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Autism research news and opinion
20 January 2015 – 27 January 2015
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Tweak to molecular scissors cuts path to turn on genes
Jessica Wright
26 January 2015
A new technique allows scientists to turn on the
expression of any gene, giving them the
unprecedented ability to explore the function of
every gene in the human genome.
“You can now look at every gene in the genome and
turn it on or turn it off and see whether or not it
plays a role in a given disease or biological process,”
says lead researcher Feng Zhang, assistant professor
of brain and cognitive sciences at the Massachusetts
Institute of Technology.
Julia Yellow
Gene editor: A revolutionary technique, CRISPR,
allows researchers to mutate or delete genes; the new
method allows them to activate genes.
The technique, described 10 December in Nature, is
a modified version of a method called CRISPR. Two
years ago, CRISPR wowed researchers by allowing
them to ‘edit’ — delete or insert mutations into —
any gene they wanted.
Like CRISPR, the new method gives researchers an
invaluable tool to study autism-linked genes. For
example, researchers could activate genes, one at a
time or simultaneously, in large duplications and deletions of DNA linked to autism, says Michael
Talkowski, assistant professor of neurology at Harvard Medical School.
“For a long time we have been continuously coming up with methods to knock down gene expression,
but there have not been really good, reliable methods to activate gene expression,” he says. “The uses
of this technology are just innumerable.”
The technique is restricted to cultured cells, including neurons made from stem cells of people with
autism, but researchers are trying to adapt it for use in animal models and, potentially, people.
Autism-linked mutations typically affect only one of two gene copies, and the new method may allow
researchers to boost activity of the ‘healthy’ gene to normal levels, says Guoping Feng, professor of
brain and cognitive sciences at the Massachusetts Institute of Technology, who was not involved in the
new study. “It will be potentially therapeutic.”
Scissor switch:
CRISPR works by allowing researchers to place an enzyme called CRISPR-CAS9, which has a
scissorlike domain, anywhere in the genome they choose. The new technique replaces the scissors
with ‘activators’ that act as landing strips for the cellular machinery that triggers gene expression.
The study is not the first to harness this approach, but earlier efforts to link activators to
CRISPR-CAS9 worked only some of the time. In a study published last year, Zhang and his team
analyzed the structure of CRISPR-CAS9 when bound to DNA and found that the bulky complex may
sit between the activators and DNA2.
In the new study, they instead placed the activators on the
small, synthetic RNA molecules that guide CRISPR-CAS9 to
specific points in the DNA. They also used multiple
activators instead of a single one.
The new method works every time, and the researchers were
able to use it to boost the expression of 12 genes that could
not efficiently be activated by previous methods.
The researchers created an open-access library of guide
RNAs that turn on every gene in the human genome. As a
proof of concept, they used the library to activate each of the
20,000 human genes in skin cancer cells. This revealed
genes that confer resistance to certain forms of
chemotherapy.
The same process could reveal genes that have
compensatory effects in autism, Zhang says. “The new
method provides a way to discover genes that, if they are
turned on, provide an advantage.”
Tricky tether: Studying the structure of the
gene-editing complex when bound to DNA
allowed the researchers to boost the
technique’s efficiency.
In another study, posted 20 December on the biology preprint server bioRxiv, researchers used
multiple activators bound to CRISPR to turn on two developmental genes in induced pluripotent stem
cells. This allowed them to consistently transform the cells into neurons in just four days, besting the
efficiency of the standard technique.
Both techniques lead to higher levels of gene expression than can be achieved with standard methods,
says George Church, professor of genetics at Harvard Medical School and lead researcher on the stem
cell study. This is crucial for screening large numbers of genes and finding their links to conditions
such as autism, he says. “In practice, you’re going to want to get as high activation as possible.”
Before the technique can be applied to animals, researchers need to control the expression levels of
the activated genes and target specific organs, such as the brain.
“That’s the ultimate goal,” says Zhang. “We’re working on it, because I really would like to be able to
use this system to study the brain. Hopefully, other people will help out, too, to make it quicker.”
News and Opinion articles on SFARI.org are editorially independent of the Simons
Foundation.
