Human derived 3D brain cultures provide insights into brain size changes in 16p11.2 conditions

People with copy number variations (CNVs) resulting in either deleted or duplicated DNA on chromosome region 16p11.2 have a much higher risk of developing autism spectrum disorder (ASD) and other neurodevelopmental conditions. Typically, people with 16p11.2 deletions have increased head and brain size (macrocephaly), whereas those with 16p11.2 duplications have decreased head and brain size (microcephaly). A recent study by SFARI Investigators Lilia Iakoucheva and Alysson Muotri, which was supported in part by a SFARI Research Award, sheds light on how 16p11.2 CNVs cause changes in brain size during early brain development (Urresti et al., Mol. Psychiatry, 2021).

Critical to this study was the researchers’ use of cortical organoids, a human-based cellular model system. Iakoucheva, Muotri and colleagues created cortical organoids using skin cells from people with both 16p11.2 deletions and 16p11.2 duplications who participate in SFARI’s Simons Searchlight— first converting these skin cells into induced pluripotent stem (iPS) cells and then reprogramming them to become brain cells. These cells were then grown into a three-dimensional structure, allowing the various types of brain cells to develop in a manner that closely resembles that seen in the human fetal brain (Lancaster et al., Nature, 2013).

The study found that cortical organoids developed from people with deletions in 16p11.2 were larger, similar to the larger brain size seen in these people. In contrast, cells from people with 16p11.2 duplications resulted in smaller cortical organoids. Because cortical organoid development happens in a culture dish, the researchers were able to carefully look at what cellular changes were causing these differences in brain size — finding that the development of neurons from their pre-neuron progenitor stage to fully functioning neurons was altered, with deletion cultures making more neurons and duplication cultures less. Looking at RNA and protein differences in these cultures provided further support for these findings and suggested that changes in the amount of 16p11.2 affect how mature neurons function.

The findings also showed that both deletion and duplication of 16p11.2 reduced the ability of neurons to move into their proper location. Similar changes in neuron migration have been seen in other neurodevelopmental disorders such as lissencephaly and periventricular heterotopia. As with those conditions, changes in a particular molecular signaling pathway — RhoA — play a role. The study found that blocking RhoA signaling allowed neurons to now migrate normally in both deletion and duplication cultures.

The findings from this work provide valuable insights into potential molecular and cellular deficits that contribute to the changes in brain size seen in individuals with 16p11.2 deletions and duplications. Importantly, the use of human-derived culture systems means such findings are being examined in the context of relevant human genetic backgrounds. It will be interesting to see what new insights will come through the use of SFARI iPS cell lines developed from participants in Simons Simplex Collection and Simons Searchlight in studies of this and other autism-related disorders.


Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism.

Urresti J., Zhang P., Moran-Losada P., Yu N.-K., Negraes P.D., Trujillo C.A., Antaki D., Amar M., Chau K., Pramod A.B., Diedrich J., Tejwani L., Romero S., Sebat J., Yates J.R. III, Muotri A., Iakoucheva L.

Mol. Psychiatry 26, 7560-7580 (November 29, 2021) PubMed

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