Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons

Abstract

We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Wholetranscriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.

Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism

“…Males and females were similarly affected, consistent with fully penetrant inheritance. While the SRAC patients were of Middle Eastern descent, similar phenotypes have been reported for ACTL6B mutant individuals of French-Canadian, Sicilian, and Finnish descent (29,40,41,44,45). The high penetrance and perfect segregation of mutant alleles with ASD indicate a causal relationship between ACTL6B mutation and autism.…”

“…S1C) (25). Individuals with recessive ASD-like phenotypes linked to biallelic ACTL6B mutations have also been identified in recent case studies (29,40,41). Cumulatively, these findings implicate mutations in ACTL6B as an important cause of recessive autism.…”

“…Recent findings link mutations in nearly every constitutive member of the BAF complex to ASD or intellectual disability (ID), including syndromic forms such as Coffin-Siris and Nicolaides-Baraitser syndromes (16)(17)(18). Implicated subunits include the following (protein/gene): BAF250b/ARID1B, BAF250a/ARID1A, BAF200/ARID2, BCL11A/BCL11A, BRG1/SMARCA4, BRM/ SMARCA2, BAF155/SMARCC1, BAF170/SMARCC2, BAF45a/ PHF10, BAF45d/DPF2 BAF47/SMARCB1, BAF57/SMARCE1, BAF53a/ACTL6A, BAF53b/ACTL6B, BAF60a/SMARCD1, and β-actin/ACTB (17,(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29). BAF mutant forms of ASD share overlapping clinical features such as corpus callosal hypoplasia, epilepsy, ID, lack of speech, craniofacial abnormalities, developmental delays, and fifth-digit shortening (17).…”

A roadmap for neurodevelopmental disease modeling for non-stem cell biologists

“…Variants or mutations that show increased frequency in disease cases but which are still present in controls should be avoided, though these are admittedly important sources of disease causing variation. In our work, we avoid missense mutations (rare variants in genes suspected to cause disease because they are private to the individual being studied) unless there is a measureable effect of the mutation (frameshift to affect RNA or protein for example). Our preference is for modeling small variants that cause stop or frameshift mutations, because these are easier to edit and cause a measurable output in the cell.…”

The npBAF to nBAF Chromatin Switch Regulates Cell Cycle Exit in the Developing Mammalian Cortex

“…Consistent with the diverse roles played by these complexes during neural development, mutations in BAF subunits are frequently associated with neurodevelopmental diseases, including autism spectrum disorders (ASD), intellectual disability (ID), and speech disorders. Mutations in SMARCB1 (encoding BAF47), ARID1a/b (encoding Baf250a/b) or SMARCA4 (encoding Brg1/Brm) cause Coffin-Siris and Nicolaides-Baraitser syndromes [12][13][14][15][16] , while mutations in ACTL6B (encoding BAF53b) cause ASD 17 . Finally, GWAS studies have implicated sequence variation in PBRM1 (encoding BAF180) in exceptional intellectual ability 18,19 .…”