long been built and used for projects that require a large amount of computing power. In a quote from Vijay Pande, leader of the Pande Lab at Stanford University, he states how instead of using one computer for 1,000,000 days, you can use 100,000 individual computers for 10 days and complete the same amount of data analysis. Grid-computing allows this high speed information analysis to happen. Grid-computing is beneficial for a number of reasons: (1) it is more cost efficient, (2) it is useful for tasks requiring vast amounts of computing power, and (3) when the computers are networked they can work in concert to achieve a common goal efficiently. In short, the power of grid-computing is infinite. The ability to analyze large amounts of data quickly is dependent upon the number of volunteers willing to use their personal to computer.
The purpose of understanding grid-computing is because some of the work currently being done affects all of us. For example, many grid-computing efforts concern the analysis of folding proteins. Diseases such as Alzheimer’s, Amyotrophic Lateral Sclerosis ALS, and Huntington’s Disease are all because of misfolding of certain proteins. Grid-computing allows researchers to analyze data from the protein folding, which ultimately will allow us to better understand how these specific proteins misfold. Our end goal is that we hope the research being done will lead to cures and/or preventative measures to aid in these diseases. Our group, specifically, is running the grid Folding@Home, which performs analysis on Huntington's Disease.
What makes the HD gene detrimental is because of how the gene is oriented. The gene includes a series of trinucleotide, CAG, repeats, which ultimately can lead to the over production of the huntingtin protein. For the huntingtin protein a normal allele would include 26 or few CAG repeats. The disease causing alleles would have to include over 36 CAG repeats, and there are two types of HD-causing alleles. Reduced-penetranc HD causing alleles have 36-39 CAG repeats, and full-penetrance HD causing alleles have greater than 40 CAG repeats. Reduced-penetrance means that in some cases the person inheriting the HD allele may or may not be symptomatic. Full-penetrance means that the individual will be symptomatic.
Huntington's disease presents with many different symptoms. Some of the most common symptoms are:
- Dystonia
- Involuntary Movements
- Chorea - twisting and jerking motions
- Dementia
- Aphasia
- Depression
- Lack of Coordination
- Death
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