Posts Tagged ‘epigenetics’

What is epigenetics, and what does it have to do with autism?

January 20, 2012 11 comments

This week’sGot Questions?” answer comes from Alycia Halladay, PhD, Autism Speaks director of research for environmental sciences

If you’ve been following autism research in recent years, you have probably read—many times—that familial, or inherited, risk is seldom the whole picture. A few inherited genes are sufficient by themselves to cause autism. But most so-called “autism genes” only increase the risk that an infant will go on to develop this developmental disorder. As is the case in many complex diseases, it appears that autism often results from a combination of genetic susceptibility and environmental triggers.

This is where epigenetics comes in. Epigenetics is the study of the factors that control gene expression, and this control is mediated by chemicals that surround a gene’s DNA. Environmental epigenetics looks at how outside influences modify these epigenetic chemicals, or “markers,” and so affect genetic activity.

It is important to remember that scientists use the term “environment” to refer to much more than pollutants and other chemical exposures. Researchers use this term to refer to pretty much any influence beyond genetic mutation. Parental age at time of conception, for example, is an environmental influence associated with increased risk of autism, as are birth complications that involve oxygen deprivation to an infant’s brain.

Because epigenetics gives us a way to look at the interaction between genes and environment, it holds great potential for identifying ways to prevent or reduce the risk of autism. It may also help us develop medicines and other interventions that can target disabling symptoms. We have written about epigenetics previously on this blog (here and here). So in this answer, I’d like to focus on the progress reported at a recent meeting hosted by Autism Speaks.

The Environmental Epigenetics of Autism Spectrum Disorders symposium, held in Washington, D.C. on Dec. 8, was the first of its kind. The meeting brought together more than 30 leaders in autism neurobiology, genetics and epidemiology with investigators in the epigenetics of other complex disorders to promote cross-disciplinary collaborations and identify opportunities for future studies.

Rob Waterland, of Baylor College of Medicine in Texas, described epidemiological studies and animal research that suggested how maternal nutrition during pregnancy can affect epigenetic markers in the brain cells of offspring.

Julie Herbstman, of Columbia University, described research that associated epigenetic changes in umbilical cord blood with a mother’s exposure to air pollutants known as polycyclic aromatic hydrocarbons (PAHs). PAHs are already infamous for their association with cancer and heart disease.

Rosanna Weksberg, of the Hospital for Sick Kids in Toronto, discussed findings that suggest how assisted reproductive technology may lead to changes in epigenetically regulated gene expression. This was of particular interest because assisted reproduction has been associated with ASD. Taking this one step further, Michael Skinner, of Washington State University, discussed “transgenerational epigenetic disease” and described research suggesting that exposures during pregnancy produce epigenetic changes that are then inherited through subsequent generations.

Arthur Beaudet, of Baylor College of Medicine, discussed a gene mutation that controls availability of the amino acid carnitine. This genetic mutation has been found to be more prevalent among children with ASD than among non-affected children, suggesting that it might be related to some subtypes of autism. Further study is needed to follow up on the suggestion that dietary supplementation of carnitine might help individuals with ASD who have this mutation. Caution is needed, however. As Laura Schaevitz, of Tufts University in Massachusetts, pointed out, studies with animal models of autism suggest that dietary supplementation may produce only temporary improvements in symptoms of neurodevelopmental disorders.

So what does this all mean for research that aims to help those currently struggling with autism? The meeting participants agreed that the role of epigenetics in ASD holds great promise but remains understudied and insufficiently understood. For clearer answers, they called for more research examining epigenetic changes in brain tissues. This type of research depends on bequeathed postmortem brain tissue, and Autism Speaks Autism Tissue Program is one of the field’s most important repositories. (Find more information on becoming an ATP family here).

The field also needs large epidemiological studies looking at epigenetic markers in blood samples taken over the course of a lifetime. One such study is the Early Autism Risk Longitudinal Investigation (EARLI). More information on participating in EARLI can be found here.

