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Mitochondria and Autism Symposium

July 8, 2010 38 comments

For the second year in a row autism was featured at the United Mitochondrial Disease Foundation meeting. Following last year’s well-attended afternoon symposium, Robert Naviaux, M.D., Ph.D. (UCSD), in conjunction with Autism Speaks’ science team, successfully applied for an NIH conference grant to support a more extensive full-day meeting that included a family “Ask the Doc” panel discussion.

Why Mitochondria?

Mitochondria are the primary energy factories for all cells in the body.  When these factories reduce their output, critical cell functions begin to flicker or fade.  The energy is produced through a process called oxidative phosphorylation—an elaborate process that converts oxygen in body tissues to energy used for all cell functions. Although the metaphor of “energy factory” is the most common way to think of mitochondrial function, mitochondria are responsible for much more.  Mitochondria were once — long ago in the history of evolution — single-celled organisms like bacteria that functioned independently, responding to the environment and producing their own proteins encoded by a small circle of DNA.  Several billion years later, mitochondria are fully integrated into our cells, co-opting proteins encoded by the much larger nuclear genome of each cell to serve different functions. Proper mitochondrial function is tuned for each cell type since skin cells, heart cells, and brain cells all have different energy needs.  Mitochondria, like their bacterial predecessors, remain exquisitely sensitive to the local environment and as such function differently in developing versus mature cells, and also in response to differing temperatures, toxins and immune challenges.

Genetics and Epilepsy: finding common ground

The Saturday scientific session began with two primers, one on Autism Spectrum Disorders from Sarah Spence, M.D., Ph.D. (NIMH) and one on mitochondrial disorders from Salvatore DiMauro, M.D. (Columbia University). This background allowed the audience of parents, researchers and clinicians with different specialties to find some common ground for the later presentations and discussion.

One of the unique aspects of this meeting was the pairing of two talks on a topic, one taking the perspective of autism and the other mitochondrial disorders. Abha Gupta, M.D., Ph.D. (Yale) informed the group about our current understanding of autism genetics and focused specifically on what can be learned about the biology of autism by discovering rare mutations. Dr. Naviaux then wove the perspective of traditional mitochondrial genetics into a broader tapestry for the audience to consider. Over 1100 proteins are active in the mitochondria, and the DNA that codes for these proteins is scattered throughout the mitochondrial genome and all the chromosomes in the nuclear genome. This scatter and spread makes mitochondrial function an easy target for random mutations. Also, mutations in one gene can have complex effects on the expression of other genes.

Another area of Dr. Naviaux’s research has focused on a mitochondrial disease called Alper’s syndrome, in which the patient develops typically until a relatively mild viral infection stresses the system and uncovers the mitochondrial deficit, resulting in the onset of severe symptoms. Research into genetic vulnerabilities revealed by environmental stressors is relevant to our understanding in autism of the interaction of genes and the environment. In his presentation, Carlos Pardo, M.D., (Johns Hopkins University) considered the interaction with the immune system by focusing on how components of the immune system serve key roles in development. Dr. Pardo surprised the autism research world in 2005 when he showed clear marks of neuroinflammation—signs of an activated immune system in the brain—using postmortem tissue from individuals with autism. This intersection of immunology and the brain has been a major focus of his lab. At the symposium, Dr. Pardo showed how a specific class of receptors that are important for marshaling resources to fight infection and healthy brain development also affect mitochondrial function. The converse was also noted– the metabolic breakdown products from dysfunctional mitochondria can adversely affect this unique receptor system.

A second set of presentations focused on epilepsy.  Russell Saneto, D.O., Ph.D. (University of Washington) offered his clinical perspective from treating many cases of epilepsy in mitochondrial disorders.  Depending on the underlying cause of epilepsy in mitochondrial disease, different types of treatment tend to be more effective.  This theme was echoed in a presentation from autism expert Roberto Tuchman, M.D. (University of Miami) who talked about “the epilepsies” as a related group of disorders, but noting that optimal treatment comes from identifying underlying biological conditions when possible. A particular type of epilepsy called West syndrome was described by both speakers.  This severe form of epilepsy is thought to involve a dysfunction in a component of neural circuits known as “fast-spiking interneurons” that inhibit the activity of neighboring cells.  These fast-spiking cells are particularly expensive from an energetic perspective.  Therefore, any mitochondrial dysfunction would especially affect these energy-demanding cells.

