Multiple Sclerosis
Genetics Group Winter 2010 Dear Friends, It is with pleasure and great enthusiasm that we send to you our 2010 MS Genetics Research newsletter. It has been a very productive time for us in the laboratory and inside these pages we hope to share with you the amazing progress that has been made in understanding the genetic factors that influence MS susceptibility and progression. Because of you, we have been able to expand our biological repository to include over 11,000 study participants. This is the largest collection nationwide, and using these valued materials we are currently in the midst of a new genome-wide association scan that is being conducted at the renowned Sanger Institute in Cambridge, UK, just a few miles away from where the famous double helix, twisted-ladder structure of DNA was discovered in the early 1950s. This study is combining your samples with other samples from people with MS across Europe and beyond to produce an impressive dataset of 17,000 individuals. When completed, we will compare these results to data already available on control samples. We believe this groundbreaking experiment will identify additional susceptibility genes. A major effort is underway to collect even larger numbers of samples which should allow us to identify even more subtle genetic variations that contribute to the disease. UCSF is committed to acquiring 3,000 new patient samples during the next 18 months, which will be combined with other samples from around the world. This new dataset will be used to confirm any results we obtain from ongoing experiments and to add to our ever expanding biological repository. The advances we make (and continue to make) are important ones, but our understanding of MS genetics remains incomplete. It is still too early to use this information in the clinical setting, though we believe it will one day help us improve diagnoses and make better decisions regarding patient care. As so many Americans have to do these days, we too are doing our share of belt-tightening. Thus, we have made the difficult decision to have this newsletter be the last one mailed through the US Postal Service. Instead, we will send future issues via the internet. You can also periodically follow our activities at http://neurology.ucsf.edu/msdb. We have included a section in the “Let’s Keep In Touch reply page” where you can tell us whether or not you would like for us to use your email, with space to provide the address should the answer be yes. Even if you don’t want to receive email updates we ask that you please take a moment to complete the remainder of the reply page. It provides us with important updates on your family and current contact information and can be mailed back to us free of charge. As always, we thank you and wish you the very best for 2010. Your participation is the foundation for all that we do, and we are grateful for your support. Sincerely,
Stephen L. Hauser, M.D. Professor and Chair
The UCSF MS Genetic Susceptibility Project Recent Progress To advance MS genetics research and to share available resources, the UCSF Genetics Group co-founded the International MS Genetics Consortium (IMSGC) that has brought together leading scientific groups worldwide. A wide ranging study was carried out and published in 2007 by the UCSF team in conjunction with the IMSGC. A first of its kind in MS, the study identified the Interleukin-7 Receptor (IL-7R), the Interelukin-2 Receptor (IL-2R) and the Lymphocyte Function-Associated Antigen 3 (LFA3 – also known as CD58) as susceptibility genes for MS. The study was completed using the two largest collections of MS genetics material worldwide (UCSF and Cambridge, UK), which contributed significantly to the “MS genomics map.” A letter was sent to all of our study participants at that time notifying them of the results and thanking them for their participation.
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Following this success of identifying these additional susceptibility genes, Jorge Oksenberg, Ph.D., led a new scientific analysis of the EPIC cohort (please see page 5 for more information on the EPIC Project), supplemented with another population of MS patients of equal size from our colleagues based in Amsterdam and Basel.This combined dataset represented the largest genome-wide association analysis (GWAS) performed in an MS cohort. In this study, 177 new associated variants were detected outside of the HLA region. One of the most significant findings in this study was an association for a gene called GPC5. This gene may play a role in the control of cell division and growth. Unexpectedly, we also identified significant associations between several genes and different MS traits, including the amount of brain tissue involved (e.g. lesion load), brain atrophy and age of onset. This study really highlights the need for large numbers of participants to identify genetic effects that are important in MS. The goal now is to understand the mechanisms by which these genes influence MS susceptibility and/or disease progression. It is important to remember that genetic variants associated with MS are most likely normal that many people without MS also inherit. Our research is testing the hypothesis that the genes associated with MS include some variations that may be common in the population and some of these variations may be advantageous to have. We believe that a specific combination of genes predispose some individuals to develop MS after exposure to an environmental factor or factors.
