Researchers develop new tool to study genes associated with autism spectrum disorder

Researchers have developed a novel technology to analyze the function of different types of genes found in many types of cells in a living organism, at the same time. The team involved scientists from Harvard University, the Broad Institute of MIT and Harvard, and MIT.

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Using the large-scale technique, the researchers investigated dozens of genes that are linked to autism spectrum disorder and found how certain types of cells in the developing mouse brain are affected by mutations.

Published in the Science journal, the “Perturb-Seq” technique provides an efficient approach to detect promising biological mechanisms implicated in autism spectrum disorder. This represents a crucial first step toward designing novel treatments for this complex disorder.

Besides this, the technique is widely relevant to other organs, allowing investigators to better interpret a broad range of diseases and regular processes.

For many years, genetic studies have identified a multitude of risk genes that are associated with the development of autism spectrum disorder. The challenge in the field has been to make the connection between knowing what the genes are, to understanding how the genes actually affect cells and ultimately behavior.”

Paola Arlotta, Study Co-Senior Author and Golub Family Professor of Stem Cell and Regenerative Biology, Harvard University

Arlotta continued, “We applied the Perturb-Seq technology to an intact developing organism for the first time, showing the potential of measuring gene function at scale to better understand a complex disorder.”

The research work was also headed by the study’s co-senior authors Aviv Regev and Feng Zhang. Regev was a former core member of the Broad Institute during the analysis and is presently an Executive Vice President of Genentech Research and Early Development, while Zhang is a core member of the Broad Institute and is also an investigator at the McGovern Institute of MIT.

For large-scale analysis of gene function, the team integrated two robust genomic technologies. They applied CRISPR-Cas9 genome editing to make accurate perturbations, or changes, in as many as 35 different genes associated with the risk of autism spectrum disorder.

Then, using single-cell RNA sequencing, the researchers studied the variations in the developing mouse brain. This single-cell RNA sequencing technique enabled them to observe how the expression of genes changed in more than 40,000 individual cells.

By examining at the level of individual cells, the investigators could compare how different types of cells in the cortex are affected by the multitude of risk genes; the cortex is the part of the brain that accounts for complex functions, like sensation and cognition. The team also investigated networks of risk genes collectively to identify the common effects.

“We found that both neurons and glia—the non-neuronal cells in the brain—are directly affected by different sets of these risk genes,” stated Xin Jin, the study’s lead author and a Junior Fellow of the Harvard Society of Fellows. “Genes and molecules don’t generate cognition per se—they need to impact specific cell types in the brain to do so. We are interested in understanding how these different cell types can contribute to the disorder.”

Therefore, to understand the model’s promising relevance to the human disorder, the team compared their results with the data obtained from post-mortem human brains. Overall, they observed that in the case of post-mortem human brains afflicted with autism spectrum disorder, a few of the major genes with modified expression were also impacted in the Perturb-seq data.

“We now have a really rich dataset that allows us to draw insights, and we're still learning a lot about it every day,” added Jin. “As we move forward with studying disease mechanisms in more depth, we can focus on the cell types that may be really important.”

The field has been limited by the sheer time and effort that it takes to make one model at a time to test the function of single genes. Now, we have shown the potential of studying gene function in a developing organism in a scalable way, which is an exciting first step to understanding the mechanisms that lead to autism spectrum disorder and other complex psychiatric conditions, and to eventually develop treatments for these devastating conditions.”

Paola Arlotta, Study Co-Senior Author and Golub Family Professor of Stem Cell and Regenerative Biology, Harvard University

Arlotta is also an institute member of the Broad Institute and part of the Stanley Center for Psychiatric Research at the same institute.

Arlotta continued, “Our work also paves the way for Perturb-Seq to be applied to organs beyond the brain, to enable scientists to better understand the development or function of different tissue types, as well as pathological conditions.”

Through genome sequencing efforts, a very large number of genes have been identified that, when mutated, are associated with human diseases. Traditionally, understanding the role of these genes would involve in-depth studies of each gene individually. By developing Perturb-seq for in vivo applications, we can start to screen all of these genes in animal models in a much more efficient manner, enabling us to understand mechanistically how mutations in these genes can lead to disease.”

Feng Zhang, Investigator, McGovern Institute, MIT

Zhang is also the James and Patricia Poitras Professor of Neuroscience at MIT and a professor of brain and cognitive sciences and biological engineering at the same institute.