Carolyn Schanen, M.D., Ph.D.  (University of Delaware) presented data on individuals with autism spectrum disorder that have a duplication in the long arm of chromosome 15. These individuals, who frequently present with epilepsy, exhibit an interesting pattern of gene expression and show evidence of mitochondria dysfunction in postmortem brain tissue. The portrait of this subgroup of autism punctuated the need for pursuing research studies of mitochondrial function in autism and simultaneously highlighting the immediate need for better diagnostic and treatment options.

Diagnosing and treating mitochondrial autism

Richard Haas, M.D. (UCSD) presented the state-of-the-art for diagnosing mitochondrial disorders. The diagnosis of mitochondrial dysfunction is dependent on the results of a series of tests, some of which, like a muscle biopsy or lumbar puncture, are relatively invasive. This presents a situation in which patients and parents need to elect how much testing to do with advice from an informed mitochondrial expert. Although there is no definitive test for mitochondrial disorders, there are agreed-upon checklists based on test results that indicate “likely” or “probably” mitochondrial dysfunction. Dr. Haas pointed to a set of “red flags” that should lead primary care doctors, including pediatricians, to consider a referral to evaluate mitochondrial function.

Treatments for mitochondrial disorders also share a commonality with autism—many complementary and alternative therapies exist with unfortunately little evidence as-of-yet to support their use. Bruce Cohen, D.O., M.D. (Cleveland Clinic) evaluated what we know about vitamin and supplement therapy. Few overall conclusions could be drawn, given the heterogeneity of presentation of mitochondrial dysfunction, but it is clear that more randomized clinical trials are needed especially in subgroups of patients. Until we have more data, exercise is recommended as therapy for all those living with mitochondrial disorders, and certain supplements to support good mitochondrial function and minimize reactive oxygen species may be used under the supervision of a physician to monitor benefit.

Ask the Doc

A group of parents and patients were fortunate to have five leading pediatric neurologists addressing their questions and concerns about mitochondrial disorders and autism. The panelist included Drs. Richard Haas, Sarah Spence, Bruce Cohen, Pauline Filipek, M.D. (University of Texas at Houston) and Roberto Tuchman.

Parents began by asking questions about the prevalence estimates for both autism and mitochondrial disorders, for which we have little population data in the US.  However, the panelists explained that data from a large Portuguese study and several smaller studies would suggest that approximately 5-10% of cases of autism may also have a likely mitochondrial dysfunction.

A lot of discussion centered around the utility of genetic testing, with the panel carefully making the distinction between the need to pursue genetic studies for research but taking caution to not put too much weight on genetic studies for individual diagnostics.  A comparative genomic hybridization (CGH) array study is definitely recommended as a good place to start for suspected mitochondrial disorders.

Questions surrounding treatment were another hot topic.  As noted previously, we would like to get to evidence-based medicine standards for the treatment of autism spectrum and mitochondrial disorders but that is difficult with disorders that present with such unusual heterogeneity.  Among the panelists, there was a general consensus that therapies such as chelation and hyperbaric oxygen were not recommended for this population due to a lack of evidence for positive effects paired with substantial evidence for the potential to harm.  In particular with hyperbaric oxygen therapy, the panelists were concerned about the potential for reactive oxygen species that can emerge from exposing a weakened mitochondrial system to more of what it can’t process well (that is, turning oxygen into energy).  For more innocuous potential therapeutic strategies (such as dietary interventions including some supplements), the panelists suggest that patients (or their parents) work with their physicians to conduct their own trials.  There was great hope for pharmacogenomics in that therapies of the future can be targeted to support a known deficit.

The meeting closed on a note of enthusiasm both for this topic and the pervasive sense of collaboration at this meeting.  Autism Speaks looks forward to more collaboration between our communities for continued progress in understanding and awareness of mitochondrial disorders in autism.

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The Next Big Thing?

June 14, 2010 10 comments

This post is from Guest Blogger, Stanley Nelson, M.D. Dr. Nelson is the Director for the UCLA Site of the NIH Neuroscience Microarray Consortium, and Professor of Human Genetics and Psychiatry at the David Geffen School of Medicine at UCLA. Dr. Nelson was also a co-author on last week’s collaborative Nature paper.


Investments in the genetics of autism have been substantial and the results are beginning to come forth, with last week’s announcement of the latest findings from our collaborative Autism Genome Project adding to previously identified genes and copy number variations that made last year’s Top 10 Autism Research Achievements of 2009.  The latest results, funded in large part by the tremendous efforts of Autism Speaks, are interesting alone, and I hope that all have learned that there are indeed novel genes being identified that lead to autism.  However, there is a perhaps more important message from the paper which relates directly to the couple hundred thousand families directly affected by an autism spectrum disorder in the US alone.

