autism and genetics

Posted on Autism

Autism gene study finds widespread impact to brain’s growth signaling network

A side-by-side look at the brains of a normal newborn mouse and one lacking the autism and intellectual disability risk gene Dyrk1a. CREDIT Damon Page Lab, Scripps Research

 Damage to the autism-associated gene Dyrk1a, sets off a cascade of problems in developing mouse brains, resulting in abnormal growth-factor signaling, undergrowth of neurons, smaller-than-average brain size, and, eventually, autism-like behaviors, a new study from Scripps Research, Florida, finds.

The study from neuroscientist Damon Page, PhD, describes a new mechanism underlying the brain undergrowth seen in individuals with Dyrk1a mutations. Page’s team used those insights to target the affected pathway with an existing medicine, a growth hormone. It restored normal brain growth in the Dyrk1a mutant mice, Page says.

“As of now, there’s simply no targeted treatments available for individuals with autism spectrum disorders caused by DYRK1A mutations,” Page says. “This represents a first step in evaluating a potential treatment that could be used in the clinic.”

Their study appears Thursday in the journal Biological Psychiatry.

To track the effects of missing Dyrk1a genes, Jenna Levy, the paper’s first author and a graduate student in Page’s lab, engineered mice to have one or two broken copies of Dyrk1a in their developing brain tissue. The brains of both sets of mice developed abnormally, she found, displaying decreased brain size and number of neurons, as well as reduced number of other brain cells.

Downstream effects

The scientists also conducted “unbiased” proteomic studies, to see if the mutant mice had abnormally high or low levels of other unknown proteins that might impact brain development. Using a technique called “high-resolution tandem mass spectrometry coupled to liquid chromatography,” they found that the Dyrk1a mutant mice had reduced levels of 56 cellular proteins, and increased levels of 33. Many of those were known autism risk genes, some implicated in sending growth signals, Levy says.

“The specific signaling cascades we found altered in Dyrk1a mutants are implicated in multiple causal mechanisms of autism,” Levy says.

A computational biology technique called Ingenuity Pathway Analysis helped them find altered proteins. There were changes to those involved in nerve signaling, creation of synapses, and growth of axons, the long, insulated extensions that give neurons their distinct shape. Also, multiple forms of the protein Tau were depleted in the Dyrk1a mice.

“These data implicate signaling cascades that were previously not known to be altered by Dyrk1a mutations,” Page says.

Many autism genes

At least 200 different high-confidence risk genes for autism spectrum disorders have been identified, Page says, but little has been known about their roles and relationships, complicating diagnosis and treatment development efforts.

Page estimates that fewer than 1 percent of people diagnosed with autism spectrum disorder carry Dyrk1a mutations. Half of those show autistic behavioral traits, and about 70 percent have short stature. But many more people with autism diagnoses display microcephaly, or smaller-than-average head circumference, around 1 in 20, he says.

“Importantly for treatment considerations, this study suggests there may be a point of convergence for multiple autism causes,” Page says. “Abnormal activity of this pathway appears to be shared across various genetic causes of autism, pointing to the possibility of common molecular target for therapeutics.”

Previously, Page’s lab has found autism-linked mutations to a gene called Pten can cause an opposite effect, brain overgrowth, or macrocephaly.

“What we didn’t know before is that the signaling disruptions that cause microcephaly, brain undergrowth, appear to be the flip side of the coin of the signaling disruptions that cause macrocephaly, brain overgrowth,” Page says.

Because of that, they hypothesized that restoring growth signaling at a high level, using a known growth hormone, might rescue the brain undergrowth.

“We thought that treating with insulin-like growth factor 1, IGF-1, should increase the activity of the downstream signaling cascade, which should result in increased growth,” Levy says. After treating Dyrk1a mice from birth to day 7, she found that was the case. The observed microcephaly improved, and under the microscope, the brain tissue showed normalized neuron growth.

Toward targeted treatments

Based on those results, more investigation is warranted on the potential for growth hormone treatment to benefit a minority of children with autism, those with Dyrk1a mutations, or related downstream mutations and manifestations, including microcephaly, Page says.

Many questions remain. Whether IGF-1 treatment in the newborn Dyrk1a mice might also improve autism-like behaviors in the mice is still under investigation, Levy adds. Also, it’s still unclear whether there is a critical treatment window during mouse brain development, and if so, how large that window may be.

In humans, neural progenitor cells begin forming in the third week of pregnancy. By the seventh week, actual neuron production starts. It’s a short window–neuron production in the billions is mostly finished by around the 20th week of gestation. As neurons are made, each migrates to its final destination in the forming brain. Once there, it starts making connections with other neurons, elongating and branching out, literally wiring the developing brain. Rapid brain development continues with experience and growth after birth.

