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Posts Tagged ‘genetics’

What lies beneath: differences in brain connections

November 11, 2010 60 comments

A new Autism Speaks-funded study reveals differences in brain connections in areas that redirect attention, mediate social interactions and modulate emotional responses.

Reconstructed axons

Science is one step closer to understanding how the brains of individuals with autism process information.  Over the past decade it became clear that neural communication is disrupted in autism, although the details, and the causes, remained elusive.  Two hypotheses emerged to explain the information processing differences found in individuals with autism spectrum disorder (ASD).  First, scientists identified over-activity at the level of the synapse—the point where two neurons connect.  Second, imaging studies showed that the balance of local versus long-range connections was skewed in autism in favor of strong local connections but weak long-range connections between distant brain regions.  Complex behavior, such as language and social interaction, depend upon such long range connections.  Although the findings supporting the two hypotheses were likely related, the mechanism relating over-activity at the synapse and biased local versus long-range connectivity was unclear.

Now, taking advantage of recent technical developments that facilitate the measurement of small structures within the brain, Autism Speaks’-funded researchers at Boston University have bridged these two hypotheses. Basilis Zikopoulos, Ph.D., and Helen Barbas, Ph.D., reconstructed the intricate fabric of neural “wires”—called axons—that connect prefrontal cortex with neighboring and distant brain regions. The prefrontal cortex is a collection of brain areas that are involved in higher cognitive functions such as attention, planning, social interactions, and abstract thinking.  Using postmortem brain tissue generously donated by families of individuals with and without autism, the team measured features of the different axons traveling beneath the cortical surface.

Talking to itself

In comparison to the control samples, autism brain tissue had fewer large axons connecting regions of the prefrontal cortex to the other areas of cortex.  Added to this connection imbalance is a thinner coat of axon insulation, called myelin. Myelin is a fatty substance that insulates axons to ensure faithful delivery of neural signals over long distances. Prefrontal axons from autism brain tissue traveling to distant brain areas have less myelin. Zikopoulos and Barbas also found more thin axons that connect neighboring regions in the prefrontal cortex in the autism brain tissue versus the control samples.  This biased pattern of connectivity creates a situation in which prefrontal cortex is not efficiently exchanging information with other brain areas, but rather is operating in a solo fashion.

Pursuing the reason for the abundance of thin axons, the researchers first checked to see whether this was due to more neurons in the cortex just above.  Detailed examination of neuron density showed no more neurons, just more axons.  This finding led the team to speculate that atypical axon branching had occurred in the autism samples.  By painstakingly tracing individual axon branches through a volume of tissue, Zikopoulos and Barbas confirmed that the abundance of thin axons emerged from overzealous branching. The thin axons found in autism samples formed tree-like braches that connected with many more cells in neighboring areas than is typical.  This pattern of branching furthered the bias for local versus long-range communication.

neuron

Differences in axons and their insulation may offer some links between the two hypotheses that aim to explain disrupted communication in autism.  Fewer large axons travel to distant brain regions. Thin axons form too many branches that make extra connections locally. These factors can handily explain the local over-connectivity and long-range under-connectivity observation made through imaging studies.  The fact that small axons seem to branch more frequently would also lead to an over-abundance of synaptic connections in a neighboring region.  This result can help to explain the synaptic connection hypothesis.  Taken together, the results lead us to a deeper understanding of how information may be processed quite differently in the brains of individuals with autism.

Anatomy offers a closer look

Imaging studies aiming to understand brain connectivity use techniques such as magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI). These techniques focus on the large swaths of axons, often called “white matter” because of myelin’s fatty white hue.  While many of these studies have suggested an imbalance favoring local connectivity in the brains of individuals with autism and served as a stimulus for this study, the level of detail that comes from quantitative anatomy is much richer.  “The study of brain tissue at high resolution is needed to pinpoint defects in the brain’s communication system, which is prerequisite to developing rational therapies. Studying pathways using DTI is comparable to looking down from a plane at 35,000 feet – you can see some of the major highways below but not the exits, and certainly not the driveway to your house to see if the car is there,” states Dr. Barbas.

