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Loss-of-Function Mutation in BAF Subunit Gene Tied to Recessive Autism

NEW YORK – Loss-of-function mutations affecting the ACTL6B gene cause a recessive form of autism by affecting chromatin repression in nerve cells, a new study has reported.

The ACTL6B gene encodes a subunit of an ATP-dependent chromatin remodeler called BAF that is expressed in neurons. Fourteen BAF subunits have previously been found to be mutated in autism, indicating that it is a major contributor to autism spectrum disorder.

A University of California, San Diego-led team of researchers examined a cohort of patients with recessively inherited autism to home in on a loss-of-function mutation in the ACTL6B gene. Patients with this alteration had destabilized ACTL6B proteins, and, in animal models, this genetic change was associated with underdevelopment of the corpus callosum and autism spectrum disorder-like behaviors. Additionally, mutated ACTL6B protein affected chromatin accessibility and changes in transcription factor activity, as the researchers reported in the Proceedings of the National Academy of Sciences Monday.

"ACTL6B loss is thus an important cause of recessive ASD, with impaired neuron-specific chromatin repression indicated as a potential mechanism," UCSD's Joseph Gleeson and his colleagues wrote in their paper.

The researchers examined a cohort of 135 individuals with autism spectrum disorder from the Simons Recessive Autism cohort who underwent whole-exome sequencing. They compared their exomes to a control group of 256 individuals with a recessive neurodevelopmental disorder, but not autism spectrum disorder. From this they zeroed in on the neuronal BAF complex subunit gene ACTL6B.

The patient variants, they noted, were protein truncating, frameshifting, or missense at highly conserved residues. When expressed in human and mouse cell lines, the researchers found the patient mutations destabilized the ACTL6B protein, which led to the formation of nBAF complexes without that subunit.

The researchers replaced the fly ortholog of the ACTL6B gene with the human wildtype or the mutated human version. Flies with the mutated human version similarly exhibited a loss of function. 

The flies with the mutated human version additionally had reduced perfect dendritic retargeting in which nerve dendritic trees project incorrectly. The researchers suspected this might reflect a feature of BAF-mutated ASD among humans: a reduced or absent corpus callosum, which mediates communication across the two hemispheres of the brain. ACTL6B knock-out mice further have a decreased corpus callosum. 

These mice further exhibited behaviors equivalent to those of humans with autism spectrum disorder, such as reduced social interactions, increased repetitive behaviors, memory impairment, and hyperactivity.

Through a proteomic analysis, the ACTL6B knockout mice appeared to have complete nBAF subunit assembly, though they exhibited reduced interactions with certain proteins. However, instead of forming with the ACTL6B subunit, the researchers found that the complex formed using the highly similar ACTL6A subunit in its place. Though the proteins share 95 percent sequence similarity overall, they differ at a particular subdomain, which affects the proteins with which the complex can interact. In particular, the alteration leads to a decrease in interactions with histone H1, indicating impaired BAF-chromatin interactions as a result of this mutation.

At the same time, an ATAC-seq-based analysis found neurons from ACTL6B knockout mice had more accessible chromatin. This, they reported, led to increased AP1 transcription factor activity in resting neurons and the abnormal expression of early response genes.

Based on these findings and reports regarding a related gene, the researchers wrote that the de-repression mechanism might stem from a functional breakdown of the BAF complex. 

"This is consistent with the fact that BAF mutations cause similar forms of ASD," they added. "We speculate that abnormal AP1 activation may be a common mechanism in BAF mutant ASD."