Autism is a constellation of disorders with multiple causes, meaning that targeted, individualized treatments will be needed to assist people who seek them, Page says. Prevalence of autism diagnoses has been rising steeply since the 1990s. Research from the U.S. Centers for Disease Control and Prevention now estimates 1 in 59 children have an autism spectrum disorder. The mutations to Dyrk1a that cause autism appear to be sporadic, meaning they aren’t typically inherited, but rather appear randomly, Page says.

Page stresses that the study is preliminary, not grounds for off-label use of IGF-1 as a possible autism treatment. He’s often asked by families what they can do for their children diagnosed with autism. He suggests asking their doctor for a genetic testing as a first step.

“It helps with understanding of what’s going on, it allows them to connect and find support, and also to be aware if clinical trials begin,” Page says. “It’s too soon for affected families to go to their pediatrician and say, ‘Give my child this.’ This is a first step in evaluating whether a potential treatment could be used in the clinic.”

Posted on Autism

Prenatal BPA exposure may contribute to the male bias in autism


Prenatal exposure to BPA disrupts autism-candidate genes involved in neuronal viability, neuritogenesis, and learning/memory. Changes in the expression of these genes are correlated in a sex-dependent manner with disruptions in neuronal characteristics and behaviors that occur in response to BPA. Surangrat Thongkorn et all

A new study by researchers from Chulalongkorn University, Tohoku University, and The George Washington University is the first to identify autism candidate genes that may be responsible for the sex-specific effects of bisphenol A (BPA) on the brain. It suggests BPA may serve as an environmental factor that contributes to the prevalence of male bias in autism .

The research was published in the journal Scientific Reports.

BPA is widely used in many products in our daily life and abundant in micro/nanoplastics found in the environment, food, or the human placenta. It is thought to be an environmental influence on autism- a neurodevelopmental disorder characterized by impaired social communication, restricted interests and repetitive behaviors. Autism is a major public health challenge around the world, with roughly 1 in 54 children in the United States being diagnosed.

“Many studies have shown BPA impairs neurological functions known to be disrupted in autism, making scientists believe that BPA may be one of the key environmental risk factors for autism. However, we still do not know how BPA can cause or increase the susceptibility of autismand whether it also plays a role in the male bias of the disorder,” said assistant professor Dr.Tewarit Sarachana, head of the SYstems Neuroscience of Autism and PSychiatric disorders (SYNAPS) Research Unit at the Faculty of Allied Health Sciences, Chulalongkorn University.

“In fact, one of our recent studies has demonstrated that prenatal exposure to BPA altered the expression of several ASD candidate genes in the hippocampus in a sex-dependent pattern, but the link between the dysregulation of ASD candidate genes and impaired neurological functions is still lacking.”

“In this study, we showed exposure to BPA during the gestational period decreased neuronal viability and neuronal density in the hippocampus and impaired learning/memory in only the male offspring. Interestingly, the expression of several ASD-related genes in the hippocampus was dysregulated and showed sex-specific correlations with neuronal viability, neuritogenesis, and/or learning/memory. Under prenatal BPA exposure, these genes may play important roles in determining the risk of ASD and its higher prevalence in males,” said Surangrat Thongkorn, a Ph.D. candidate and first author of the study.

“The sex differences in the effects of BPA found in our study strongly suggest that BPA negatively impacts the male and female offspring brain through different molecular mechanisms. We are progressively working on these issues to identify the sex-specific molecular mechanism of BPA in the brain. Understanding the effects of BPA and its molecular mechanisms in ASD may lead to changes in the policy regarding the use of BPA or even the discovery of molecular targets for ASD treatment in the future,” concluded Dr.Sarachana.

Posted on Autism

Study finds neglected mutations may play important role in the autism spectrum


UC San Diego and UCLA researchers find tandem repeats, which are also associated with Huntington’s disease, may contribute to autism.

Mutations that occur in certain DNA regions, called tandem repeats, may play a significant role in autism spectrum disorders, according to research led by Melissa Gymrek, assistant professor in the UC San Diego Department of Computer Science and Engineering and School of Medicine. The study, which was published in Nature on Jan. 14, was co-authored by UCLA professor of human genetics Kirk Lohmueller and highlights the contributions these understudied mutations can make to disease.

“Few researchers really study these repetitive regions because they’re generally non-coding–they do not make proteins; their function is unclear; and they can be difficult to analyze,” said Gymrek. “However, my lab has found these tandem repeats can influence gene expression, as well as the likelihood of developing certain conditions such as autism.”

In the paper, the lab studied around 1,600 “quad” families, which include mother, father, a neurotypical child and a child with
autism . Specifically, they were looking for de novo mutations, which appear in the children but not the parents. This analysis, led by UC San Diego graduate student and first author Ileena Mitra, identified an average of 50 de novo mutations at tandem repeats in each child, regardless of whether they were affected by autism.