Martha Herbert, M.D., Ph.D., of Massachusetts General Hospital and LADDERS, an imaging expert who was not involved with this study, was enthusiastic about the new results.  “Zikopoulos and Barbas have given us a paper about the cellular level of white matter changes in autism that has needed to be written for quite some time.  Their analysis is meticulous and comprehensive, and goes far in providing microscopic details to answer provocative questions raised by the larger scale observations in so many brain scan studies in autism.  Their findings suggest that the insult occurs later in brain development, after the neurons migrate to where they will live in the brain. The time when these neurons hook up with each other through white matter is crucial and during this period environment and immune factors as well as genes may play a role in the observed changes. These specific details about white matter in autism matter greatly for how we understand autism and how we go about providing the help people with autism need.”

Modeling the development of axon differences

The new axon data may also offer suggestions of what occurred to lead to this state of altered connectivity.  Combining the axon data with what is known about the development of the cerebral cortex, the researchers devised a model that links differences in axons below frontal areas to a cascade of events in development that affects the growth of axons and their insulation.  The hypotheses proposed are testable, and point to specific pathways that could to be targeted for the development of therapeutic interventions in autism.

One pathway that Zikopoulos and Barbas analyzed in detail was GAP-43, one of a myriad of signals that are exquisitely timed to encourage the proper growth and integration of developing neurons.  GAP-43 stimulates axon branching.  GAP-43 also interacts with other signals to prevent premature myelination, and is turned down after myelination begins.  In the anterior cingulate cortex, a region of the prefrontal cortex that was the most profoundly affected in the brains studied, the neurons are sensitive to GAP-43 signals for an especially long duration in development.  This is an important point because environmental agents such as estrogen-like compounds can increase the GAP-43 signal altering the timing of different aspects of neural development.

One take-home message from this study is how important it is to have diverse lines of inquiry investigating autism.  The axon results were consistent across individuals studied. For example, the same changes were found regardless of whether or not the individual experienced seizures. Zikopoulos and Barbas also note that many of the genes that have been associated with autism exert effects on neural connectivity. Dr. Barbas says, “Genome-wide association studies are valuable in pointing out potential vulnerability in affected individuals. Our study suggests further that environmental factors (in utero, after birth, or both) can lead to abnormal connectivity because external factors up-regulate signals such as GAP-43 that regulate axon growth. We need studies to take into account all of these aspects of autism, not just one.”

This work was published in the Journal of Neuroscience and featured on the cover of the November 3 issue.

This research was made possible through funding from Autism Speaks and brain tissue supplied by Autism Speaks’ Autism Tissue Program. These groundbreaking results came from the brain tissue of ten generous individuals who chose to make a lasting gift to science.  Importantly, only a small portion of each donated brain was needed for this study, making other sections of this incredibly valuable research resource available to others to uncover new insights into autism spectrum disorders. Please consider making a lasting gift to science by participating in the ATP.

Rats Rising: Using the Rat as a Model Organism for Autism Research

October 28, 2010 Leave a comment

Autism Speaks has partnered with SAGE Labs, a division of Sigma Life Science, to create and validate the first line of rat models of autism.  Previous rodent models of ASD, which are important for understanding the biological basis of autism and drug discovery, have used mice.  Such models allow scientists to examine the downstream effects of genetic mutations on brain development and behavior.    For studies of behavior, learning and cognition, the rat is the animal of choice due to its complex behavioral repertoire. With these new genetically modified rats, the richness of previous behavioral and physiological research can be leveraged and applied directly to autism.  These new rat models will now be validated in the laboratories of several scientists who will be studying brain development and behavior of the animals.

Edward Weinstein, Ph.D., director of Sage Labs

Edward Weinstein, Ph.D., the Director of SAGE labs, answers some questions about the new model animals and how they will benefit autism research.

1) Generally speaking, why do we need a rat model of autism when mouse models exist?

Dr. Weinstein: Researchers have been able to create genetically modified mice for the past 25 years, so a large number of mouse models have been created, addressing all sorts of human diseases and disorders.  But mice are not always the best model system for every condition.  For example, researchers who study ocular disease greatly prefer the rabbit.  And the rat is an excellent model for toxicology, cardiovascular, and cognitive research.  In the past, researchers would create the best genetically modified mouse model possible to answer their scientific questions. Now they can create the most relevant genetically modified model in whatever species best models the condition they are studying.

2) Why can’t the same technology that one uses to make a genetically modified mouse work with rats?

Dr. Weinstein:  Genetically modified mice, also sometimes called knockout mice, are created by making changes to the DNA in a mouse embryonic stem cell.  Researchers tried unsuccessfully for decades to develop rat models using the same technology. SAGE labs has developed a new technology, called  zinc finger nuclease technology, which allows us to create knockout rats without the use of embryonic stem cells.