Within the recent Nature paper are compelling new findings demonstrating that autism can be caused by genetic mutations in a wide range of different genes, but the findings highlight how complex the genetic causes will be, likely in the hundreds. With this level of complexity, it is also clear that this sized sample that took 15-20 years to collect at the cost of tens of millions of dollars including molecular testing and analytical effort, we were only able to find genetic causes for a small minority of the children with autism (a few percent). So detecting the meaningful gene variants is largely a game of statistics.  With the relatively small size of the autism samples available to us today, many gene mutations that may be causative in an individual with autism will go ‘undetected’ because our sample size lacks the statistical power to identify them as definitively associated with autism. This is because these causative variants are each “rare” in the whole autism population. Even though rare, each gene variant that confers risk is important.  Why?  When considered together, these gene variants will collectively explain the majority of cases of the disorder, as well as inform us greatly about the still largely unresolved biological causes, both genetic and environmental. To get us to the next phase of understanding the genetic risk of autism, we need a way to cost-effectively recruit tens of thousands of affected individuals and their families to enable the appropriate large scale genetic studies needed to address this pressing scientific need. My attitude is well described in an interview written by Nancy Shute at US News and World Report.

Until recently, we have not had a nationwide infrastructure that could allow anyone in the US to participate with a child with a diagnosis of autism. That has changed with the initiation of the IAN Genetics Project, funded by Autism Speaks through the High Risk, High Impact Initiative. Using the web portal of the IAN Genetics Project, families provide information about their child through simple web-based questionnaires that require only a few hours effort from home, anytime. Families also give consent for the DNA collection portion of study online. Interested families may participate in this study by taking their child to one of 1,600 blood draw sites nationwide with our corporate partner, Labcorp. This is all made possible through the Interactive Autism Network, and more information can be found at IANPROJECT.ORG, where I encourage all families with an affected child to register and complete the requested questionnaires. For those interested in learning more about the DNA Study, specific information can be found by following this link.   Any questions about the project can be answered by IAN staff, who can be reached through the link.

Please register at IANPROJECT.ORG, even if not interested in the DNA Study. Simply filling out the online forms provides powerful new data to researchers that can only come from many thousands of individual families taking the time to help solve the complex issues of autism beyond genetics alone. Together we can take this next step to help reveal the causes of autism and help alleviate the struggles of those living with autism today.

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Geri Dawson Reflects on AGP Phase 2 Results

June 10, 2010 18 comments

By Geri Dawson, Chief Science Officer, Autism Speaks

Science moves so slowly and is so labor-intensive that we don’t often have moments to celebrate an achievement or breakthrough that has resulted from our investments. With this week’s announcement of Phase 2 results from the Autism Genome Project, we are celebrating such an achievement.

Several years ago, when I was a professor at the University of Washington, I remember a phone call from Andy Shih, Ph.D. (Autism Speaks VP, Scientific Affairs) who asked if he could take my colleague, Jerry Schellenberg, and me out to breakfast. Over coffee, Andy described to us an idea he had: Would we be willing to collaborate with other scientists around the world and add the genetic data we have been collecting to a combined database? While each of us at that time had been working independently to try to discover autism risk genes, we knew that ultimately we would need much larger samples to deal with the significant heterogeneity that exists in autism spectrum disorder. After a lot of discussion and questions, Andy convinced us that this would be a worthwhile effort and thus we became part of what became known as the “Autism Genome Project,” or the AGP. Eventually, Andy talked with over 50 groups worldwide and cajoled each of them to join the effort. What ensued was a series of monthly conference calls, complex negotiations and agreements that Andy helped broker, the creation of a combined database, and yearly meetings during which the goals for analysis and future data collection would be discussed. Today, the AGP is considered a driving force in autism genetic research.

Meanwhile, Clara Lajonchere, Ph.D. (Autism Speaks VP, Clinical Programs) was spearheading an effort to create a database of multiplex families called the Autism Genetic Resource Exchange (AGRE). She was leaving most of us collecting similar samples in the dust as she quickly assembled the largest private genetic individual data base that exists. Her ability to form partnerships with families, engaging them in the process of scientific discovery, was a model for us all. Not surprisingly, Clara readily agreed to join the AGP since AGRE’s basic premise was “collaboration and data sharing.”