Predicting relapses in individuals with a first attack of MS Led by Sergio Baranzini, Ph.D., we completed an important gene expression profiling study in patients with an initial attack of MS (known as clinically isolated syndrome [CIS]). The formation of MS lesions is thought to be caused by an activated (e.g. “turned on”) cell found in blood (called a CD4+ T cell) that moves into the brain and initiate a damaging inflammatory reaction. In this study, we isolated these CD4+ T cells from the blood of people experiencing their first attack of MS and using gene chip technology obtained a “gene-activity expression profile” of several thousand genes within these cells. Using powerful computer programs to help translate these images into genetic research data, unique patterns – molecular signatures – were found in the CD4+ cells that predicted with high reliability the risk of future relapse, months or years later. The specific genes involved made sense in terms of their known biological function. A gene known to put a “break” on the function of CD4 T cells (called TOB1) was under-expressed in patients at high risk for future attacks. Similarly, over-expression of genes that promote activation and production of CD4 T cells was present in the high-risk group. This finding means that a blood test to predict how MS will behave in the future may soon be at hand. We are now studying how interacting genes collectively affect the ability of CD4+ T cells to initiate the disease. What we want to know is how to keep CD4 T cells from being over-active. These data may lead to new opportunities not only to monitor but also to treat people with MS.
An example of a gene expression profile – a molecular signature. In this image, the activity of several hundred genes (columns) is depicted in a red-green barcode for 13 individuals (rows). While red indicates high activity, green indicates low activity for a particular gene. This global view allows for the identification of patterns (patches of red or green areas ) across several genes or individuals. This facilitates the biological interpretation of the complex gene regulation process and the identification of individuals with similar expression signatures that may correlate with clinical observations, such as response to therapy or disease progression. 3
Network Analyses To identify these combinations, we further investigated genetic information using a technique called network analysis. Here, we used novel computer algorithms to look at genes of interest to see how they interact with each other biologically. We assembled a “network” with all experimentally determined interactions and conducted searches for “sub-networks” (also know as modules) that contain markers associated to MS. This resulted in a number of modules that were related to each other by their participation in the same biological pathway. We were able to identify, for the first time, “modules” involved in nerve cell axon guidance and in receptors for the transmitter and nerve toxin glutamate as susceptibility factors in MS. Mathematical models have been developed by our team to capture the coordinated behavior of multiple genes associated with the development of multiple sclerosis.
EPB41L2
GRID2
GRIK1
HOMER1
GRIA1
GRIK2 GRIK4
GRIA4 DLG1 GRIN2A KCNJ2 ERBB4
DLG2
In this example, interacting genes involved regulating the chemical signals between neurons and other cells (the glutamate pathway) are shown to affect susceptibility to the disease. Each node (circle) represents a gene component of the network. The colors represent the location in the genome (chromosomes). The size of each network node is proportional to the strength of the effect of each gene, and the connections (lines) represent the strength of the interaction.
To see if these modules were specific to MS, we examined genetic data from 8 other diseases including 3 autoimmune and 2 neurological diseases. The analysis identified modules specific for each disease but also some that were overlapping. Not surprisingly, HLA genes were identified as common susceptibility factors to MS, rheumatoid arthritis and type 1diabetes. These diseases are all considered autoimmune diseases. This finding may begin to explain why people with MS sometimes belong to families in which other autoimmune diseases also occur.
African American Study- Ancestry can influence clinical outcome Led by Dr’s Jorge Oksenberg and Bruce Cree, UCSF has been at the scientific forefront in studying MS in African Americans. Previous work found that African Americans are less likely to develop MS, but that once MS begins, the symptoms are often more severe than in white-Americans.
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We are well on our way to identify the genetic factors that contribute to susceptibility and disease severity in this community, but to reach the finish line we will need much larger numbers of MS patients, family members and friends to participate. Only through analysis of very large numbers of participants will we have the the ability to identify these genetic factors.
Moving forward with the MS Genetics Research Group Building on our early success, we have now expanded the International Multiple Sclerosis Genetics Consortium to include 33 other scientific investigators in 18 additional countries worldwide. We are truly global, sharing resources and talents in every way possible to end this devastating disease. We are currently in the midst of an exciting project with the newly expanded IMSGC. A new generation genome-wide association scan is being conducted at the Sanger Institute in the UK that takes advantage of new cutting-edge technology to study human genetic variation, with a level of resolution unimaginable just a year ago. This study is relying on the UCSF biological repository and other MS patient samples from populations across Europe to produce an impressive dataset of 17,000 patient samples. When completed, we will compare these results to data already available on control samples – which we undoubtedly will identify additional susceptibility genes and hopefully complete most of the MS genetic puzzle. Once this experiment has been completed, we know we will need an equally impressive number of new participants to confirm results. Thus, the clinical coordinator office and the bio-repository staff are fully entrenched in an ambitious project to recruit and enroll 3000 new MS research subjects over the next year and a half. To help reach our goal we have had the good fortune to team up with The North American Research Committee On Multiple Sclerosis (NARCOMS) and their MS Patient Registry. Through NARCOMS, we sent a letter to registry members inviting them to participate in our genetic susceptibility research study. We have had a wonderful response and are working hard to reach each registry member who agreed to participate. This will take us many months and a round-the-clock effort to complete, but we couldn’t be happier with the wonderful response that we’ve received from the entire MS community.