3) Can you describe how the Sigma technology works in a manner accessible to our community?

Dr. Weinstein: The technology is actually fairly straightforward.  We create an enzyme called a zinc finger nuclease (ZFN), which has been especially constructed to target a specific gene.  We can then inject that ZFN into a one-cell rat embryo where it will bind the targeted gene and cause a break in the DNA.  This effectively “knocks out”, or inactivates, the gene.  The one-cell embryo is then transferred into a surrogate rat and 21 days later you have a genetically modified rat that is born.  This genetically modified rat will be exactly like every other rat, with the exception of the inactivation of that one specific gene that was targeted.  Part of the beauty of this technology is that it not only works for creation of genetically modified rats, but also mice and rabbits.  It should work in virtually any animal model system.

4) What do you see are the next steps in using genetically modified rats for autism research?

Dr. Weinstein: We have worked to create a suite of genetically modified rats that we hope will be useful for autism research.  The real challenging work, however, comes in the validation of the models.  Testing these rats to see if there really are behavioral differences in them will be key to determining their usefulness.

In addition, autism research is still at the stage where new genetic links are continuously being uncovered.  We hope to continue to serve the research community by expanding our platform of autism models as rapidly as possible.

5) Genetics is only one component of the autism puzzle.  Research has identified environmental agents that either alone or in combination with a genetic vulnerability lead to the altered neurodevelopment we see in autism.  Can environmental and gene-environment interaction questions be posed using these new rats?

Dr. Weinstein: We get kind of hung-up when we say “genetic model.” We absolutely can do these experiments. Using the genetically modified rats, we can carefully time exposures both in utero and during early post-natal life. Gene-environment interactions are extremely important to understand and we hope that researchers will seek answers to those questions with these new autism model rats.

6) Why did you partner with Autism Speaks for your foray into rat models of genes important in autism?

Dr. Weinstein: We have a lot of expertise in the use of Zinc Finger Nucleases and the creation of genetically modified animals.  However, we don’t have the in-depth expertise or background in autism that is necessary for determining which are the best models to create.  Working with Autism Speaks has been critical from a scientific aspect.  Also, members of Autism Speaks are so well connected to the research community, you know that when you get scientific advice from Autism Speaks, you are getting advice from an entire field of researchers.

We look forward to sharing the results of the behavioral and physiological evaluations of these new rats as scientists begin working with them.

Read a press release about the partnership.

New CNVs on Chromosome X

September 16, 2010 15 comments

Guest blog by Dr. John Vincent, who is a Scientist and Head of the Molecular Neuropsychiatry and Development Laboratory of the Psychiatric Neurogenetics Section in the Neuroscience Research Department and an Associate Scientist of The Centre for Applied Genomics at The Hospital for Sick Children, Toronto.

The group here in the Molecular Neuropsychiatry & Development Lab at CAMH, along with our collaborative partners at Sick Kids and elsewhere report the identification of PTCHD1 as a gene for autism spectrum disorder, as well as intellectual disability, on the X-chromosome. The finding stems from attempts to find differences in specific strands of DNA, called copy number variants (CNVs) in the DNA of autistic individuals that might be linked to the condition. If the human genome can be thought of as a book containing the DNA code written out in words and sentences, we each of us have our own unique book, with many words spelled differently from each other, but mostly without changing the overall meaning of the words and sentences. Traditional genetic studies would try to identify spelling mistakes that compromise the meaning of a sentence, and thus lead to an incorrect message, i.e. resulting in a clinical condition. In our current study we have been looking instead for whole sentences, paragraphs or pages that are either deleted or duplicated (i.e. CNVs), thus altering the meaning of the message, and leading in this case to autism.

We were particularly interested, in our study, to look at CNVs on one of the 2 sex chromosomes, the X, as it might explain some of the bias towards boys having autism over girls. In our initial screen of over 400 autism patients, we identified a large deletion disrupting the PTCHD1 gene. In an analysis of CNVs in genomes from over 1000 more autism individuals, deletions just next to this gene were the most significant finding. These deletions are likely to disrupt DNA sequences that may regulate how the PTCHD1 gene is expressed. In addition, we identified many single letter changes in the PTCHD1 gene that may affect the “meaning”. These changes were not found in the DNA of many control individuals.