Autism Speaks remains committed to supporting and guiding environmental epigenetics as a highly important area of research.  We look forward to reporting further results in the coming year and years.

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Read more autism research news and perspective on the science page.

Thank You for Supporting our Pioneering Research

January 10, 2012 8 comments

Guest post by epidemiologist Daniele Fallin, PhD, of Johns Hopkins Bloomberg School of Public Health

My work focuses on autism and understanding how genes and environments interplay to cause this developmental disorder. Much of this work is funded by federal grants, but there can be gaps in what these grants can support, especially in new fields of research. Support from Autism Speaks has been amazing in helping fill these gaps.

In particular, Autism Speaks provided important support for two of my current projects. The funding is allowing us to study families with autism and, so, gain insights into  interactions between autism risk genes and environment exposures.

The Early Autism Risk Longitudinal Investigation (EARLI) is a national study of families that have at least one child on the autism spectrum and anticipate having more children. By following these high-risk families we seek to identify causes and risk factors—be they genetic, environmental or a combination of both. Information is regularly collected from mothers enrolled in the study, and their newborns receive free developmental assessments until 3 years of age.

The second study is a genome-wide investigation of DNA methylation, or epigenetics. It will allow us to investigate how various environmental exposures can affect gene expression in ways that increase—or potentially decrease—the risk of autism. This study will place special focus on environmental exposures during crucial periods of prenatal brain development.

Autism Speaks realizes the importance of these new areas of research and has put forth great effort to ensure we can explore and, hopefully, uncover risk factors for autism that, over the long term, may lead to prevention and improved treatments.

We continue to recruit study participants. Specifically we are enrolling mothers who have one or more children with autism and who may become pregnant or who are currently less than 28 weeks pregnant. They must live near an EARLI research site (California, Maryland or Pennsylvania). For more details, please visit or our Facebook page.

On behalf of the EARLI research team, I want to extend a special thanks to Autism Speaks supporters for helping make this pioneering research possible.

Explore more of the studies our supporters are funding with our Grant Search Engine. And read more autism research news and perspective on the science page.

Environmental Epigenomics and Susceptibility for Developmental Disorders: Findings from the Keystone Symposium

April 19, 2011 5 comments

By Guest Blogger, Jennifer T. Wolstenholme, PhD, Postdoctoral Fellow at the University of Virginia, Charlottesville, VA, working with two Autism Speaks-funded researchers, Emile Rissman, Ph.D. and Jennifer Connelly, Ph.D.

In recent work in our lab, we have established a mouse model for gestational exposure to an endocrine disrupting compound, bisphenol A (BPA), at human physiological levels. We asked if a low BPA dose ingested during pregnancy (20 ug BPA/kg body weight/day) would affect the social behaviors of the juvenile offspring mice. In addition, we continued to breed the mice from these litters to ask if these effects could be transmitted to future generations that were not directly exposed to dietary BPA. We also examined a handful of genes known to be affected by BPA or involved in social behaviors to determine if BPA also changed the expression of these genes in the brain during embryogenesis. The take home message is this: we do not know if exposure to endocrine disrupting chemicals causes any neurobiological disorders, including autism spectrum disorders (ASD).  However, the data are interesting enough to cause us and others to continue to test the hypothesis that exposure to BPA during gestation may result in modified social behaviors in juvenile mice.

Bisphenol A (BPA) is a man-made compound used to make polycarbonate plastics (i.e. food and water containers), epoxy resins (i.e. canned food linings) and thermal register receipts. Human exposure to this chemical is wide spread and nearly unavoidable as it has been detected in urine in 90% of all humans sampled [1, 2]. Public health concerns have been fueled by findings that BPA exposure can reduce sex differences both behaviorally and in the brain. In rats and mice, perinatal exposure to BPA is associated with aggressive behavior, cognitive impairments, increased novelty seeking and impulsivity [3-5].  BPA can also influence social interactions and anxiety in rodents [6-10]. This list of associations have suggested to some that BPA may be somehow related to human neurological disorders, such as ASD. However, such a conclusion at this time is premature.

