Brain chimeroids offer window into relationships between genetics and exposures

Researchers at the Harvard Department of Stem Cell and Regenerative Biology (HSCRB) and the Broad Institute of MIT and Harvard have developed a new platform for modeling at the cellular level how the human brain responds to a variety of stimuli. Described in Nature, these ‘brain chimeroids’ provide an approach for studying how genetic background can affect the outcome of neurotoxic exposures, disease-associated genetic variants, and potential therapeutic compounds. 

Chimeroids are brain organoids made up of cells representing multiple cell types found in the human brain (neurons, glial cells, etc.), derived from induced pluripotent stem cells generated from several human donors. By incorporating cells from many individuals, chimeroids allow researchers to observe in vitro how cells and brain circuits from individuals with unique genetic backgrounds, including those with family histories of neurodevelopmental or neuropsychiatric disorders, respond to the same stimulus. 

People carry a vast reservoir of genetic variation; any two individuals differ from each other at about one base pair out of every 1,000 across the three billion-base pair genome. Risk for conditions like schizophrenia or autism spectrum disorder (ASD) often arises from the complex interplay of many genetic variations, rather than from variations in a single gene. By incorporating large numbers of individuals across a spectrum of polygenic risk, chimeroids allow researchers to leverage this genetic diversity to understand its functional effects on the brain.

"The idea of generating organoids that contain cells from multiple donors was directly motivated by our long-term interest in modeling psychiatric conditions, such as schizophrenia, and developmental disorders, such as autism spectrum disorder," said senior author Paola Arlotta, chair of HSCRB and an institute member in the Stanley Center for Psychiatric Research at Broad. "The ability to grow cells from distinct donors within the same organoid opens the door to investigating at scale and in a controlled way the responses of brain cells of many different individuals to many different types of stimuli, from genetic mutations, to infections, to drugs, and more."

Embracing variation

Brain chimeroids build on a decade of research by the Arlotta lab, which has pioneered the use of human organoids to study neuropsychiatric disorders. The process of creating a chimeroid involves several steps. First, pluripotent stem cells — which can be generated from any donor (healthy or patient) — from multiple people are differentiated in individual 3D cultures and coaxed to become neural progenitors, particularly those of a brain cortical fate. Next, the cells are removed from culture, disassociated from each other, and reassembled.

The resulting 3D chimeroids are composed of multiple brain cell types from multiple donors, each contributing to the overall structure. The researchers used cells from five different donors for this study, but the platform is designed to be flexible and scalable, potentially accommodating hundreds of donors in future studies.

"In this context, the goal was to develop a way of looking at different cells of the brain that are affected by a trigger in a more scalable way and develop a platform to read solid responses in these different cells," said Irene Faravelli, a postdoctoral researcher in the Arlotta lab and co-first author of the study with postdoctoral fellow Noelia Antón-Bolaños.

The development of chimeroids was not without its challenges, such as ensuring that the cells from different donors maintained a balanced proportion over time. "A major technical challenge was that single donors would take over the culture over time, even if mixes were donor-balanced initially," Antón-Bolaños recalled. Overcoming this challenge required a deep understanding of embryonic brain development and innovative computational analysis techniques.

Putting exposure in context

To test their system, the team exposed chimeroids to two compounds with well-known neurotoxic effects in the developing brain: ethanol and valproic acid. Ethanol exposure during pregnancy can lead to fetal alcohol spectrum disorder, while valproic acid (VPA), a drug used to treat mood disorders and seizures, has been linked to an increased risk of ASD. Clinicians have long noted that not all children exposed to these compounds experience the same outcomes, suggesting that genetic variations may influence susceptibility.  

Using a transcriptomic readout, which allows researchers to explore cells' molecular responses to stimuli, the team identified significant changes in the cell type composition of ethanol- or VPA-exposed chimeroids compared to unexposed controls. They also found that the proportion of cells from specific donors changed within exposed organoids, as did the gene expression profiles of cells from different donors in response to VPA. 

The team believes chimeroids may accelerate the study of complex polygenic states associated with psychiatric disorders like schizophrenia and ASD, or could enable prediction of responses to new therapeutics, which could have significant implications for personalized medicine. This could lead to more accurate preclinical trials and better predictions of clinical outcomes.

"Success in this area would mean that organoids could become pre-clinical trial 'avatars' informing on the differential responses of the cells of the brain of each individual to begin to predict clinical outcomes," Arlotta said. "What if one day we could use chimeroids as avatars to predict individual responses to new therapeutics before testing it in a trial? Or to stratify and better classify and diagnose patients to tailor more effective therapeutics to them? I like to imagine that future, frankly." 

Adapted from a story published by the Harvard Department of Stem Cell and Regenerative Biology.