References:
1: Konermann S. et al. Nature Epub ahead of print (2014) PubMed
2: Nishimasu H. et al. Cell 156, 935-949 (2014) PubMed
Small snippets of genes may have big effects in autism
Kate Yandell
22 January 2015
Small pieces of DNA within genes,
dubbed ‘microexons,’ are abnormally
regulated in people with autism,
suggests a study of postmortem brains
published 18 December in Cell1. These
sequences, some as short as three
nucleotides, moderate interactions
between key proteins during
development.
“The fact that we see frequent
misregulation in autism is telling us
that these microexons likely play an
important role in the development of
the disorder,” says lead researcher
Benjamin Blencowe, professor of
molecular genetics at the University of
Toronto.
Network analysis: Many genes containing abnormally regulated
microexons are linked to autism (red).
Genes are made up of DNA sequences
called exons, separated by swaths of
noncoding DNA. These exons are
mixed and matched to form different
versions of a protein. This process,
called alternative splicing, is thought to
be abnormal in autism.
Many sequencing studies tend to skip over microexons because they are not recorded in reference
sequences. Although researchers have known about microexons for decades, they were unsure
whether the small segments had any widespread purpose.
The new study confirms microexons’ importance, suggesting that these tiny sequences can have big
effects on brain development.
“It’s really a new landscape of regulation that’s associated with a disorder,” says Blencowe. “We have a
big challenge ahead of us to start dissecting the function of these microexons in more detail.”
Blencowe and his team developed a tool that flags short segments of RNA flanked by sequences that
signal splice sites. They used the tool to identify microexons in RNA sequences from various cell types
and species throughout development.
In the brain, microexons are highly conserved across people, mice, frogs, zebrafish and other
vertebrates. Alternatively spliced microexons are more likely to be present in neurons than in other
cell types, suggesting that they have an important, evolutionarily conserved role in neurons.
Irregular splicing:
The researchers analyzed patterns of microexon splicing in the postmortem brains of 12 people with
autism and 12 controls between 15 and 60 years of age.
Nearly one-third of alternatively spliced microexons are present at abnormal levels in autism brains
compared with control brains, they found. By contrast, only 5 percent of exons longer than 27
nucleotides are differentially spliced in autism brains.
Genes with microexons that are misregulated in autism tend to be involved in the formation of
neurons and the function of synapses — the junctions between neurons. Both of these processes are
implicated in autism.
Microexons are particularly likely to be misregulated in
autism-linked genes, such as SHANK2 and ANK2. What’s
more, the expression of a gene called nSR100, which regulates
splicing of microexons, is lower in the brains of people with
autism than in those of controls.
One future goal is to determine the biology underlying these
differences, says Daniel Geschwind, director of the University
of California, Los Angeles Center for Autism Research and
Treatment. nSR100 belongs to a module of genes that includes
transcription factors — which regulate the expression of other
genes — and those that modify chromatin, which helps
package DNA into the nucleus. Many of these genes have
known links to autism.
Related content:
Method predicts impact of
DNA variants on gene
expression
Genetics: Splicing gene
alters expression of autism
genes
Online tool can predict
effects of genetic variants
New resource catalogs
RNA-binding sites of many
proteins
To look at microexon splicing throughout development,
Blencowe and his team sequenced RNA from mouse
embryonic stem cells as they differentiated into neurons.
Microexon levels tend to spike after the cells finish dividing, hinting at a role in the late stages of
neuronal maturation.
Studying microexon regulation at various stages of normal development in people is another logical
next step, says Lilia Iakoucheva, assistant professor of psychiatry at the University of California, San
Diego, who was not involved in the study. “Then, of course, we can study gene expression in autism
brains and then talk about what’s regulated correctly and what’s misregulated.”
As a complement to the postmortem data, the researchers could also look at how microexons are
regulated in developing neurons derived from people with autism, says Chaolin Zhang, assistant
professor of systems biology at Columbia University in New York, who was not involved in the study.
“We should not underestimate the potential of more detailed characterization of these splicing
variants,” he says. “They really expand the genome and [its] complexity in an exponential way.”
Yang Li, a postdoctoral fellow at Stanford University in California also applauds the attention to the
microexons. “There’s still not enough recognition that different [forms of proteins] can have very
different functions,” he says. “This is especially true in the brain.”
In an independent study published in December in Genome Research, Li and his colleagues reported
that microexons in the brain tend to encode amino acids in locations that are likely to affect protein-
protein interactions2. They also found that the autism-linked RBFOX gene family regulates microexon
splicing in the brain.