Many laboratories have suggested that BPA exposure disrupts normal brain development and behaviors through its actions on the steroid receptors [18, 19].  BPA acts as an analog of steroid hormones.  Steroid hormones organize the brain during neonatal development [11-13]. BPA has steroid-like properties and binds estrogen receptors, (ERa, ERb [14]), as well as androgen and thyroid receptors [15-17].

In addition to steroid-related effects, BPA may have even more global actions as it can alter DNA methylation [20].  Dysregulation of DNA methylation during critical developmental windows could disrupt the normal progression of brain and endocrine system development causing robust changes in the developing embryo that can persist into adulthood or even beyond if effects extend to germ cells that later serve reproduction as sperm or egg cells. Embryonic development is a particularly sensitive period, specifically when the body’s germ line cells undergo epigenetic programming and experience a wave of DNA de-methylation and re-methylation.

Skinner et al. have shown trans-generational effects for several endocrine disrupting compounds, but at much higher doses than humans are typically exposed [21, 22]. Specifically, endocrine disruptors found in plastics, pesticides, hydrocarbons and herbicides can affect embryonic testes development and lead to deficits in sperm production in adulthood.  These effects are trans-generational in rodents directly exposed to these chemicals during gestation (F1 generation) and through to the great, great grandchildren (F2, F3 and F4 generations).

We use a paradigm in which inbred female mice are placed on control diet free of any phytoestrogens, or control diet with BPA (5mg BPA per kg diet). This diet produced BPA blood levels equivalent to those reported in humans. A week after the start of the diet females were mated. At birth, pups were fostered to control dams to limit BPA’s effect only to gestation. Three generations of offspring were tested for social behaviors at 21 days after birth.

BPA exposure had effects on several social and non-social behaviors and some of these differences between mice on control and BPA-containing diets persisted over generations. The great, great grandchildren of the BPA lineage (the F4 generation) were never directly exposed to dietary sources of BPA, yet social interactions resembled those of mice exposed during gestation. Some of these behavioral effects are correlated with different levels of gene expression in the brains of mice directly exposed to BPA compared to mice that were never exposed to dietary BPA. More work needs to be done to discover if the relationships between the affected genes and the behavioral changes are causal. Since exposure to BPA appears to alter social interactions in young mice, this compound may contribute to the risk of developing neurological disorders such as autism spectrum disorders, but further studies, especially in humans are needed to show a causal relationship. 


1.         Fujimaki, K., et al., [Estimation of intake level of bisphenol A in Japanese pregnant women based on measurement of urinary excretion level of the metabolite]. Nippon Eiseigaku Zasshi, 2004. 59(4): p. 403-8.

2.         vom Saal, F.S., et al., Chapel Hill bisphenol A expert panel consensus statement: integration of mechanisms, effects in animals and potential to impact human health at current levels of exposure. Reprod Toxicol, 2007. 24(2): p. 131-8.

3.         Kawai, K., et al., Aggressive behavior and serum testosterone concentration during the maturation process of male mice: the effects of fetal exposure to bisphenol A. Environ Health Perspect, 2003. 111(2): p. 175-8.

4.         Miyagawa, K., et al., Memory impairment associated with a dysfunction of the hippocampal cholinergic system induced by prenatal and neonatal exposures to bisphenol-A. Neurosci Lett, 2007. 418(3): p. 236-41.

5.         Tian, Y.H., et al., Prenatal and postnatal exposure to bisphenol a induces anxiolytic behaviors and cognitive deficits in mice. Synapse, 2010. 64(6): p. 432-9.

6.         Dessi-Fulgheri, F., S. Porrini, and F. Farabollini, Effects of perinatal exposure to bisphenol A on play behavior of female and male juvenile rats. Environ Health Perspect, 2002. 110 Suppl 3: p. 403-7.

