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Organoid Study Sheds Light on How Autism Risk Gene Mutations Affect Brain Development

NEW YORK — Variants in three different genes associated with autism spectrum disorder risk have similar effects on neuronal development, a new organoid-based study has found.

Hundreds of genes have been implicated in autism spectrum disorder but how variants in those genes lead to the condition has been unclear. By developing organoids with mutations in one of three different autism-linked genes — SUV420H1, ARID1B, and CHD8 — researchers from Harvard University and their colleagues have begun to tease out the effects of these alterations on neuronal development.

As they reported on Wednesday in Nature, they found that the effect of mutations in those genes converges on two types of neurons in particular, the inhibitory γ-aminobutyric-acid-releasing (GABAergic) neurons and the deep-layer excitatory projection neurons, though they act on them through different molecular pathways.

"Much effort in the field is dedicated to understanding whether commonalities exist among the many risk genes associated with autism. Finding such shared features may highlight common targets for broad therapeutic intervention, independent from the genetic origin of disease," senior author Paola Arlotta, a professor of stem cell and regenerative biology at Harvard, said in a statement. "[Our] results encourage the future investigation of therapeutic approaches aimed at the modulation of shared dysfunctional brain properties."

The researchers generated organoid models of the human cerebral cortex from different human induced pluripotent stem cell lines and engineered them to harbor heterozygous protein-truncating indels in SUV420H1, ARID1B, or CHD8. They profiled the organoids at various developmental time points using single-cell RNA sequencing and ATAC-sequencing as well as proteomic analyses and calcium imaging. In all, they analyzed more than 745,000 cells.

Alterations in these risk genes shifted the times at which neuronal development occurred in the organoids compared to control organoids. In particular, the researchers found that GABAergic neurons were present earlier in development in organoids with risk variants. At the same time, deep-layer excitatory projection neurons developed more quickly in cortical organoids with alterations in risk genes. An imbalance in excitatory and inhibitory neurons in the cortex has been implicated in autism etiology, the researchers noted.

"The cortex is made in a very orchestrated way: each type of neuron appears at a specific moment, and they start to connect very early. If you have some cells forming too early or too late compared to when they are supposed to, you might be changing the way circuits are ultimately wired," co-first author Martina Pigoni, a former postdoc in the Arlotta lab, said in a statement.

The researchers noted that the genomic context in which these changes were made had an influence, as the severity of the effects differed in organoids derived from different cell lines.

Further, these alterations affected largely different molecular pathways. The researchers compared gene expression changes across the altered organoids to find that while they shared enrichment for gene ontology categories, the differentially expressed genes did not overlap much. Similarly, a proteomic analysis found few overlapping differentially expressed proteins between the organoid lines.

These findings indicated that the three risk genes have similar ultimate effects but act through different pathways and on different proteins.

The next goal will be to better understand the effect of these mutations on the developing brain. "By mapping the alterations in brain circuits when genetic variations are present, we can take the tentative next step in the direction of better diagnoses and uncover new avenues for therapeutic exploration," said Steven Hyman, who was not involved in the study, but who is the director of the Broad's Stanley Center where the research took place.