Annual Report 2020

Highlights of SFARI-Supported Autism Research From 2020

Autism Research Initiative (SFARI)

In 2020, the Simons Foundation Autism Research Initiative (SFARI) supported nearly 300 investigators in the United States and abroad who have pushed forward the frontiers of autism research in many directions. The following are some highlights of SFARI Investigators’ research in the past year.

Representative images of cultured hippocampal (top) and dorsal root ganglion (bottom) neurons expressing the GFP gene alone (left), or with WT-PTEN (middle) or PTEN-C124S (right). Credit: K.L. Post et al./Nature Communications 2020

Spotting harmful missense. Many families and individuals with autism participate in sequencing studies in the hope of receiving a definitive genetic explanation for their condition. Sometimes, this wish is fulfilled: Genetic sequencing uncovers a mutation that clearly sabotages the protein encoded by a known autism risk gene. But other times, only a “missense” mutation in the gene is found — one that switches a single amino acid in the corresponding protein, perhaps destroying the protein’s function, but perhaps not. Missense mutations are thought to underlie many cases of autism, but it’s hard to tell which missense mutations are deleterious and which are benign.

A study led by SFARI Investigator Kurt Haas of the University of British Columbia offers a systematic framework for assessing which missense mutations are likely to be damaging. As they reported on April 29, 2020, in Nature Communications, the researchers examined 106 mutations in the autism risk gene PTEN in five model systems: yeast, roundworms, fruit flies, rats and human cells. The team tested the functional impact of the mutations in a variety of ways, such as by examining larval development in fruit flies and the structure of neurons in rats.

Many of the mutations had harmful impacts, and these impacts tended to correlate across the different organisms. The correlations were especially strong in the case of mutations that weaken the protein’s stability, suggesting that assessing protein stability might be a quick first test for spotting disruptive mutations. The team has since used its testing platform to study missense variants in another autism risk gene, SYNGAP1. As more genes go through this pipeline, the pool of individuals with autism who can receive a conclusive genetic explanation may greatly expand.

Rescuing plasticity. The autism-linked gene SHANK3 is essential to brain plasticity, according to a new study that illuminates the gene’s role in enabling neurons to adjust to changes in sensory input. The study, led by SFARI Investigator Gina Turrigiano of Brandeis University, also found that the mood-stabilizing drug lithium mitigates repetitive behaviors and disruptions to brain plasticity in rats and mice missing SHANK3, which is mutated in about 1 percent of people with autism.

The researchers, who reported their findings in the June 3, 2020, issue of Neuron, disrupted SHANK3 expression in cultured rat neurons, and then temporarily blocked the neurons’ ability to fire. Once the block was removed, the cells failed to return to their normal firing rate, suggesting they were unable to adapt to this change. Lithium restored the neurons’ ability to adjust their firing rates.

The team next glued one eye shut in mice lacking SHANK3 and used multielectrode arrays to study their visual cortex. Neurons in the mutant mice decreased their firing rate more gradually than those in control mice, suggesting that they took longer to adjust to the decrease in visual input. And then, while neurons in the control mice compensated for the loss of vision and resumed firing after a couple of days, neurons in the mutant mice never returned to their original firing rates. 

The mutant mice also groom themselves excessively, but this behavior was eliminated by lithium treatment. The findings imply that lithium may be useful for treating people with SHANK3 mutations. Although lithium is often poorly tolerated, understanding why it works may also open the door to better treatments.

Mutated motion. A machine learning algorithm that breaks down motion into discrete behavioral chunks can tell the difference between control mice and ones with a particular autism-linked mutation, a new study shows. The algorithm was able to identify hyperactivity in the mutated mice, and it also detected how a widely used autism drug affected their motion.

The study, led by SFARI Investigator Sandeep Robert Datta of Harvard University, used MoSeq, an algorithm Datta and his team developed in 2015 to break down motion into discrete “syllables” without human assistance. The researchers, who published their findings on September 21, 2020, in Nature Neuroscience, examined the motion of mice with two mutated copies of the gene CNTNAP2. MoSeq identified 16 motion syllables that are different in these mice than in controls.

The drug risperidone, the team found, restored seven of these syllables to normal, and improved seven others. The researchers also examined the motion of control mice that were given one of 15 different drugs for depression, anxiety, psychosis or other disorders, and found that MoSeq was able to figure out which mice had received which drug. The software might help researchers quickly screen drug candidates to see which ones show promise for alleviating hyperactivity, repetitive movements and other traits linked with autism.

Mapping autism’s genetic terrain. A new genetic analysis of people with autism and their families offers the most expansive view yet of the landscape of autism risk genes, identifying 102 genes strongly associated with autism, including 30 that had not been previously linked to the condition. The study — a large collaborative effort that involved SFARI Investigators Stephan Sanders and Matthew State of the University of California, San Francisco, Bernie Devlin of the University of Pittsburgh, Kathryn Roeder of Carnegie Mellon University, and Michael Talkowski of Harvard University, under the auspices of the Autism Sequencing Consortium — looked at the exomes (the protein-coding regions of the genome) of more than 35,000 individuals from the Simons Simplex Collection and other cohorts, making this the largest exome-sequencing autism study to date.

The researchers, who published their findings in Cell on February 6, 2020, applied an enhanced version of their previously developed statistical method, called TADA, to determine which gene variants are likely to be harmful. The 102 genes that emerged from this analysis tended to cluster in groups that affect gene expression or neuronal communication. In cells from the human cortex, the team found that the expression of these genes is enriched in both excitatory and inhibitory neurons starting in early development. Some lines of research have suggested that autism stems in part from an imbalance between excitatory and inhibitory signaling, and the new study indicates that there may be multiple biological pathways toward this imbalance.

Editing Angelman syndrome. Altering mouse DNA using CRISPR gene-editing technology can prevent many characteristics of the autism-related condition known as Angelman syndrome, researchers reported in Nature on October 21, 2020. The therapy’s benefits lasted for the entire 17 months that the researchers monitored the mice, and may be lifelong.

Angelman syndrome, whose core traits include developmental delays, motor dysfunction and speech impairments, typically results from a mutation blocking the maternal copy of the gene UBE3A. The paternal copy of this gene is normally silent, and treatments that activate this copy in mice can ameliorate some traits of the condition. However, these improvements typically wear off over time.

The new study, led by SFARI Investigator Mark Zylka of the University of North Carolina at Chapel Hill, used the CRISPR-Cas9 gene editing approach to deactivate the RNA molecule that ordinarily silences paternal UBE3A. The therapy, which was delivered to the cortical neurons of embryonic and infant mice in two doses, activated the paternal copy of the gene in 58 percent of cortical neurons. Mice that received the therapy showed improved motor coordination and reduced anxiety and repetitive behaviors.

The researchers also found that the therapy activated paternal UBE3A in cultured human neurons, suggesting that it might be effective in people as well as mice. But the approach is considered risky because it can make unpredictable cuts in DNA. So Zylka’s team next plans to examine alternate versions of CRISPR therapy that can activate paternal UBE3A without cutting DNA, and thus may be safer for human use.