7.         Negishi, T., et al., Behavioral alterations in response to fear-provoking stimuli and tranylcypromine induced by perinatal exposure to bisphenol A and nonylphenol in male rats. Environ Health Perspect, 2004. 112(11): p. 1159-64.

8.         Ryan, B.C. and J.G. Vandenbergh, Developmental exposure to environmental estrogens alters anxiety and spatial memory in female mice. Horm Behav, 2006. 50(1): p. 85-93.

9.         Cox, K., et al., Gestational exposure to bisphenol A and cross-fostering affect behaviors in juvenile mice. Horm Behav, 2010. 58(5): p. 754-61.

10.       Porrini, S., et al., Early exposure to a low dose of bisphenol A affects socio-sexual behavior of juvenile female rats. Brain Res Bull, 2005. 65(3): p. 261-6.

11.       McEwen, B.S. and S.E. Alves, Estrogen actions in the central nervous system. Endocr Rev, 1999. 20(3): p. 279-307.

12.       Phoenix, C.H., et al., Organizing action of prenatally administered testosterone propionate on the tissues mediating mating behavior in the female guinea pig. Endocrinology, 1959. 65: p. 369-82.

13.       Negri-Cesi, P., et al., Sexual differentiation of the brain: role of testosterone and its active metabolites. J Endocrinol Invest, 2004. 27(6 Suppl): p. 120-7.

14.       Kuiper, G.G., et al., Interaction of estrogenic chemicals and phytoestrogens with estrogen receptor beta. Endocrinology, 1998. 139(10): p. 4252-63.

15.       Sohoni, P. and J.P. Sumpter, Several environmental oestrogens are also anti-androgens. J Endocrinol, 1998. 158(3): p. 327-39.

16.       Xu, L.C., et al., Evaluation of androgen receptor transcriptional activities of bisphenol A, octylphenol and nonylphenol in vitro. Toxicology, 2005. 216(2-3): p. 197-203.

17.       Bonefeld-Jorgensen, E.C., et al., Endocrine-disrupting potential of bisphenol A, bisphenol A dimethacrylate, 4-n-nonylphenol, and 4-n-octylphenol in vitro: new data and a brief review. Environ Health Perspect, 2007. 115 Suppl 1: p. 69-76.

18.       Fujimoto, T., K. Kubo, and S. Aou, Prenatal exposure to bisphenol A impairs sexual differentiation of exploratory behavior and increases depression-like behavior in rats. Brain Res, 2006. 1068(1): p. 49-55.

19.       Rubin, B.S., et al., Evidence of altered brain sexual differentiation in mice exposed perinatally to low, environmentally relevant levels of bisphenol A. Endocrinology, 2006. 147(8): p. 3681-91.

20.       Dolinoy, D.C., D. Huang, and R.L. Jirtle, Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc Natl Acad Sci U S A, 2007. 104(32): p. 13056-61.

21.       Anway, M.D., et al., Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science, 2005. 308(5727): p. 1466-9.

22.       Chang, H.S., et al., Transgenerational epigenetic imprinting of the male germline by endocrine disruptor exposure during gonadal sex determination. Endocrinology, 2006. 147(12): p. 5524-41.

23.       Patisaul, H.B. and H.L. Bateman, Neonatal exposure to endocrine active compounds or an ERbeta agonist increases adult anxiety and aggression in gonadally intact male rats. Horm Behav, 2008. 53(4): p. 580-8.

24.       Farabollini, F., et al., Effects of perinatal exposure to bisphenol A on sociosexual behavior of female and male rats. Environ Health Perspect, 2002. 110 Suppl 3: p. 409-14.

Meeting highlights environmental influences on genetic risk factors for ASD

March 15, 2011 19 comments

Everyone knows that some environmental factors can have adverse effects on health, especially early in development.  For example, we know that exposure to cigarette smoke is particularly bad for infants and young children, increasing risk for Sudden Infant Death syndrome, respiratory challenges and middle ear infections.  While we are still learning what kinds of environmental factors might impact the intricate process of brain development, and exactly how these impacts occur, we all want to know how environmental factors influence risk for autism.