“I definitely think that microexons are important because of how conserved they are in terms of brain
function,” says Li. “But I don’t know if they cause autism.”
News and Opinion articles on SFARI.org are editorially independent of the Simons
Foundation.
References:
1. Irimia M. et al. Cell 159, 1511-1523 (2014) PubMed
2. Li Y.I. et al. Genome Res. 25, 1-13 (2015) PubMed
Method charts lifetime expression of DNA in brain
Kate Yandell
21 January 2015
A new database that maps changes in gene expression
in the prefrontal cortex shows that autism-linked
genes are expressed differently than other genes
through six stages of life. The results were published
15 December in Nature Neuroscience1.
Most studies that measure gene expression rely on
lists of genes and their protein-coding subunits, called
exons. As a result, they miss sequences not on those
lists.
The new study takes advantage of a method called
‘derfinder’ that identifies clusters of adjacent DNA
base pairs, called differentially expressed regions
(DERs), that change in concert2. This captures
changes in gene expression in regions of the genome
that are not yet fully understood.
Christos Georghiou/Shutterstock.com
Cortex clock: Gene expression in the prefrontal
cortex, a brain region implicated in autism, shifts
dramatically from fetal development to old age.
The researchers tested the method in the prefrontal
cortex — a brain region implicated in several
developmental and degenerative disorders, including
autism. They studied a total of 72 samples from the
postmortem brains of fetuses, infants, children,
teenagers, adults and older adults.
The method identified 50,650 DERs in the prefrontal cortex that are associated with progression
through the six life stages. Roughly 41 percent of these DERs reside in introns — DNA segments that
are edited out before genes are translated into proteins. Another 8 percent lie in the genetic material
between genes.
The researchers hypothesize that some of these DERs code for subunits of proteins that were never
noted in gene and exon maps, whereas others may code for regulatory RNAs.
The researchers investigated whether changes in gene expression over different life stages correlate
with shifts in the brain, such as an increase in the proportion of support cells called glia. Instead, they
found that the changes reflect developmental changes within neurons as they mature.
The researchers used the method to analyze preexisting gene expression data and found that DERs are
conserved across multiple brain regions. Humans and mice also express similar DERs in fetal versus
adult brain tissue.
Genes linked to neurodegenerative diseases tend to include DERs expressed late in life, whereas those
implicated in neurodevelopmental disorders contain more DERs in the fetal prefrontal cortex. DERs
are overrepresented in autism-linked genes, suggesting that the expression of these genes changes at
key times in early development.
The database is freely available on the University of California, Santa Cruz Genome Browser, and
derfinder is available for download on Bioconductor. Researchers can surf the dataset for genetic
regions of interest or apply the tool to their own samples.
News and Opinion articles on SFARI.org are editorially independent of the Simons
Foundation.
References:
1. Jaffe A.E. et al. Nat. Neurosci. 18, 154-161 (2014) PubMed
2. Frazee A.C. et al. Biostatistics 15, 413-426 (2014) PubMed
Researchers urge caution in studies of mice and microbes
Sarah DeWeerdt
20 January 2015
Over the past several years, researchers have
begun to investigate links between the trillions of
bacteria that inhabit our digestive tract and
autism. These studies reflect the undeniable
presence of gastrointestinal symptoms in autism,
as well as a growing appreciation for the so-called
microbiome and its role in overall health.
HerPhotographer/flickr
A new review raises caution, however, about using
mice to model the human microbiome. Published
in this month’s issue of Disease Models &
Mechanisms, it serves as an important reminder
for autism researchers to interpret such studies
with skepticism.
One reason for this caution comes down to
anatomy. Compared with people, mice have a
proportionally larger large intestine and cecum — the pouch at the beginning of the large intestine
where bacteria ferment undigestible plant material. These differences reflect different diets: Although
mice, like humans, are omnivores, they eat a greater proportion of plants.
The two organisms also have different distributions of goblet cells and Paneth cells in the gut wall.
These cells help to coordinate immune responses in the gut and so are likely to influence the
composition of the microbial community.
The types of resident bacteria also vary between people and mice. Both microbiomes are dominated
by two major bacterial groups: bacteroidetes and firmicutes. But their precise composition is difficult
to compare because researchers have usually used different methods to study them.