The EPIC Project (Expression, Proteomics, Imaging and Clinical) Multiple Sclerosis is a dynamic, constantly changing disease. The EPIC project (previously known as the GeneMSA study) is a unique and ambitious longitudinal study whereby UCSF investigators follow 500 people with MS each year for a total of 5 years with the purpose of capturing these changes and learning the factors that control the evolution of the disease. Since each participant must come to UCSF for clinical assessments and yearly state-of-the-art MRI scans, in general only people who live locally are able to participate. Its specific goals are to intensively study MS at the bedside using the most advanced tools of modern biology in order to develop biomarkers that predict 1) who is likely to develop MS; 2) how MS will behave once it begins, and 3) what the best therapy for an individual should be. Ultimately, it is our goal to use this information in making routine clinical care decisions for individual MS patients. Only through studying people living with MS are the fundamental answers to this disease likely to be discovered. We want to fully understand MS genetics, the biology of inflammation, neurodegeneration and brain repair in order to – at long last – have safe and effective interventions to prevent, treat, and cure MS.
An Integrated Biomarker Approach to MS EPIC Longitudinal MS Dataset, N=500
Clinical Characterization
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Visual Imaging
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Data Integration
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Gene Expression
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Brain tissue segmentation: MRI image (left) is processed using computer software to study in detail the tissue loss from separated brain compartments (cerebrospinal fluid, gray matter and white matter).
MRI image
cerebrospinal fluid
gray matter
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Scientific highlights of the EPIC Project Relationships between Genetics and MRI Measures (genotype-phenotype):
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Led by Daniel Pelletier, M.D., using state of the art MRI imaging, we have been able to characterize the clinical expression of multiple sclerosis in a way that has never been possible before. As a first step, we focused on the relationship between the strongest susceptibility gene known in MS (HLA-DRB1*1501) and disease severity. We found that patients carrying this gene had increased white matter lesions visible on brain MRI scans, increased axonal injury, increased brain atrophy and increased cognitive impairment (measured by PASAT-3, neuro-cognitive test) compared to patients who did not carry that gene (HLADR1*1501). Secondly, the depth and richness of the data collected from the research patient cohort enabled us to study and establish, for the first time, the link between brain injury (white matter lesions and brain atrophy) and patient self-reported health-related qualify of life (QOL) measures. These measures are more comprehensive in capturing the overall impact of MS than are scales of physical disability. Despite normal or only mildly abnormal neurological examinations, MS patients most often report a reduced quality of life. Using high-resolution MRI images, we demonstrated that the patients’ perceptions of how MS impacts fatigue and reductions in emotional and cognitive health correlate with MRI lesions and brain atrophy, particularly in the gray matter. These associations persisted independent of treatment status, an important finding since disease-modifying therapies by themselves have been shown in some studies to influence QOL. In an early form of MS, voxel-based morphometry (VBM) analysis shows volume loss in the thalamus (a gray matter structure in the middle of the brain, shown here).
Using this same group of subjects, we have developed new processing image analysis methods to detect regional brain atrophy and to establish the direct connection between white matter lesions and grey matter loss. Subsequently, using techniques called diffusion tensor imaging and fiber tracking in vivo we found that only
lesions within the white matter tracts connecting the thalamus and the cortex of the brain were correlated with thalamic atrophy. This work suggests that neurodegeneration in MS is the direct result of the injury to myelin.
Example of two brain fiber bundles (red) traveling through MS plaques (blue) connecting the thalamus (green) and the gray matter cortex (not shown).
Quantitating Neurodegeneration in the Retina of the Eye
Why do patients with MS become disabled? Why is it difficult for physicians to predict if, or when, a patient with MS will become disabled? Over the last twenty years we have learned a great amount about the role of immune dysregulation in MS. As a result, we have discovered, tested and implemented a generation of therapies (interferons, glatiramer acetate, and natalizumab). These treatments are the first to affect the underlying course of MS. They do this by preventing attacks (exacerbations) and reducing the number of new MS lesions detectable on MRI. However, existing therapies are only partially effective against the disease and have their greatest impact early in disease course. Currently, little can be done for patients once they are becoming, or have become, disabled. Because disability in MS takes many years to develop (on average 15-25 years), it has been very difficult to design therapies to help address this aspect of the disease. Led by Ari, Green, M.D., we are investigating visual dysfunction in MS and using this newly acquired knowledge to better understand the disease process as a whole. We employ novel methods for evaluating structural and functional integrity of the visual system to help us understand the neurodegenerative process in MS. The EPIC study has made possible some of our most interesting and important discoveries in this area. Over the last two years we have performed more than 500 visual evaluations in patients with MS. We perform basic visual tests (high contrast acuity, color vision, low contrast vision) followed by retinal imaging techniques and visual electrophysiology when indicated. One of our standard methods of examination is optical coherence tomography (OCT). OCT is an important clinical tool that can provide high-resolution imaging of the retina.