Last week the Society of Toxicology met in Washington D.C. to discuss not only environmental effects, but how they may interact with our genes to confer autism risk.  The most popular topic of  this 50th anniversary meeting was epigenetics —literally changes made “above the genome”.   Different epigenetic changes have the effect of making the genetic code more or less available for reading and the production of  proteins.  In other words, the environment can actually turn off the functions of genes, resulting in downstream effects on brain and behavioral development.

During a special symposium organized by autism researcher Isaac Pessah, PhD from the University of California at Davis and Cindy Lawler, PhD at the National Institute of Environmental Health Science, , scientists discussed new data and examples of how environmental factors can lead to changes in autism risk.  Animal models of autism are essential for carrying out tests such as these, as different amounts of exposure to a particular substance can be carefully delivered and the outcomes observed with all other variables controlled.

Janine LaSalle, PhD at the University of California at Davis studied the effects of a flame retardant on behavioral development and cognitive function.  She and her colleagues showed that these cognitive effects, which are similar to those found in autism, are dependent on both the sex of the animal and proper function of epigenetic mechanisms that turn a collection of other genes “on” or “off”.

Researchers in the Tanguay lab at Oregon State University are using the humble zebrafish to study a newly discovered type of gene expression.  The research team is studying the effects of alcohol (ethyl alcohol, both the type found in beverages and and as a biofuel additive to gasoline) and a common acne treatment ingredient (retinoic acid, a metabolite of vitamin A ) on gene expression in the zebrafish.  They are finding that disruptions in this new type of gene expression (microRNAs) can have surprisingly large effects on the rest of the genome.

We know from many previous studies that duplications or deletions of collections of genes—called copy number variants or CNVs—can be associated with increased autism risk.  Scott Selleck, PhD, from Penn State University reported on his study which looked at the genetic background of children in the CHARGE study at UC Davis (  Individuals with ASD showed increased lengths of CNVs at certain points in the genome. His lab reasons that these CNVs may be areas of what he calls “genomic instability” where environmental chemicals affect gene expression.   We need to know more about these CNVs and whether or not they are the reason some individuals are more susceptible to environmental factors in development.

Genes and environment interact, yes, but another important factor is when.  Timing of the environmental insult can be crucial.  Studies of neural stem cells are showing us that there exist critical periods in the development of these immature brain cells that include times in which cells divide, and also a later time when the immature cells become either neurons or another type of brain cell known as glia.  It is at these times when environmental influences might have their biggest effect.

Pat Levitt, Ph.D. from the University of Southern California spoke on how the combination of genetic vulnerabilities and  environmental factors can converge to disrupt brain development and function.  One example involves the MET gene, which controls the development of a special class of inhibitory neurons. Previous research showed mutations in MET to be associated with autism, especially in individuals with gastrointestinal dysfunction.

Dr. Levitt and his colleagues demonstrated that exposure to chemicals in diesel fuel exhaust also decreases proper expression of the MET protein.  This reduction in expression leads to changes in complexity and length of neurons as they reach to connect with other neurons.  These changes may contribute to the previously observed effects on brain development.  Interestingly, a recent report notes an increased risk for autism in children whose mothers lived within 1000 feet of a major highway during pregnancy.

Autism Speaks is actively supporting a number of research projects investigating the role of epigenetics in autism, including how environmental factors interact with genetic mechanisms to influence behavior.  A primary focus of research invited for submission to Autism Speaks in 2011 is the mechanism of gene/environment interactions, including epigenetics.

