A recent study published in Nature suggests that a specific genetic sequence, which does not produce proteins, plays a significant role in the core behavioral features of autism in males. By examining human genetics alongside genetically altered mice, scientists found that missing sections of this genetic material lead to social difficulties and repetitive behaviors without affecting general intelligence. These findings provide evidence that targeting specific brain circuits might eventually help support individuals with autism.
Autism spectrum disorder presents with primary characteristics like differences in social communication and repetitive behaviors. Roughly one in 50 children and youth in Canada have the condition. Despite the diverse ways people experience autism, changes in social interaction and repetitive actions are common across the spectrum. Many individuals with autism also experience additional conditions, such as intellectual disability or attention issues.
Separating the biology of core autism traits from these other conditions remains a significant challenge in genetics. Most known genetic variations linked to autism encode proteins and tend to influence broad brain development, making it hard to pinpoint what drives specific social and repetitive behaviors. A large international research team led by scientists at The Hospital for Sick Children, or SickKids, in Toronto initiated this project to study a specific genetic region on the X chromosome known as PTCHD1-AS.
This genetic region produces long non-coding ribonucleic acid, commonly known as RNA. Unlike typical genes that provide instructions for making proteins, long non-coding RNA molecules act as functional regulators within the cell. By interacting with other genes and cellular machinery, they help control how and when other genetic instructions are turned on or off. Researchers targeted PTCHD1-AS because it sits in a region close to other protein-coding genes that together have been linked to autism and intellectual disability.
“PTCHD1-AS gives us a new entry point to study the biology of ASD, sharpening our understanding of how specific biological pathways relate to key autism traits,” says Stephen Scherer, senior scientist of genetics and genome biology and chief of research at SickKids, and director of the McLaughlin Centre at the University of Toronto. “This is essential, because no new therapeutics in clinical trials are designed to modulate the main features of ASD.”
To begin their research, the scientists analyzed whole-genome sequencing data from more than 9,300 individuals in global databases. They identified 27 male individuals with autism from 23 unrelated families who were missing small pieces of DNA in the PTCHD1-AS gene. The scientists focused on males because the gene is located on the X chromosome, and females possess a backup X chromosome that provides protection. Statistical analysis indicated that these missing segments increased the odds of an autism diagnosis by more than two and a half times.
Notably, clinical records for these specific individuals showed fewer instances of intellectual disability or attention issues compared to the general autism population. When the researchers expanded their view to a broader group of 118 individuals with neurodevelopmental disorders, they found that those with PTCHD1-AS deletions predominantly exhibited core autism traits. This clinical profile provided evidence that the PTCHD1-AS region might specifically govern the core social and repetitive traits of autism.
To understand how this genetic deletion works in the brain, the scientists created two distinct genetically modified mouse models. In both models, they used gene-editing tools to delete a specific segment of the mouse equivalent of the PTCHD1-AS gene. They then subjected these male mice, along with genetically typical control mice, to a variety of behavioral and physiological tests.
The behavioral assessments revealed that the genetically modified mice engaged in significantly less social interaction. In a standard test using a three-chambered enclosure, these mice showed equal interest in a lifeless object as they did in another live mouse. They also spent significantly more time engaged in repetitive self-grooming compared to control mice.
The scientists also tested how the mice reacted to social odors, which rodents rely on heavily for communication. Typical mice will intensely sniff a new scent, like the urine of another mouse, and then lose interest over time. The genetically modified mice showed very little interest in new social odors and failed to adapt to them, indicating limited social responsiveness.
To assess communication, the researchers recorded the high-frequency sounds that mice make to each other. The mice missing the genetic segment produced fewer distinct vocalizations and communicated less intensely. At the same time, the researchers tested the mice on memory and complex learning tasks. The genetically modified mice performed just as well as the control mice on tasks involving navigating a puzzle box and remembering spatial cues.
“Our findings suggest there is a different biology involved with our PTCHD1-AS model compared to other ASD protein-coding models,” says Lisa Bradley, first author and research associate in The Centre for Applied Genomics at SickKids. This behavioral profile in mice perfectly mirrored the human data. It suggests that the PTCHD1-AS gene influences social and repetitive behaviors independently of learning and memory.
To see if the brains of these mice developed differently, the researchers scanned 50 mice repeatedly from their early postnatal period into adulthood. They observed subtle developmental differences in specific brain structures, such as the anterior cingulate cortex, and in nerve fiber tracts associated with sensory processing. To find out what was happening inside the cells, the research team examined brain tissue, focusing on an area called the striatum. The striatum is a deep brain structure involved in processing rewards, controlling movement, and regulating habits.