Fast forward to this week when the AGP published the largest and most comprehensive study of copy number variations (CNV) – small deletions or duplications in our genome that can disrupt gene function – in autism families. By comparing CNVs found in 1,000 individuals with autism with those from 1,300 individuals without autism, the AGP reported the following:

  • Several novel ASD genes were discovered, and many genes previously implicated by other studies were confirmed. Some of these genes are involved with communication between neurons, while others help regulate cell growth and how they respond to environmental stimuli.
  • It was confirmed that autism risk genes are rare variants in our genome that occur very infrequently or not at all in the general population, and each person with ASD may have a unique risk gene or set of risk genes. Some of these genes are “highly penetrant” meaning that, if you carry this risk gene, you very likely will develop ASD, whereas other only raise the risk for ASD and need to combine with other genetic and/or environmental risk factors to cause ASD. Some of these are inherited, but many appear “de novo” meaning that they only exist in the child and not the parents.
  • In the not-so-distant future, we will start to see more comprehensive genetic testing being conducted in the clinic to provide parents with information about whether their child may be at risk for ASD, so they can watch for signs or better understand the cause of their child’s ASD. It will be important to consider carefully what tests are appropriate and interpret them in a manner that is responsible and helpful for parents.
  • Although the fact that so many rare genes can be related to risk for autism seems to form an overwhelmingly complex picture of autism, there is a path forward:  These genes appear to cluster around specific biochemical pathways in the brain and, thus, point to new directions for developing drugs that could potentially help recover function of these pathways. This is good news for families.

Most of all, I see the publication of this report as a celebration of the fruitful partnership between the families and the scientific community. While Autism Speaks staff like Andy and Clara helped create and implement unique and productive scientific endeavors like the AGP, ultimately, it is the families who contributed their time and literally a part of themselves that is helping us put together this puzzle called autism piece by piece.

Human Genetics at IMFAR

May 27, 2010 4 comments

Guest staff blogger: Vlad Kustanovich, Ph.D.

Genetic research is one of the exciting avenues of investigation that was highlighted at this year’s IMFAR meeting.  The section on human genetics started with a description of the largest study of autism twins to date. This study, described by Dr. Joachim Hallmayer, has concluded the data collection  phase and is beginning to shed new light on how much autism can be explained by genes and how much by environment.   Because identical twins share 100% of their DNA while fraternal twins share only approximately 50%, geneticists can compare the relative contribution of genes and environment, since it is assumed that for each twin pair, the environment is the same.  Clearly, both environment and genes are involved but this study may help to identify to what extent.

Dr. David Ledbetter described his effort to gather anonymous genetic information on chromosomal microarays from hundreds of thousands of patients with autism spectrum disorder and developmental delay.  He is doing this by forming partnerships with over 120 clinical labs throughout the U.S. Dr. Ledbetter, a world-reknown expert in cytogenetics, has the knowledge and respect of the scientific community to achieve the goal of creating data standards and pooling information to show which chromosomal changes are most often identified in these groups.   Deletions in regions on chromosomes 16 and 22 are identified consistently.  Although still rare, an understanding of altered genes in these regions may lead us to identify new subtypes of autism.

Other talks focused on studies of brain and face development (since these happen at the same time) in families with autism from the Autism Genetic Resource Exchange, an update from the Autism Genome Project, and a fascinating talk from Sun-Chiao Chang (working with Dr. Susan Santangelo) on sex-specific effects in autism spectrum disorder.   Ms. Chang identified several genes which seem to have an effect only in males, possibly helping to explain the common finding that there are four times as many males with autism as there females.

To read complete coverage from IMFAR, please visit http://www.autismspeaks.org/science/science_news/imfar_2010.php.

How does genetic research benefit people living with autism today? And why do scientists do autism research on mice?

May 24, 2010 2 comments

Guest Blogger: John Elder Robison, author, advocate, adult with autism and member of Autism Speaks scientific advisory board.

Those are two of the questions I discussed with researchers at this year’s IMFAR autism science conference. We’ll start with genetics, an area of study that’s often misunderstood…

The available evidence suggests that autism has both genetic and environmental components. When you study autistic minds at the cellular level, it’s possible to find many subtle differences between the brain cells and structures of people with autism and our typical counterparts. Researchers are working hard to look at those differences and why they occur. At first, scientists thought we were born a certain way, but that thinking has evolved. Now most scientists believe our genes give us a predisposition toward something but both genes and the environment shape the final result.

Adding to the complexity is that “environment” is a catch-all word for many different things, including the air we breathe, our food, our water, and even the social community where we’re parented and raised. We are truly the product of the genetic material we start with and everything we encounter from that point forward.