To read about all the research Autism Speaks is funding in this area, click here

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Feeling exposed? Insights from a new meeting on environmental impacts in autism

December 11, 2010 10 comments

by Sallie Bernard, Autism Speaks’ Board Member, co-founder and Executive Director of Safe Minds

Given the historic inattention of the scientific establishment to the environmental contributions to autism, it was nice to see a day-long conference on the topic held this week by a major research center. “Exploring the Environmental Causes of Autism and Learning Disabilities” was put together by the Children’s Center for Environmental Health at the Mount Sinai School of Medicine in New York City. The center is run by Dr. Phil Landrigan, who has been a prominent researcher on the harmful effects of environmental toxicants for decades. He told the incredible story of the harms of lead exposure on children’s cognition and behavior, and how the successful effort to remove leaded gasoline from the market in the 1970s resulted in rising IQ scores and economic gain to the country. I hope this same massive effort will be applied to autism and the chemicals which underlie the increase in its prevalence.

Also of note was the presence at the meeting of Linda Birnbaum. Dr. Birnbaum is the director of the National Institute of Environmental Health Sciences (NIEHS) which holds the autism/environment portfolio at NIH. The Mt. Sinai meeting follows on a workshop held at NIEHS several months ago which explored the role of the environment in autism. Large scientific initiatives in the field fall to the NIH, so without its support, gains will be painfully slow. Hopefully Dr. Birnbaum’s personal involvement signals a heightened interest at NIEHS to look at autism. Although Dr. Birnbaum stated at the conference that her institute spends $30 million on children’s environmental health, at a Senate hearing earlier this year, it was shown that just $8 million of this is for autism specifically.

A few interesting bits of information came out of the conference. One was the definition of “environment” that the insiders use. It covers synthetic chemicals like pesticides, flame retardants and plasticizers; heavy metals like arsenic, lead and mercury; combustion and industrial by-products; diet and nutrients; medications, medical interventions, and substance abuse; infections; the microbiome; heat and radiation; and lifestyle factors. Some may be harmful; others protective. They may operate before conception, during pregnancy or in early life, and some may alter gene expression through epigenetic modifications to chemicals surrounding our genes. Craig Newshaffer, who runs the EARLI study to look at environmental factors among younger autism siblings, referred to the concept of the “exposome”, that is, everything we are exposed to and its effects on health. Dr. Birnbaum’ made the point that health does not equal medicine, and prevention through reduction in chemical exposures is of equal importance to health. Colleen Boyle from the CDC stated that the next prevalence report will be issued in April 2011. We will see if the 1 in 110 number from last year’s report has changed. New research from Korea was unable to confirm increased risk of autism due to parental age or low birth weight, which have been identified as risk factors in Western studies.

The most informative talk was by Dr. Irva Hertz-Picciotto from UC-Davis. She explained how changes in diagnosis do not account for most of the increase in autism rates, and how recent research by their group on mercury and flame retardant blood levels do not address whether these substances are causative for autism because the blood samples were taken years after the autism diagnosis. A paper out this week from UC-Davis found that proximity to traffic air pollution during pregnancy almost doubles the risk of autism. Another paper just accepted by a journal has found higher antibodies to cerebellar tissue in children with autism relative to controls, highlighting the immune component in autism.

Other than these interesting items, the conference covered minimal new ground as far as the science goes. Rather, the points of the meeting seemed to be to make the case that environmental factors research in autism must now be considered mainstream science and to showcase the work being done or about to be done to investigate the issue. Dr. Landrigan made the case for an environmental role by noting that the rate of autism has increased too much to be solely genetic, and that at most, genetics alone will end up explaining 40% of autism cases with the likely percentage much lower.

Autism Speaks provided funding for the conference so that families could attend for free. Alycia Halladay, who runs our environmental science portfolio, noted that environmental factors and how they interact with genetics became one of Autism Speaks 5 priority areas for science in 2010. Autism Speaks also co-funded the NIEHS workshop on the environment earlier this year. Mt. Sinai plans to make video excerpts of the conference available in a few weeks.

Read more about this meeting in The Daily Green.

What is epigenetics? Does this new field hold promise for understanding the causes of ASD?

November 19, 2010 9 comments

“Got Questions?” is a new weekly feature on our blog to address the desire for scientific understanding in our community.  We received over 3000 responses when we asked what science questions were on your mind. We answered a few here and the Autism Speaks Science staff will address the other themes we received in this weekly post.