There are at least 79 subgroups, or genera, of bacteria that exist in both mice and people. However,
the relative abundance of genera may differ between the two. For example, Prevotella appears to be
abundant in the human gut but rare in the mouse; the opposite is true of Lactobacillus.
Despite these differences, mouse models have helped to uncover the interrelationships between diet,
the microbiome and obesity in people. Dietary manipulations in mice produce microbiome changes
similar to those seen in people, for example.
On the other hand, researchers have struggled to create mouse models of inflammatory bowel disease
that accurately reflect the human condition. Some microbiome changes are similar between the two
organisms but others are puzzlingly inconsistent. For example, a bacterium called Akkermansia is
scarce in people with inflammatory bowel disease but more abundant than normal in one mouse
model of the disease.
No research tool is perfect, and the idea that mice do not always accurately model a human condition
is hardly news to autism researchers. After all, the field
continues to debate which mouse behaviors best correspond to
the social and communication deficits seen in autism. Some
researchers go so far as to question whether it’s even possible
to model autism in an animal that strays so significantly from
people in terms of social behavior and cognition.
Still, I think there’s great potential for mouse microbiome
studies of autism because there are so many mouse models of
the disorder. Researchers could compare the microbiomes of
different mouse models to look for subsets that have similar
changes. They could also manipulate the mouse microbiome to
tease out the relationships between gut bacteria,
gastrointestinal symptoms and autism traits — even if this
practice only provides clues about those relationships in
people.
Related content:
Clinical research: Gut
bacteria prevalent in autism
Studies implicate gut
bacteria in autism
Cognition and behavior:
Epilepsy drug alters rodent
gut
Study finds no link between
autism and gut microbes
Finally, researchers could test whether drugs being developed for specific forms of autism affect the
microbiome and whether such changes are key to a drug’s effectiveness. An imperfect model can
nevertheless be a perfect opportunity.
News and Opinion articles on SFARI.org are editorially independent of the Simons
Foundation.
Toddlers with autism show few symptoms during brief exams
Nicholette Zeliadt
23 January 2015
Many children with autism show early signs of
the disorder, such as lack of eye contact and
repetitive behaviors. A pediatrician’s ability to
spot these subtle signs during a routine exam
opens the door to early intervention.
But many toddlers with autism display so few
abnormal behaviors during brief exams that they
evade the diagnostic eye of even expert clinicians,
according to a study published 12 January in
Pediatrics. This suggests that behavioral
observation alone is not enough for doctors to
detect the disorder in young children.
The researchers recorded two 10-minute videos
for each of 42 children as they underwent
thorough diagnostic exams for autism. The study
included 14 children with autism, 14 children
with language delay and 14 controls, all between 15 and 33 months of age.
Monkey Business Images/Shutterstock.com
Two autism experts, both of whom were unaware of the children’s diagnoses, reviewed the videos.
They measured the number of times each child performed certain behaviors, such as playing with
toys, making sounds or responding to their name being called, and rated each behavior as ‘typical’ or
‘atypical.’ They then decided whether each child’s overall behavior warranted a referral for an autism
evaluation.
Based on these observations, the autism experts incorrectly flagged 39 percent of the children with
autism as not needing further evaluation. That may be because they thought these children showed
typical behavior 89 percent of the time. In other words, the atypical behaviors occur so seldom that
they are overshadowed by typical ones, the researchers suggest.
This doesn’t necessarily mean that pediatricians and family physicians are missing children with
autism, as mainstream news reports suggested last week. Beyond making behavioral observations,
doctors typically consider a child’s family history, the results of autism screening tests and parental
reports of symptoms displayed outside the doctor’s office.
The findings highlight just how difficult it can be to diagnose autism based on behavior. When rating
typical behaviors, the experts in the study agreed 97 percent of the time, but this fell to 35 percent for
atypical behaviors. If anything, the study underscores the need for more objective measures of autism
symptoms.
News and Opinion articles on SFARI.org are editorially independent of the Simons
Foundation.
Webinar: The female autism conundrum
Greg Boustead
20 January 2015
Due to the winter weather emergency affecting the
northeastern U.S. this week and its potential effect on
operational resources at the Simons Foundation, we
are unfortunately forced to reschedule the webinar
on 28 January featuring David Skuse and William
Mandy. We apologize for the inconvenience.