On average, there were more mutations in autism children, and while the increase was statistically significant, it was also relatively modest. However, using a novel algorithmic tool developed by UC San Diego bioengineering undergraduate and second author Bonnie Huang, the researchers showed tandem repeat mutations predicted to be most evolutionarily deleterious were found at higher rates in autistic children.

“In our initial analysis, the ratio between the number of mutations in autistic children and neurotypical children was around 1.03, so barely above one,” said Gymrek. “However, after we applied Bonnie’s tool, we found relative risk increased about two-and-a-half fold. The kids with autism had more severe mutations compared to the controls.”

Finding so many previously undiscovered tandem repeat mutations is significant, as it matches the number of point mutations (single alterations in the A, C, G, T bases that make up DNA) typically found in each child.

The study also produced a wealth of information about the many factors that can influence these de novo mutations. For example, children with older fathers had more tandem repeat mutations, quite possibly because sperm continues to divide – and accumulate mutations – during a man’s lifetime. However, the changes in repeat length coming from mothers were often larger, though the reasons for this are unclear.

“The mutations from dad tended to be plus or minus one copy,” said Gymrek. “However, mutations from mom were usually plus or minus two or more copies, so we’d see more dramatic events when they came from the mother.”

This approach highlighted a number of genes that had already been linked to autism, as well as new candidates, which the lab is now exploring.

“We want to learn more about what these novel autismgenes are doing,” said Gymrek. “It’s exciting because repeats have so much more variation compared to point mutations. We can learn quite a bit from a single location on the genome.”


Posted on Autism

Advances in understanding autism, based on “mosaic” mutations

Mutations and chromosome deletions/duplications during embryonic development contribute to autism risk


Two studies in today’s Nature Neuroscience, led by researchers at Boston Children’s Hospital, Brigham and Women’s Hospital (BWH), and Harvard Medical School (HMS), implicate mosaic mutations arising during embryonic development as a cause of autism spectrum disorder (ASD). The findings open new areas for exploring the genetics of ASD and could eventually inform diagnostic testing.

Mosaic mutations affect only a portion of a person’s cells. Rather than being inherited, they arise as a “mistake” introduced when a stem cell divides. A mutation in a stem cell will only be passed to the cells that descend from it, producing the mosaic pattern. When mosaic mutations occur during embryonic development, they can appear in the brain and affect the function of neurons. The earlier in development a mutation happens, the more cells will carry it.

Characterizing mosaic mutations in the brain

The two studies were part of the Brain Somatic Mosaicism Network, funded by the National Institute of Mental Health. The first study used deep, ultra-high-resolution whole-genome sequencing to quantify and characterize mosaic mutations in the frontal cortex of people with and without ASD. It was led by Rachel Rodin, MD, PhD and Christopher Walsh, MD, PhD, of Boston Children’s, and Yanmei Dou, PhD and Peter Park, PhD, of HMS.

When the researchers examined samples of brain tissue from 59 deceased people with ASD and 15 controls — the largest cohort of brain samples ever studied — they found that most of the brains had mosaic “point” mutations (alterations in a single “letter” of genetic code). They calculated that embryos acquire several such mutations with each cell division, and estimate that about half of us carry potentially harmful mosaic mutations in at least 2 percent of our brain cells.

In the brains of people with ASD, however, mosaic mutations were more likely to affect parts of the genome that have a pivotal role in brain function. Specifically, they tended to land in “enhancers,” portions of DNA that do not code for genes but regulate whether a gene is turned on or off.

“In the brains of people with autism, mutations accumulate at the same rate as normal, but they are more likely to fall into an enhancer region,” says Rodin, first author on the paper. “We think this is because gene enhancers and promoters tend to be in DNA that’s unwound and more exposed, which probably makes them more susceptible to mutations during cell division.”

“Mutations in enhancers are a hidden kind of mutation that you don’t see in typical diagnostic exome sequencing, and it may help explain ASD in some people,” notes Walsh, chief of genetics and genomics at Boston Children’s and co-senior author on the paper with Park, who led the study’s computational analyses. “We also need to better understand the effects of these mutations on neurons.”

Mosaic deletions and duplications

The second study is the first large-scale investigation of copy number variants (CNVs) in people with ASD that occur in a mosaic pattern. As opposed to point mutations in a single gene, CNVs are deletions or duplications of whole segments of a chromosome, which may contain multiple genes.

A team led by Maxwell Sherman, MS of BWH, Po-Ru Loh, PhD of BWH, Park, and Walsh studied blood samples from about 12,000 people with autism and 5,500 unaffected siblings provided by the Simons Simplex Collection and the Simons Powering Autism Research for Knowledge (SPARK) datasets. They used blood as a proxy for brain tissue and applied novel computational techniques to sensitively detect mosaic mutations that likely arose during embryonic development.