Scientists have long wondered how experiences during a person’s lifetime can alter behavior and body functioning.  In the early 1800’s Jean Batiste Lamarck suggested that giraffes’ necks grew long through many generations of stretching to reach distant leaves.  That theory eventually fell to evolution–pressures from the environment selectively amplify or quiet certain traits that are variably present within a population. Later, the DNA code was found to be the mechanism for inheritance and the level at which selective pressure acts.

Today’s scientists see hints of Lamark as they peer into the molecular biology of inheritance.

Consider DNA to be a library of books that encode genes. These “genetic books” must be read so that proteins can be formed from the code.  Some genetic books are open and available for reading by the cell’s molecular machinery.  Others maybe temporarily unavailable and still others are in the restricted section—essentially permanently unreadable.

Experiences throughout an individual’s life create tags on the genetic code, marking it as available or not for reading. The molecular methods that control the availability of the genetic code are collectively referred to as epigenetic mechanisms. Literally meaning “above the genome”, epigenetic mechanisms tag DNA with different chemical marks, such as methyl or acetyl groups.  Certain tags can increase the reading frequency, resulting in more protein building-blocks transcribed from the DNA code, and more of that gene “expressed”.  Other tags result in a particular piece of the genetic code to be skipped during reading.

A host of environmental agents and interactions may leave epigenetic marks on the genome.  Early life stress, smoking, exposure to toxins may all leave epigenetic marks either creating or removing barriers for protein creation.

Here is where Lamark comes in.  Most epigenetic marks are removed before the sperm and egg meet to form an embryo, but sometimes, epigenetic marks remain.  This is one mechanism by which environmental exposures can be passed along from parent to child.

The study of epigenetics and gene expression in autism is underway and early findings are exciting.  Some of the genetic syndromes associated with autism, such as Angelman and Prader-Willi syndrome, result from epigenetic marks that render one parent’s genetic contributions unreadable.  Recently, gene expression studies from the blood and even brain tissue of individuals with autism have shown differences in the activity of patterns of genes that are involved in brain development and function.

This is an exciting area of research and we look forward to sharing more details as we learn more from the science.

Read more about epigenetics on or blog.

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:

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:

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:

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.

Categories: Science Tags: , ,

Many journeys to the same location – methods that 21st century scientists are using to identify genes that cause autism

April 15, 2010 11 comments

We have asked several scientists who gave presentations at the April 10-11 DAN! conference in Baltimore to share their research and perspectives from the meeting with you here on the blog.  The following piece is from Dr. Simon G. Gregory, Ph.D. Dr. Gregory is an Associate Professor in the Center for Human Genetics, Duke University Medical Center His primary area of research involves identifying the complex genetic factors that give rise to cardiovascular disease and multiple sclerosis, Dr. Gregory’s group is also applying high-resolution genomic arrays to the discovery of chromosomal abnormalities and identification of epigenetic factors associated with autism.

For decades scientists have relied on traditional genetic approaches to identify genes that contribute to the development of autism. These approaches have included collecting extended, multi-generation families that contain one or more individuals with autism. Once a sufficient number of these families have been collected, hundreds of DNA markers that can highlight differences between us all at a genetic level (a bit similar to DNA fingerprinting used in CSI) are used to identify a region of the genome is linked with the disorder in the families. More recently, higher resolution technologies that benefitted from the completion of the human genome project have been developed to allow us to look at hundreds of thousands of markers simultaneously. This approach differs from the family-based approach in that it uses thousands of unrelated cases and age/sex/ethnicity matched controls. Together, both approaches have been successful in identifying genes, or at least regions of our chromosomes, that play a role in the development of autism. However, we know that many more genes will likely contribute to autism spectrum disorders (ASDs) and that not all mechanisms that disrupt the normal function of a gene will be based on a single DNA mutation or a variant present in the general population.