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On the right, an OCT image of the retina shows the classic thinning of the temporal nerve fiber layer (made up of axons). The space between the two yellow lines is where injury is most pronounced. The image is taken from a circle (green) surrounding the optic disc (red arrow, left image). The bright white band in the upper part of the OCT image is the nerve fiber layer.
The retina is the only part of the central nervous system that can be visualized non-invasively. Retinal injury is very common in MS and we have recently discovered it involves more parts of the retina than we previously thought. Predominant injury occurs in the inner retina and by measuring and tracking retinal injury using OCT we can complement clinicians’ ability to follow MS using their clinical exam and MRI. We plan to use these methods to help develop new therapies aimed at reversing or forestalling neurodegeneration in MS. Thanks to the voluntary participation of EPIC study participants, we have accumulated more retinal imaging data than any other site in the world. With your help, and state of the art retinal imaging, we have made two important discoveries. 8
First, inner retinal injury in MS is not uniform but appears concentrated in the fibers that mediate central vision. This may serve as a very useful measure for tracking neurodegeneration in MS. Furthermore, investigating why some neurons are prone to injury may lead us to understand the basis for this relative selectivity for injury. Second, OCT measures of retinal injury correlate with measures of nerve cell injury in the brain. This likely occurs as a consequence of the spread of degeneration from one neuron to another which may help us understand why MS takes so long to become disabling. One of the great strengths of the EPIC project is the extensive genetic, imaging and clinical evaluations that each patient undergoes annually as part of his or her participation. In 2010 we plan to use this genetic dataset to learn more about what leads to neuronal loss in the visual pathway in MS. We have also recently acquired new instruments for even higher resolution imaging of the retina (spectral domain-OCT). The new tools and techniques will hopefully bring us a closer to our goal of finding ways to stop the debilitating effects of MS. If you participate in the EPIC study and have not yet had an OCT vision exam, and would like to, please contact Dr. Green’s coordinator, Ami Cuneo, at 415-353-2707 or email her at ami.cuneo@ucsf.edu.
3-Dimensional OCT images of the optic disc of a volunteer without MS (left) and an MS patient with an active optic neuritis (right). Swelling (axoedema) occurs when axons cannot transport proteins and fluid down the length of the axon. The patient in the right image did not have symptoms besides minor eye pain. This suggests that MS patients may at times have subclinical optic neuritis that could contribute to later injury.
Let’s Keep in Touch! Reply Page Please drop us a line. Providing us with current contact information and updates on you and your family allows us to keep in touch with you. Please provide us with any new contact information so that we can continue to send you updates about our research. Name
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Frequently Asked Questions Q.
May I have my personal results of the genetic testing?
A.
Since the results of the genetic analyses are not yet able to be used for clinical diagnosis or treatment, research participants may not have access to any individual genetic results. Data and results of our genetic analyses are published as pooled data, not as individual findings.
Q.
Will I be notified of study results & findings?
A.
Preliminary results and research findings are published periodically. The UCSF MS Genetics website (http://neurology.ucsf.edu/msdb) lists the papers published in professional journals that results from our research projects. We will also email periodic newsletters highlighting the activities of the group.
Q.
Why do studies need healthy controls to participate?
A.
Genetic studies like ours need controls (persons who do not have MS or other autoimmune diseases) to participate. By comparing genetic profiles in MS and in non-MS individuals we will be able to confirm that any results we generate are actually due to the person’s disease and not just a genetic variation that occurs in the healthy population as well.
Q.
Do I need to keep you updated when my contact information changes?
A.
Yes! We would like to have your current contact information to keep you updated with current information on our research. (such as this newsletter).
Q.
After I participate in the study, will I be contacted to provide any further information?
A.
It is likely that you will be contacted in the future for new information. As our research progresses, new questions on MS sometimes arise. We occasionally send follow-up questionnaires that are designed to obtain new or updated information about you and your medical history.
Our work is supported by: The National MS Society The National Institutes of Health The Nancy Davis Foundation and The Ostby Foundation
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