The PTCHD1 gene makes a protein with as yet unknown function, however it shows similarities to several known proteins that function as cell-surface receptors for an inter-cellular signaling pathway known as Hedgehog, crucial in determining how brain cells develop and mature. The preliminary data we present in the paper shows that PTCHD1 appears to have similar properties to the two Hedgehog receptors already known, leading us to speculate on a role for Hedgehog-related processes in autism.
These findings give us another important gene that we can screen for in at risk children, and will allow earlier therapeutic interventions, thus increasing the likelihood of success.

For more information, please see the press release.

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Common language: Exploring community collaboration in the translation of genetics discoveries

September 13, 2010 3 comments

The past several years have seen significant advances in our understanding of the genetics of autism spectrum disorders (ASD). As result, many researchers and companies have begun exploring the possibilities of translating these discoveries into clinical applications, especially those that could help with diagnosis. By detecting and understanding genetic risk factors for autism, it is possible to  provide earlier diagnosis and intervention, which typically leads to better outcomes.  In addition, it can help identify subgroups within our community, that because of shared risk factors, may benefit from more targeted or specific treatment.  Finally, some genetic etiologies are associated with specific medical conditions, such as seizures, cancer, and GI problems.  Thus, information about specific genetic etiologies can have significant clinical implications. Using this kind of approach, it may also be possible to identify individuals who are predisposed to particular environmental risk factors and help improve our understanding of the role of gene-environment interactions in autism.

Most importantly, Autism Speaks is interested in encouraging the development of real world solutions that can help families make more informed healthcare decisions and improve their overall quality of life. While it has long been known that autism involves genetic factors and genetic testing is already being conducted for some genetic etiologies, such as Fragile X syndrome, recent studies have identified many other autism risk genes that are not routinely screened for during a diagnostic exam.  Including more comprehensive genetic screening could be of real benefit to persons with ASD.  However, we recognize that the science is still evolving, and there are many uncertainties and important issues such as ethics and risk communication that must be carefully weighed and considered to maximize potential benefits to individuals as well as families in our community.

In order to better understand the state of the science and opportunities and barriers in translating autism genetics discoveries into diagnostic tests, Autism Speaks and several partners, including the National Institutes of Health (NIH), Canadian Institutes for Health Research (CIHR), and the UK’s Medical Research Council (MRC), organized an educational symposium, “Genetic Risk Factors for Autism Spectrum Disorders: Translating Genetic Discoveries into Diagnostics,” in Toronto, Canada, on September 1-2, 2010.  By bringing together a multidisciplinary group of about 80 international experts and stakeholders, including government officials, funding agencies, scientists, clinicians, ethicists, lawyers, biotech companies, parents and self-advocates, the symposium aimed to develop some consensus around two key questions: (1) Is the science ready for translation of genetic findings to clinical diagnostics? And if so, (2) how can the professional and stakeholder communities work best together to ensure that genetic diagnostic testing is a benefit to persons with ASD?

With an audience as diverse as the one at this symposium, a variety of opinions was expected. Some researchers thought this discussion was a bit premature because the science is still evolving and the interpretation of microarray-based clinical genetics findings can be oftentimes be complicated. Others, however, advocated for a cautious but firm push to help families by establishing an authoritative reference database and clarifying regulatory guidelines. Developing guidelines for the use of interpretation of genetic testing is especially important since several companies are already providing genetics testing services for the medical community.  The FDA acknowledged the new terrain, but clearly preferred greater oversight to help protect consumers. Medical geneticists and genetic counselors pushed back that more regulations may not be necessary because of the professionals’ well-established track record in helping individuals and families interpret and understand complicated genetic findings.  Bioethicists and communications experts left the attendees more appreciative of important non-technical issues that should be a part of any deliberation on the risks and benefits of genetic diagnostics for autism. Parents and self-advocates, while optimistic about the promise of the technology, also highlighted the need to address the implications of this technology on important community issues about identity and choice [Read John Elder Robison’s blog on this topic in Psychology Today].

After a packed and intense one and a half days, including breakout sessions where many vigorous and fascinating discussions ranged from community impact to next generation of diagnostic devices, the participants achieved consensus on several important issues, the details of which will be published via a peer reviewed journal and other dissemination channels in the near future. Suffice to say, while there was a general appreciation for how much work we still need to do, there was also enthusiasm for an opportunity to work together to help individuals and families benefit from the translation of latest genetics discoveries.

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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.

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