My group at the Duke Center for Human Genetics recently embarked on a journey to identify autism genes using an approach that looks at chromosome content, and yet we reached an interesting finding using another technique that doesn’t rely on the sequence of our DNA. For many years it has been known that ASDs can be caused by loss (deletion) or gain (duplication) of chromosomes. These genomic rearrangements can be large or small and some have been shown to cluster in particular regions of the genome, for example on the long arm of chromosome 15 (15q11-13). Our journey began by assessing the genomic content of 119 unrelated autistic children from families that we had collected over a number of years. We used genomic microarrays (microscope slides with printed content spanning our genome) to identify novel or common regions of deletion or duplication within one autistic child from each family. Although we identified a handful of novel regions and confirmed dozens of rearrangements that have increasingly been shown to exist within the ‘normal’ population, we decided to focus on a single deletion in one individual. The deletion, which contained five genes, sparked our interest because one of the genes, the oxytocin receptor (OXTR), had been previously implicated in autism. Previous studies using the traditional genetic approaches (mentioned above) had shown that OXTR was genetically associated with autism, other studies had shown that levels of oxytocin (a neurotransmitter that the receptor binds to OXTR) is important for pro-social behavior and that a knock-out of the receptor in mice can affect this behavior, and very recent studies have tested the supplementation of oxytocin in adults with autism.

After identifying the deletion in the one affected child we screened his family to see if it was novel and causative of his autism, or if he inherited the deletion from his parents. Somewhat disappointingly, his mother also had the deletion, but interestingly she had self reported obsessive compulsive disorder (OCD) for which OXTR has also been implicated. Although we could have stopped the journey at this point, we decided try a different approach. Previous studies have shown that OXTR is controlled in the liver by a chemical group (methyl –CH3) that sits on top of the DNA but which doesn’t change its sequence (click here for more information on epigenetic changes as they relate to autism). The phenomena of DNA methylation is a normal mechanism by which our cells silence parts of the genome that they don’t want to be active (mainly repeat and retro-viral sequences) but they also use it as a switch to turn on or turn off genes for protein production. Significant in our journey was that the child with autism who had the OXTR deletion also had an affected brother. This is significant because when we assessed the methylation status of the whole family we noticed that the affected brother has very high levels of methylation in five different CG bases (among the A’s C’s G’s and T’s of our genome where the methyl group resides) in a 1,600 base pair window that had previously been identified as being methylated in the liver OXTR.

Differential methylation isn’t a novel finding as a possible cause of autism. Previous studies in Rett syndrome, which has ASD like symptoms, have shown that mutations in the methyl CpG binding protein 2 (MECP2) gene not only contributes to the development of Rett syndrome but that these mutations affect the normal functioning of the gene which regulates the expression of other genes by altering their DNA methylation state. Additionally, imprinting (the silencing of a maternal or paternal copy of a chromosome by DNA methylation) has also been established as the basis for the development of Angelman and Prader-Willi syndromes that, again, have ASD like symptoms. Our next step was to validate the observation that increased methylation of OXTR in the affected brother may be a causal mechanism of autism. We expanded our analysis to include evaluation of the methylation status of OXTR in the peripheral blood of 20 controls and 20 individuals with autism, and in a second dataset of the post-mortem samples of temporal cortex tissue (a center for language and learning) in eight controls and eight children with autism. In both datasets we were pleased to see that the individuals with autism had higher levels of methylation than the controls. We next measured the level of gene expression of OXTR because we would expect that increased DNA methylation would result in decreased gene expression – which it did in a very small number of samples that we could test.

So you’re asking yourself, how, if all these other studies had pointed to OXTR being implicated in autism, is this discovery significant? Well, we hope that we have found a unique autism-associated DNA methylation signature in a receptor for a neurotransmitter that is important in social cognition in autism. The next more exciting journey will be to substantiate what we have found in a larger number of samples and to establish if oxytocin treatment can help

Gene-Environment Interactions: Context Matters

March 23, 2010 3 comments

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