Researchers have been cataloging autistic differences for some years now. Essentially, they start with the observable manifestation of a difference (like ignoring the people around you or failing to communicate in the normal ways) and work backward until they find a possible biological reason why. For example, a first clue might be an area of the brain that’s too large or too small. Research biologists look at smaller and smaller structures until they get to the smallest difference, which might be an error in the DNA code for those cells.

Having found an abnormal part of the brain, and a possible genetic explanation, they now need to test their ideas out. That’s where the mice come in.

You may have read stories about our gene splicing and engineering skills. Genetic engineering has given us many things, from cloned sheep to drought resistant corn. It also gives us a powerful tool to study complex disorders in humans. In these experiments, mice stand in for people. By introducing the genetic mutations we discover into mice, we are able to observe changes in their brains and even their behavior.

Why mice?

As it happens, mice are uniquely suited for this work. They are genetically very similar to humans, with over 99% similarity in the areas of the brain we’re studying in autism research. Almost every human gene has its analogue in a mouse. Mice are also social animals, making it possible to observe the impact of genetic changes in their behavior. Finally, mice grow fast and are relatively inexpensive to raise.

The human genome has about 3.2 billion base pairs, with about 25,000 actual genes. In a stroke of great fortune for scientists, almost every human gene can be found in a mouse. Mice have fewer base pairs than humans, but their gene count is about the same.  Scientists can insert actual human DNA into mice genes and then breed a population of altered mice for study. This sort of work has been extraordinarily valuable to medical science, giving us insights we just couldn’t get any other way.

When we introduce a human genetic aberration into a mouse we are able to see for sure whether that change introduces a structural change in the mouse’s brain. But more importantly, we get a chance to learn how such a change impacts the mouse’s behavior. Indeed, we are finding genetic differences that do actually translate into autistic behaviors in mice. For example, some differences make normally social mice totally ignore other mice in a cage. Other differences make the mice wring their “hands” and flap in a pattern of behavior that’s striking similar to human autistic stimming.

Once scientists have a mouse that exhibits a particular autistic trait, it is then possible to experiment with therapies to correct the problems. That’s where we are now with a number of genetic differences associated with autism. We are also able to study the relationship between a genetic difference and the environment with mice.

Some of the best-known examples of this work can already be seen in the grocery store, or the hardware store. Just look at the label warnings that tell you repeated exposure to a certain chemical causes cancer. We see those warning labels on packages everywhere. We identify cancer-causing chemicals by exposing mice to a particular compound and seeing if they develop cancer. In the autism world, researchers have looked at exposure to high levels of lead, mercury, and other chemicals to learn how they affect the developing or developed mouse brain.

One day, thanks to this sort of research, we might have labels that say, “Warning – Exposure to xxxx can cause autism.”  There may indeed be environmental toxins that trigger autistic regression in people, and there may be chemicals that make autism like mine worse. If I knew what they were I’d be sure to avoid them – any of us would – but science needs to identify them first.

We know some chemicals are dangerous. Most of us already avoid heavy metals and other known toxins. My concern is that we may find other common but currently ignored compounds that are safe for some people but dangerous to others of us on the spectrum. For many of us, that knowledge cannot come soon enough.

On a hopeful note, we can also try various drugs, some of which can minimize or fix damage that started in the genetic code. For example, researchers have recently found that people with autism have excessive brain plasticity. Plasticity is the ability of your brain to change in response to life circumstances. Plasticity is essential to learn new skills, but too much of it can prevent you from learning much at all, because your mind can’t “take a set.”

We know how to create mice with excess plasticity, and we are now studying the effectiveness of drugs to reduce plasticity in abnormal mice. It’s both safer and faster to try these new drug therapies in mice, because they develop so much faster than humans. That work may – hopefully – lead to promising discoveries that can be tested in humans and perhaps ultimately lead to new therapies for that particular component of autism.

It’s important to keep in mind that we are not creating “autistic mice.” Autism is an extremely complex disorder, to the extent that many people say no two autistic people are the same. What we’re doing is modeling specific autistic differences by finding genetic codes that are associated with them.

That sounds easy, but it’s not. One problem is that a social behavior – like ignoring your fellow mice – might be associated with more than one genetic difference. In humans, we have hundreds or even thousands of subtle differences associated with autism. And no one genetic difference is common to all of us.

That’s why this is such a hard problem to unravel. We can isolate a difference, and even develop a therapy to fix the changes it causes, but that difference may only be present in 1% of the autistic human population. So what do we do for the other 99%? We continue our studies of mice and men, I suppose.

Some people are critical of genetic research in the field of autism, because they fear it may lead to prenatal screening and the abortion of autistic fetuses. I participated in many discussions last week, and I can say with certainty those ideas were not even on the table for the scientists involved.

