Breakthrough Discovery: CHOOSE System Reveals Autism Insights

In a significant leap forward for autism research, the CHOOSE system, developed by researchers from IMBA and ETH Zurich, has unveiled a profound understanding of autism’s genetic basis. This cutting-edge technology allows for an in-depth examination of genetic mutations within human brain organoids, offering unprecedented insights into the underlying mechanisms of autism and expanding its potential applications in disease research.

The CHOOSE system, an innovative fusion of brain organoids and genetics, is revolutionizing autism research by enabling detailed analysis of mutations and their impact on brain development.

Does the human brain possess a vulnerability that ultimately leads to autism? Thanks to this groundbreaking system, which combines brain organoid technology with intricate genetics, researchers can now comprehensively assess the effects of multiple mutations simultaneously and at the single-cell level within human brain organoids.

This technology, pioneered by scientists from the Knoblich group at the Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences and the Treutlein group at ETH Zurich, allows for the identification of susceptible cell types and gene regulatory networks that underlie autism spectrum disorders. This innovative approach brings a ray of hope to the field of autism clinical research.

Human Brain Development and ASD Risks

Compared to other species, the human brain exhibits unique characteristics. Human brain development relies on distinct processes that result in a complex, interconnected cortex. While these processes are unique to humans, they also render neurodevelopmental disorders, like autism spectrum disorder (ASD), more likely.

For instance, many genes associated with a high risk of developing ASD are essential for cortex development. Despite clinical evidence linking multiple genetic mutations to autism, the precise mechanisms through which these mutations affect brain development remain elusive. Due to the distinct nature of human brain development, animal models offer limited insights.

“As IMBA Scientific Director Jürgen Knoblich, one of the study’s corresponding authors, aptly puts it, ‘Only a human model of the brain can recapitulate the complexity and particularities of the human brain.'”

Innovative CHOOSE System for Genetic Screening

To unravel this enigma, researchers from IMBA and ETH Zurich, under the leadership of Jürgen Knoblich and Barbara Treutlein, developed a technique to screen a comprehensive set of key transcriptional regulator genes associated with autism. This development is particularly impactful as it allows for the simultaneous examination of genes of interest within a single mosaic organoid, heralding an era of intricate, efficient, and rapid genetic screening in human tissue.

In the newly established system, known as “CHOOSE” (CRISPR-human organoids-scRNA-seq), each cell within the organoid carries at most one mutation in a specific ASD gene. Researchers can trace the effect of each mutation at the single-cell level and chart the developmental trajectory of each cell.

Chong Li, a postdoctoral fellow in the Knoblich group and the study’s first and co-corresponding author, explains, “With this high-throughput methodology, we can systematically inactivate a list of disease-causing genes. As the organoids carrying these mutations grow, we analyze the effect of each mutation on the development of each cell type.”

A High-Throughput Systematic Approach

The CHOOSE system propels research on disease-causing genes by a substantial leap, offering researchers a versatile and high-throughput method applicable to any disease and human model system. Importantly, CHOOSE significantly accelerates the analysis compared to traditional genetic loss-of-function methods.

Knoblich emphasizes, “We can observe the consequences of every mutation in one experiment, drastically shortening the analysis time compared to traditional methods. This approach, which was previously only possible in organisms like the fruit fly, allows us to leverage a century of scientific literature on disease-causing genes.”

Simultaneously mutating several genes and tracking their effects generates vast amounts of data. To decipher this complex dataset, Barbara Treutlein, the co-corresponding author, and her team at ETH Zurich employ quantitative bioinformatics and machine learning approaches.

“Using this high-throughput single-cell expression data, we can quantify changes in cell type abundance due to a given mutation and identify sets of genes affected by each mutation. By comparing across all gene mutations, we can reconstruct the phenotypic landscape of these disease-linked genetic perturbations,” Treutlein elaborates.

Learning About Autism During Development

Using the CHOOSE system, researchers discovered that mutations in 36 genes associated with a high risk of autism lead to specific changes in cell types during human brain development. They identified critical transcriptional changes regulated by common networks known as “gene regulatory networks” (GRNs). Li elucidates, “A GRN is a set of molecular regulators that interact to control a specific cell function. We demonstrated that some cell types are more susceptible than others during brain development and identified the networks most vulnerable to autism mutations.”

Knoblich adds, “With this approach, we learned that autism-causing genes share some common molecular mechanisms. However, these mechanisms can result in markedly distinct effects in different cell types.”

Li further notes, “Some cell types are more vulnerable to mutations leading to autism, especially some neural progenitors—the founder cells that generate neurons. This suggests that autism pathology could emerge early during brain development. This underscores the importance of studying specific cell types when researching autism genes.”

To confirm the relevance of these findings to human disorders, researchers collaborated with clinicians from the Medical University of Vienna and generated brain organoids from stem cell samples of two patients with mutations in the same gene associated with autism.

Knoblich states, “The organoids from both patients exhibited developmental defects linked to a specific cell type. We validated these observations by comparing organoid structures with prenatal MRIs of one patient’s brain. This demonstrated a close alignment between organoid data and clinical observations.”

Beyond the Brain and Autism…

In addition to gaining unprecedented insights into the pathology of autism, the researchers emphasize the versatility and applicability of the CHOOSE system. Knoblich highlights, “We anticipate that our technique will find wide application beyond brain organoids in the study of various disease-associated genes.”

With this innovative technique, scientists and clinicians now possess a robust, precisely controlled high-throughput screening tool that significantly reduces analysis time and provides invaluable insights into disease mechanisms.

Reference: “Single-cell brain organoid screening identifies developmental defects in autism” by Chong Li, Jonas Simon Fleck, Catarina Martins-Costa, Thomas R. Burkard, Jan Themann, Marlene Stuempflen, Angela Maria Peer, Ábel Vertesy, Jamie B. Littleboy, Christopher Esk, Ulrich Elling, Gregor Kasprian, Nina S. Corsini, Barbara Treutlein, and Juergen A. Knoblich, published on September 13, 2023, in Nature.
DOI: 10.1038/s41586-023-06473-y

IMBA Scientific Director Jürgen Knoblich also holds the position of Professor in Synthetic Biology at the Medical University of Vienna.

Funding for this research was provided by several organizations, including the Simons Foundation Autism Research Initiative, Austrian Federal Ministry of Education, Science and Research, City of Vienna, Austrian Science Fund, European Research Council, Chan Zuckerberg Initiative, Silicon Valley Community Foundation, Swiss National Science Foundation, National Centre of Competence in Research Molecular Systems Engineering, and the European Molecular Biology Organization.

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More about Autism Genetics

• IMBA (Institute of Molecular Biotechnology)
• ETH Zurich
• Nature Journal Article
• Simons Foundation Autism Research Initiative
• Austrian Federal Ministry of Education, Science and Research
• European Research Council
• Chan Zuckerberg Initiative
• Swiss National Science Foundation
• National Centre of Competence in Research Molecular Systems Engineering
• European Molecular Biology Organization