Human language

Researchers use miniature 3D models of the human brain to advance understanding of disease

Autism spectrum disorders have been associated with hundreds of different genes, but how these distinct gene mutations converge into similar pathology in patients remains a mystery. Now researchers from Harvard University and the Broad Institute of MIT and Harvard have found that three different autism risk genes actually affect similar aspects of neuronal formation and the same types of neurons in the human brain. in development. By testing for genetic mutations in miniature 3D models of the human brain called “brain organoids”, the researchers identified similar global defects for each risk gene, although each acts through unique underlying molecular mechanisms.

The results, published in the journal Nature, give researchers a better understanding of autism spectrum disorders and are a first step towards finding treatments for the disease.

“Much effort in the field is devoted to understanding whether there are commonalities among the many risk genes associated with autism. The discovery of such shared characteristics may highlight common targets for broad therapeutic intervention, regardless of the genetic origin of the disease, indeed converge to affect the same cells and developmental processes, but through distinct mechanisms. These findings encourage future research into therapeutic approaches aimed at modulating shared dysfunctional brain properties,” said said study lead author Paola Arlotta, who is the Golub Family Professor of Stem Cells and Regenerative Biology at Harvard University and Fellow of the Stanley Center for Psychiatric Research at the Broad Institute.

The Arlotta lab focuses on organoid models of the human cerebral cortex, the part of the brain responsible for cognition, perception, and language. The models start out as stem cells and then grow into 3D tissue that contains many types of cortical cells, including neurons that can fire and connect to circuits. “In 2019, we published a method for producing organoids with the unique ability to grow reproducibly. They consistently form the same cell types, in the same order, as the developing human cerebral cortex,” said Silvia Velasco, a senior postdoctoral fellow at the Arlotta lab and co-lead author of the new study. “It is a dream come true to now see that organoids can be used to discover something unexpected and very new about a disease as complex as autism.”

In the new study, the researchers generated organoids with a mutation in one of three autism risk genes, which are named SUV420H1, ARID1Band CHD8. “We decided to start with three genes that have a very broad hypothetical function. They don’t have a clear function that could easily explain what happens in autism spectrum disorders, so we were interested in seeing if these genes did sort of similar things,” said Bruna Paulsen, postdoctoral fellow at the Arlotta lab and co-lead author.

The researchers developed the organoids over several months, closely modeling the progressive stages in the formation of the human cerebral cortex. They then analyzed the organoids using several technologies: single-cell RNA sequencing and single-cell ATAC sequencing to measure the changes and regulation of gene expression caused by each disease mutation; proteomics to measure responses in proteins; and calcium imaging to check whether the molecular changes translated into abnormal activity of neurons and their networks.

“This study was only possible through the collaboration of several laboratories that came together, each with their own expertise, to attack a complex problem from multiple angles,” said co-author Joshua Levin, a scientist at the institute at the Stanley Center and the Klarman Cell. Observatory at the Broad Institute.

The researchers found that the risk genes affected all neurons in the same way, speeding up or slowing down neuronal development. In other words, the neurons developed at the wrong time. Moreover, not all cells were affected – rather, the risk genes affected the same two populations of neurons, an inhibitory type called GABAergic neurons and an excitatory type called deep-layer excitatory projection neurons. This pointed to selected cells that might be particular targets in autism.

“The cortex is made in a very orchestrated way: each type of neuron appears at a specific time, and they start to connect very early. If you have cells that are forming too early or too late compared to when they are supposed to doing so, you could change the way circuits are ultimately wired,” said Martina Pigoni, a former postdoctoral fellow at the Arlotta lab and co-lead author.

In addition to testing different risk genes, the researchers also produced organoids using stem cells from different donors. “Our goal was to see how changes in organoids might be affected by an individual’s unique genetic makeup,” said Amanda Kedaigle, Arlotta Lab computational biologist and co-lead author.

Looking at organoids made from different donors, the overall changes in neuronal development were similar, but the level of severity varied between individuals. The effects of risk genes were refined by the rest of the donor genome.

“It is disconcerting how the same autism risk gene mutations often show varying clinical manifestations in patients. We found that different human genomic contexts can modulate the manifestation of disease phenotypes in organoids, suggesting that we may be able to use organoids in the future to untangle these distinct genetic contributions and come closer to a more complete understanding of this complex pathology,” Arlotta said.

“Genetic studies have been extremely successful in identifying genome alterations associated with autism spectrum disorders and other neurodevelopmental disorders. The next difficult step on the road to discovering new treatments is understanding exactly what these mutations do to the developing brain,” Steven said. Hyman, who is Harvard University Emeritus Service Professor of Stem Cells and Regenerative Biology, Director of the Stanley Center at the Broad, and Senior Fellow of the Broad Institute. “By mapping brain circuitry alterations when genetic variations are present, we can take the next tentative step towards better diagnostics and uncover new avenues of therapeutic exploration.”

This research was supported by the Stanley Center for Psychiatric Research, the Broad Institute of MIT and Harvard, the National Institutes of Health (R01-MH112940, P50MH094271, U01MH115727, 1RF1MH123977), Klarman Cell Observatory and the Howard Hughes Medical Institute. One of the cell lines (HUES66 CHD8) was created with support from the Simons Foundation and the National Institutes of Health.