We will announce a new date for the webinar soon. If
you've already registered for the session, you will be
sent new log-in details automatically once the new
date is confirmed.
David Skuse; William Mandy.
The webinar will feature David Skuse, professor of
behavioral and brain sciences at University College
London, and his colleague William Mandy, senior
lecturer of clinical psychology.
Skuse and Mandy are interested in exploring and
refining the current conventional definitions of autism — specifically how it manifests itself in girls.
They argue that the apparent gender gap often reported in autism is overblown due to fundamental
flaws in the way autism is diagnosed.
During this webinar, they will present evidence to support the notion that the tools available for
diagnosing girls with autism show an inherent gender bias. They will also share interviews with a
former patient to provide specific examples of the ideas they discuss.
Here’s how the presenters describe the session:
For many years, our conceptualization of autism was based on a male stereotype. There was a
widespread consensus that the sex ratio was at least 4-to-1, males predominating, and
epidemiological evidence appeared to support that assumption. An influential theory of autism
susceptibility — that it represents an ‘extreme male brain’ — has subsequently been promulgated
with great success.
This 4-to-1 ratio is not consistent across the full range of intelligence quotients (IQ), however, which
makes the observation hard to understand in terms of genetic susceptibility. No evidence for
X-linked susceptibility has been proven. Females with autism and high IQ are rarely clinically
identified, yet in those with the lowest intellectual functioning, the sex ratio is no more than 2-to-1.
One possible explanation is that our current ascertainment methods for autism are biased toward
males. A corollary of this biased ascertainment hypothesis is that so-called ‘high-functioning’
females with autism are harder to diagnose.
In this webinar, we will discuss the reasons for this bias. There are three significant factors. First,
our standardized measures of autism are derived from historical conventions based on the
stereotypical symptom profile of boys. Second, boys with autism tend to have co-occurring
symptoms and conditions that prompt clinical attention (including attention deficit hyperactivity
disorder and disruptive behavior). Girls with autism, on the other hand, tend to have more subtle
related symptoms (such as social withdrawal, depression and anxiety), so their underlying social
communication problems are often overlooked. Third, there is increasing evidence that females with
autism show a greater capacity to ‘mask’ or compensate for their difficulties, and this leads to the
development of compensatory behaviors in those who are intellectually able.
During the session, we will present empirical evidence to support these hypotheses and describe the
female phenotype.
Press policy: The SFARI Webinar Series aims to facilitate the free exchange of ideas among autism
researchers, including discussion of published and unpublished research, hypotheses and results.
Members of the press may report information presented during a SFARI webinar only if that
material has already been published elsewhere or they have first obtained express written consent
from the presenter.
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News and Opinion articles on SFARI.org are editorially independent of the Simons
Foundation.
Lecture: One brain, many genomes
Due to the winter weather emergency affecting the northeastern U.S. this
week and its potential effect on operational resources at the Simons
Foundation, we are unfortunately forced to reschedule the lecture on 28
January featuring Christopher Walsh. We apologize for the inconvenience.
We will announce a new date for the lecture soon.
About the lecture:
Christopher Walsh and his team are interested in genetic mechanisms
underlying the development of the cerebral cortex and abnormalities in this development resulting in
intellectual disability, autism and epilepsy. The lab pioneered the analysis of recessive causes of
autism by studying children with autism whose parents share ancestry.
Walsh will review recent work on ‘somatic mutations’ — de novo mutations that are present in only
some brain cells but not in all cells of the body — in several neurological conditions associated with
intellectual disability and seizures. His talk will cover the extent to which somatic mutations are an
inevitable part of normal brain development, such that the neurons in the human brain are a tapestry
of cells with distinct genomes. He will briefly discuss the possible relevance of somatic mutations to
autism.
About the speaker:
Christopher A. Walsh is chief of the genetics and genomics division at Boston Children's Hospital,
Bullard Professor of Pediatrics and Neurology at Harvard Medical School, and an investigator at the
Howard Hughes Medical Institute. He completed his M.D. and Ph.D. at the University of Chicago,
trained in neurology at Massachusetts General Hospital and has worked at Boston Children’s Hospital
since 2006.