Others criticize genetic studies because they think (wrongly) that the work won’t benefit anyone living today. However, the stated goal of much of today’s work is indeed to help the current autistic population.

No one can say what the full ramifications of any particular work may be, but I hope the ideas I’ve shared here make the importance of ongoing genetic research clearer. There is indeed a very good possibility that genetic research today will lead to therapies to mitigate certain components of autistic disability well within our lifetimes.

I sure hope so.

To read complete coverage from IMFAR, please visithttp://www.autismspeaks.org/science/science_news/imfar_2010.php.

Read John’s other IMFAR blog post here: A World of Geeks – IMFAR 2010.

Two Family Meetings on Autism Subtypes Set the Tone for IMFAR

May 20, 2010 1 comment

This is a guest post by Autism Speaks’ staff members Leanne Chukoskie, Ph.D., Jane Pickett, Ph.D., and Andy Shih, Ph.D.

One of the challenges in pursuing the causes of autism spectrum disorders is the heterogeneity of symptoms and life history of the individuals affected. On Wednesday, one day before the start of the International Meeting for Autism Research (IMFAR), meetings of two family foundations centered on specific genetic syndromes for autism moved past these challenges to offer hope for recovery.

The Phelan-McDermid Syndrome Foundation (PMSF) was one of the family foundations that hosted a meeting of international scientists, clinicians and parents to better understand PMSF. Katy Phelan, Ph.D. (Molecular Pathology Laboratory Network, TN) presented a characterization of the individuals affected, as many scientists working with animal models of this disorder have met very few, if any, persons with PMS.  Dr. Phelan reviewed the cluster of symptoms present typically early in life, including a “floppy” infant, general developmental delays and poor or absent speech.  She also reviewed evidence that led to the recognition that individuals with PMS had some form of mutation in the SHANK 3 gene on chromosome 22.

The meeting soon shifted to animal models and presentations from several researchers who presented greater detail about the role of the protein SHANK 3 at synapses, or junctions of neurons, which are crucial for learning and memory functions.  It was shown that SHANK 3 is responsible for tying together two receptors for the common excitatory transmitter glutamate at the synapse.  Through a series of careful experiments examining the structure and function of synapses when more or less SHANK 3 protein was present, Joseph Buxbaum, Ph.D. (Mount Sinai School of Medicine, NY) and colleagues learned that SHANK 3 controlled the physical connections that underlie plasticity of the synapses (the mechanism that underlies learning and memory).  After achieving this detailed understanding of how the system develops and stabilizes in the animal, the next step was to attempt to rescue normal function in these animals that lack SHANK 3.  A related set of receptors present on the cells (AMPA receptors) was targeted with the drug called IGF1. Injections of IGF1 into the mouse travelled across the protective barrier that encases the brain and had the desired effects on the cells, rescuing the structure and function of the synapses that had the atypical SHANK 3 proteins.

Lastly before a dinner gathering where parents scientists and clinicians can share ideas with each other more informally, Sarah Curran, Ph.D. (Kings College, London) presented on new technology that may allow the creation of stem cell lines for deeper analysis of the effect of a single individual’s mutations (the SHANK 3 gene can have mutations at several places, potentially leading to different effects on the functioning of the SHANK 3 protein) by analyzing a single complete hair from an affected person.

The Isodicentric 15 Exchange, Advocacy and Support group (IDEAS) is another family foundation that hosted a meeting of clinicians, scientists and parents.  Of the several genetic disorders that have a ‘causal’ relationship to autism, the duplication of a portion of chromosome 15q (IDIC15q) figures prominently in post-mortem brain research.  In fact, one out of every ten brain donors to the Autism Tissue Program comes from this specific population that is represented by the IDEAS organization.   A major concern of the group and a factor in the high brain donation rate in this group of only 650 known affected individuals is sudden unexplained deaths, a fact reviewed by Edwin Cook, MD (University of Illinois at Chicago) at the meeting.  Seizure activity is many of the individuals is thought to underlie their apparent vulnerability and the IDEAS group has been proactive in publicizing recommendations from their physician-advisors, including Carolyn Schanen, M.D., Ph.D. (University of Delaware) who gave the opening presentation at this meeting.  The physician-advisors also promote brain donation to understand the causes of death and look for developmental changes consistent with autism and/or epilepsy.