“People have been interested in CNVs in autism for a long time, and would occasionally notice that some of them were mosaic, but no one had really looked at them in a large-scale study,” says Loh, co-senior author on the paper with Walsh and Park.

From these large samples, the team identified a total of 46 mosaic CNVs in the autism group and 19 in siblings. The CNVs affected 2.8 to 73.8 percent of blood cells sampled from each subject.

Size matters

Notably, the people with ASD were especially likely to have very large CNVs, with some involving 25 percent or more of a chromosome. The CNVs spanned a median of 7.8 million bases in the ASD group, versus 0.59 million bases in controls.

“This is one of the more interesting and surprising aspects of our study,” says Sherman, the paper’s first author and a PhD student at MIT. “The kids with ASD had very large CNVs that often hit dozens of genes, and likely included genes important for development. If the CNVs were in all their cells, rather than in a mosaic pattern, they would likely be lethal.”

The study also suggested that the larger the CNVs, the greater the severity of autism as assessed with a standard clinical measure. Another surprise was that smaller CNVs already known to be associated with ASD when found in all cells, such as deletions or duplications of 16p11.2 or 22q11.2, were not associated with autism when they occurred in a mosaic pattern.

“This suggests that in order to get autism, you have to mess up a large number of cells in the brain in a pretty substantial way,” says Walsh. “We’re fairly sure that these large CNVs change the behavior of the neurons that carry them.”

“We don’t really know what cell fraction is important, or what particular chromosomes are most susceptible,” notes Loh. “These events are still very rare, even in people with autism. As larger cohorts are assembled, we hope to get some finer-grained insights.”

The findings of these studies could eventually be incorporated into diagnostic testing in children with autism. Testing could incorporate the non-coding portions of the genome, such as gene enhancers and promoters, and include higher-resolution chromosomal analysis to identify large mosaic CNVs. For now, the findings add to the ever-evolving autism puzzle, deepening the mystery of why so many different genetic mechanisms can lead to the same presentation of autism.


Posted on Autism

Single mutation leads to big effects in autism-related gene

New findings suggest that a single mutation may contribute to increased prevalence of autism in boys than in girls. Image courtesy of Roche Lab/NINDS.

A new study in Neuron offers clues to why autism spectrum disorder (ASD) is more common in boys than in girls. National Institutes of Health scientists found that a single amino acid change in the NLGN4 gene, which has been linked to autism symptoms, may drive this difference in some cases. The study was conducted at NIH’s National Institute of Neurological Disorders and Stroke (NINDS).

Researchers led by Katherine Roche, Ph.D., a neuroscientist at NINDS, compared two NLGN4 genes, (one on the X chromosome and one on the Y chromosome), which are important for establishing and maintaining synapses, the communication points between neurons.

Every cell in our body contains two sex chromosomes. Females have two X chromosomes; males have one X and one Y chromosome. Until now, it was assumed that the NLGN4X and NLGN4Y genes, which encode proteins that are 97% identical, functioned equally well in neurons.

But using a variety of advanced technology including biochemistry, molecular biology, and imaging tools, Dr. Roche and her colleagues discovered that the proteins encoded by these genes display different functions. The NLGN4Y protein is less able to move to the cell surface in brain cells and is therefore unable to assemble and maintain synapses, making it difficult for neurons to send signals to one another. When the researchers fixed the error in cells in a dish, they restored much of its correct function.

“We really need to look at NLGN4X and NLGN4Y more carefully,” said Thien A. Nguyen, Ph.D., first author of the study and former graduate student in Dr. Roche’s lab. “Mutations in NLGN4X can lead to widespread and potentially very severe effects in brain function, and the role of NLGNY is still unclear.”

Dr. Roche’s team found that the problems with NLGN4Y were due to a single amino acid. The researchers also discovered that the region surrounding that amino acid in NLGN4X is sensitive to mutations in the human population. There are a cluster of variants found in this region in people with ASD and intellectual disability and these mutations result in a deficit in function for NLGN4X that is indistinguishable from NLGN4Y.

In females, when one of the NLGN4X genes has a mutation, the other one can often compensate. However, in males, diseases can occur when there is a mutation in NLGN4X because there is no compensation from NLGN4Y.

The current study suggests that if there is a mutation in NLGN4X, NLGN4Y is not able to take over, because it is a functionally different protein. If the mutations occur in regions of NLGN4X that affect the protein levels, that may result in autism-related symptoms including intellectual deficits. The inability of NLGN4Y to compensate for mutations in NLGN4X may help explain why males, who only have one X chromosome, tend to have a greater incidence of NLGN4X-associated ASD than females.

“The knowledge about these proteins will help doctors treating patients with mutations in NLGN4X better understand their symptoms,” said Dr. Roche.