In recent decades, the zebrafish has become one of the most valuable model organisms in scientific research. For a variety of reasons, including their genetic similarities to humans, these tiny tropical fish have helped researchers unlock secrets to diseases ranging from muscular dystrophy to melanoma.
Now, Yale researchers are hoping the zebrafish will do the same for autism spectrum disorder.
In a new study, a research team generated a database of 520 U.S. Food and Drug Administration (FDA)-approved drugs and their effects on basic larval zebrafish behaviors and then used the database to identify drug candidates that reverse disrupted behaviors in zebrafish carrying mutations in autism risk genes.
These drug candidates, the researchers say, might represent targets for people carrying mutations in specific autism risk genes.
“Because autism spectrum disorder is highly clinically and genetically heterogeneous, it is challenging to identify drug candidates and many new drugs under investigation are not effective in clinical trials,” said Ellen J. Hoffman, an associate professor at the Yale Child Study Center at Yale School of Medicine (YSM) and senior author of the new study.
“Our study highlights the importance of stratifying or subgrouping autism risk genes to identify potential drug candidates using a precision medicine-based approach.”
The study appears in the journal Proceedings of the National Academy of Sciences.
Scientists have identified more than 100 genes that are strongly associated with autism. Research has shown that these genes impact fundamental biological processes in the developing brain, such as neuronal communication and regulating the expression of other genes. Researchers have struggled to identify pharmacological candidates related to autism, however, due to the limited understanding of the underlying biology of autism as well as its considerable clinical and genetic heterogeneity.
But zebrafish offer many advantages for studying the function of autism risk genes in the developing brain and identifying novel drug candidates. Zebrafish have a genetic profile that’s remarkably similar to that of humans. They’re also easy to manipulate genetically, so it’s possible to disrupt the function of multiple autism risk genes simultaneously; they produce large numbers of offspring at a time; and larval zebrafish are easy to work with in the lab, which makes them amenable to large-scale pharmacological screens.
In previous research, Hoffman and her fellow researchers identified how disrupting 10 different autism risk genes in zebrafish affected basic sleep and sensory processing behaviors. For the new study, they sought to leverage these behavioral “fingerprints” to predict and test specific drugs that “rescue” or reverse the dysregulated behaviors in zebrafish carrying mutations in specific autism risk genes.
The researchers first screened a total of 774 U.S. FDA-approved drugs using automated assays of basic sleep and sensory processing behaviors in “wild-type” larval zebrafish that don’t carry any mutations. Using statistical models, they generated a database of 520 drugs that weren’t toxic and had significant effects on zebrafish behavior.
Then they compared the behavioral fingerprints of zebrafish carrying mutations in autism risk genes to the drug behavioral fingerprints using a method called pharmaco-behavioral profiling. This allowed them to identify and screen drug candidates predicted to rescue or reverse dysregulated behaviors in zebrafish carrying mutations in two autism risk genes, SCN2A and DYRK1A .
Through their methods, the researchers revealed three major findings. First, they identified drug candidates that rescue dysregulated sleep and sensory processing behaviors associated with specific autism risk genes. These drug candidates showed central pathways relevant to these autism risk genes, including estrogens, microtubules, mitochondria, and lipid metabolism.
Second, they found that the drug levocarnitine — which transports long-chain fatty acids into mitochondria — is a top rescue drug for two genes, SCN2A and DYRK1A , and showed that it rescues dysregulated behaviors, lipid metabolic pathways, and regional differences in baseline brain activity in zebrafish. They also found that levocarnitine rescues network activity deficits in human pluripotent stem cell (hPSC)-derived glutamatergic (excitatory) neurons carrying mutations in these genes (pluripotent refers to the ability to give rise to several different cell types).
Third, based on information about the 520 U.S. FDA-approved drugs, the researchers generated a database that can be used to identify new drug candidates relevant to autism risk genes. And they created an open-source, searchable website with the behavioral profiles of all 774 drugs screened, which they hope will facilitate drug discovery across different systems and platforms.
“Our findings lay the groundwork for investigating these drug mechanisms as potential targets for individuals carrying mutations in select autism risk genes,” Hoffman said. “We can use our pharmaco-behavioral screening approach to identify new drug candidates for a growing number of autism risk genes.”
The research team also includes co-senior author Zuoheng Anita Wang, professor of biostatistics at Yale School of Public Health (YSPH); Kristen Brennand, the Elizabeth Mears and House Jameson Professor of Psychiatry at YSM; Priyanka Jamadagni, postdoctoral associate at the Child Study Center; Yi Dai, a Ph.D. candidate at YSPH; Yunqing Liu, a Ph.D. graduate of YSPH; and Hellen Weinschutz Mendes, a postdoctoral associate at the Child Study Center.
This work was supported by the National Institutes of Health, the Binational Science Foundation, the National Genetics Foundation, the Simons Foundation, the Spector Fund, the Swebilius Foundation, the Kavli Foundation, the Howard Hughes Medical Institute Gilliam Fellowship, the Autism Science Foundation, the National Institute of Mental Health and National Institutes of Health Medical Scientist Training Program, and the Interdepartmental Neuroscience Program at Yale.