The meeting brought together researchers and parent advocates in a significant effort to understand the research to date and fine tune future efforts. Jerzy Wegiel, V.M.D., Ph.D. (New York Institute for Basic Research) described neuropathology in 5 brain studies completed to date that shows unexpected ongoing production of new brain cells (neurogenesis), a atypical early migration of brain cells, and distortion of the cell structure reflecting an altered course of maturation of brain cells.  Each of these brain anomalies can contribute to seizure activity and the study of brains and clinical evaluations of the donors will continue.

In conjunction with the neuropathologic examinations of brain donors, IDEAS asked its families to participate in a seizure survey.  Preliminary results from about 85 participants shows various types of seizures and onsets; results will be posted on the IDEAS site and communicated via the Autism Speaks blog.  Since sudden deaths often occurred during sleep, Sanjeev Kothare, M.D. (Children’s Hospital, Boston, MA) was present to provide information on his studies of breathing abnormalities in patients with IDIC15q.  He reviewed the clinical spectrum of duplications on chromosome 15q: epilepsy, low muscle tone, atypical facial features, moderate-severe developmental delay, and autistic behaviors.  He speculated that the increased risk of sudden death is due to abnormalities of sleep, cardio-vascular function, mitochondrial function and epilepsy.  The results of his sleep study on 5 children with IDIC15q revealed central sleep apnea that occurs when the brain does not send proper signals to the muscles that control breathing often in conjunction with seizure activity.  This very important work will continue and many of the IDEAS families have worked with their own doctors to obtain a sleep study to determine both seizure and breathing activity.

An additional highlight of the meeting was a talk by James Sutcliffe, Ph.D. (Vanderbilt University) on one of the genes of interest in the duplicated piece of chromosome 15 – the GABA B3 receptor.  GABA is the main inhibitory neurotransmitter and any dysfunction in its receptor is thought to increase brain activity and might contribute to seizures.  He is studying rare point mutation in this gene that was also found in a condition known as Childhood Absence Epilepsy.   A presentation by Larry Reiter, Ph.D. (University of Tennessee Health Science Center) focused on a subset of 15q duplications called ‘interstitial duplications’.  These are also duplications of genes in the 15q portion of the chromosome but instead of arising de novo in the child, are inherited from the mother or father. Overall, the future goals are aimed at learning more about the conditions that affect mortality such as low muscle tone, apnea and seizures.  Further genetic studies on molecular mechanisms to find drug targets will include mouse models and analysis of DNA and brain tissue.

Taken together these meetings offered a positive view for the future. Families are working closely with clinicians and researchers to find effective new therapies for genetic syndromes that present as autism. The larger hope is that as these syndromes reveal their secrets, they will provide us with new tool with which to treat other forms of autism.

Thank you to Andy Mitz, Ph.D. of NIH for providing input on the PMSF meeting.

To read complete IMFAR coverage, please visit http://www.autismspeaks.org/science/science_news/imfar_2010.php.

Beyond genetics: What the new fields of functional genomics and epigenetics are revealing about autism

April 22, 2010 9 comments

Today’s guest post comes to us from Valerie W. Hu, Ph.D. Dr. Valerie Hu is a Professor of Biochemistry and Molecular Biology at The George Washington University Medical Center as well as a mother of a son with ASD.  She redirected her research focus towards autism about 5 years ago and has since published 6 papers on the genes and biological pathways associated with ASD.  Dr. Hu received her Ph.D. in Chemistry from Caltech and did her postdoctoral research in Membrane Biochemistry and Immunology at UCLA.  More information about her research and papers can be obtained at:  http://www.gwumc.edu/biochem/faculty_vhu.html

For many years, genetics has followed the traditional approach to identifying genes associated with various disorders, including autism.  However, the wide diversity of symptoms and behaviors associated with autism spectrum disorders (ASD) has posed a significant challenge to identifying mutations in one or a few genes that are reliably associated with ASD.  More recent attention has focused on copy number variants (CNVs) which are submicroscopic regions of chromosomes that have been found to be lost or duplicated in some individuals with ASD. Together, these studies are making progress in identifying a number of genes that function at the synapse between nerve cells. Nevertheless, the combination of all known genetic mutations still does not account for the majority of autism cases or for the association of non-neurological symptoms observed in autistic individuals.

My laboratory at The George Washington University Medical Center has taken a functional genomics approach to studying genes that may be deregulated in autism.  Rather than identify mutations in DNA, our goal has been to identify genes whose activity, as indicated by gene expression level, is altered in order to identify dysfunctional biochemical pathways and impaired cellular functions in autism.  Thus, using a method known as DNA microarray analysis to profile gene expression in cells from identical twin pairs who are differentially diagnosed with autism (one autistic, the other not reaching the threshold for an autism diagnosis), sibling pairs where only one sibling is autistic, and unrelated case-controls, we identified many genes whose expression levels (activities) are different from non-autistic individuals.  Furthermore, by subtyping the unrelated autistic individuals according to symptomatic severity across over 63 symptoms probed by a commonly used diagnostic assessment instrument (Autism Diagnostic Interview-Revised), we were able to identify gene “signatures” for each of 3 ASD subtypes studied.  These signatures not only revealed genes unique to a given subtype of autism, but also overlapping genes that presumably control common symptoms of autism across subtypes.  Interestingly, a set of genes that regulate the biological clock (that is, circadian rhythm) were found to be disrupted only in the subtype of ASD exhibiting severe language impairment.

These studies demonstrating different gene expression signatures between identical but differentially diagnosed twins as well as revealing differential expression of hundreds to thousands genes depending on ASD subtype suggest the involvement of  “master switches” (or epigenetic mechanisms) in the control of gene expression.  Two new studies by our laboratory, published in two different journals on Apr. 7, 2010, suggest that epigenetics may play a significant role in the regulation of gene expression in autism (read a blog from AS staff on epigenetics).  In one study, published in the FASEB Journal, we identified chemical tags (called “methyl groups”) on the DNA of individuals with autism that led to gene silencing. This mode of turning off a gene is potentially reversible with the proper drugs if the specific gene can be properly targeted.  The second study, which was published in the journal Genome Medicine, reports on the differential expression of microRNA in autism.  MicroRNA are recently discovered snippets of RNA (ribonucleic acid), each of which can inhibit the expression (and thus activity) of hundreds of genes.  The effects of microRNA are also reversible by treatment with complementary “anti-sense” RNA.  While methylation inhibits gene expression at the level of DNA, microRNA inhibits at the level of RNA.  These two studies together illustrate two different “epigenetic” mechanisms controlling gene activity in autism that lie beyond genetic mutations.

In the study published in the FASEB Journal, we again used cell lines derived from identical twins and sibling pairs in which only one of the twins or siblings was diagnosed with autism to identify chemical changes on DNA. We then compared the genes that showed changes in DNA tagging (methylation) with a list of genes that showed different levels of expression from these same individuals. The amounts of protein produced by two of the genes that appear on both lists were then investigated in brain tissues from the cerebellum and frontal cortex of autistic and control subjects which were obtained through the Autism Tissue Program.  We found that both selected proteins, RORA (retinoic acid-related orphan receptor-alpha) and BCL-2, as predicted by the observed increase in methylation, were reduced in the autistic brain.  Although BCL-2 has previously been reported to be reduced in autistic brain, RORA is a novel gene which is relevant to many of the observed deficits in autism.  Specifically, RORA is involved in several key processes negatively affect by autism, including Purkinje cell differentiation, cerebellar development, protection of neurons against oxidative stress, suppression of inflammation, and regulation of circadian rhythm.

These results suggest that blocking the chemical tagging of these genes may reverse some symptoms of autism if targeted removal of methyl groups from specific genes can be accomplished.  Furthermore, this study, which links molecular alterations in blood-derived cells to brain pathobiology, demonstrates the feasibility of using more easily accessible cells from blood (or other non-brain tissues) for diagnostic screening.

This research is reported in the study, titled “Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain,” which was recently published in the Federation of American Societies for Experimental Biology (FASEB) Journal, and is available online at: http://www.fasebj.org.

In the study published in Genome Medicine, we identified changes in the profile of microRNAs between twins and sibling pairs, again discordant for diagnosis of autism.  We discovered that, despite using cells derived originally from blood, brain-specific and brain-related microRNAs were found to be differentially expressed in the autistic samples, and that these microRNAs could potentially regulate genes that control many processes known to be disrupted in autism.  For example, differentially expressed miRNAs were found to target genes highly involved in neurological functions and disorders in addition to genes involved in gastrointestinal diseases, circadian rhythm signaling, and steroid hormone metabolism. The study further shows that by treating the cells with antisense RNA antagonists (inhibitors) to specific microRNA or by employing mimics of a particular microRNA, one can reverse the pattern of expression of a given target gene regulated by that microRNA.

This study, titled “Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines” was highlighted as an “Editor’s pick” in the journal Genome Medicine.  It is available online at: http://genomemedicine.com/content/2/4/23.

By integrating both DNA methylation and miRNA expression studies with gene expression data, Dr. Hu and colleagues are applying a systems biology approach to understanding this complex disorder.

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