“When we examined gene and protein expression in this area, we saw changes in genes and proteins involved in regulating synaptic plasticity as well as myelination, the process that allows electrical signals to travel faster between neurons,” Bradley says. “This gives us a molecular pattern we can use for future studies into the biological effect of this non-coding gene in the brain.”
The scientists used advanced sequencing techniques to look at the RNA from individual brain cells, allowing them to see exactly which cellular pathways were altered. They discovered that the absence of PTCHD1-AS disrupted the production of molecules responsible for creating myelin. The scientists also found alterations in support cells called astrocytes, suggesting a mild level of brain inflammation specific to the striatum.
The scientists also analyzed thousands of proteins in the brain tissue using mass spectrometry. They found alterations in proteins involved in synaptic plasticity. Synapses are the tiny gaps where nerve cells communicate with one another, and synaptic plasticity refers to the brain’s ability to adapt and fine-tune signals in response to activity. This process is how the brain learns and adapts at a microscopic level.
The researchers measured the electrical activity in slices of the striatum and the hippocampus. In the hippocampus, which handles memory, the electrical activity and plasticity were entirely normal. However, in the striatum, a specific type of synaptic depression, a process that weakens connections between neurons, was significantly enhanced in the genetically modified mice.
“Through a multi-disciplinary approach combining human genetics, mouse models, multi-omics and electrophysiology, we’ve connected a non-coding gene to measurable changes in brain function,” says study co-author Graham Collingridge, senior researcher at the Lunenfeld-Tanenbaum Research Institute at Sinai Health, director of the Tanz Centre for Research in Neurodegenerative Diseases, and professor in the Department of Physiology at the Temerty Faculty of Medicine at the University of Toronto.
“Together, our research helps clarify how unique alterations in synaptic plasticity relate to the core features of autism,” Collingridge adds.
A particular family of enzymes known as conventional protein kinase C was notably reduced in these brain regions. The researchers traced these changes to reduced enzyme activity in a specific brain circuit connecting the cortex to the striatum. When the researchers chemically blocked these enzymes in normal mice, their brain tissue behaved exactly like the tissue from the genetically modified mice. This confirmed that the genetic deletion was actively changing how striatal neurons communicate.
While these findings are highly detailed, it is important to avoid misinterpreting the results as a universal explanation for autism. The PTCHD1-AS deletion accounts for only a small fraction of autism cases globally. Animal models also cannot perfectly replicate the complexities of human neurodevelopment or human social experiences. The study focuses exclusively on male individuals and male mice, meaning the exact role of this genetic region in females remains unaddressed.
The research team notes that by linking a specific gene and biological pathway to social and repetitive behaviors, these findings may be relevant across all autism diagnoses, regardless of clinical complexity. Future research will need to explore how these striatal circuits interact with other brain regions during early development. The next steps for the researchers include deeper investigation of the molecular, cellular, and circuit-level pathways influenced by PTCHD1-AS. By identifying potential targets driving those core features of autism, the scientists hope to inform future precision therapeutics for those who seek them.
Scherer, who is also a professor in the Department of Molecular Genetics at the Temerty Faculty of Medicine at the University of Toronto, notes the broader implications of the findings. “Beyond significantly advancing our understanding of autism as a human condition, the study shows how small changes in DNA can influence complex human behavior,” Scherer says. “It’s amazing to me how much of our disposition is genetically ‘hardwired,’ even in the traits that shape how we connect and interact.”
Scientific efforts of this scale require extensive backing from public and private institutions. The research received funding from multiple organizations, including Autism Speaks, the Autism Science Foundation, the Canada Foundation for Innovation, the Canadian Institutes of Health Research, Genome Canada, Ontario Genomics, the Government of Ontario, the Ontario Brain Institute, the Province of Ontario Neurodevelopment Disorders Network, the Simons Foundation Autism Research Initiative, the University of Toronto McLaughlin Centre, and the SickKids Foundation.
The study, “An X-linked long non-coding RNA, PTCHD1-AS, and the core features of autism,” was authored by Clarrisa A. Bradley, Sangyoon Y. Ko, Meng Tian, Liam T. Ralph, Lia D’Abate, Jinyeol Lee, Tianyi Liu, Junhui Wang, Patrick Tidball, Marla Mendes, Xiaolian Fan, Jennifer L. Howe, Roumiana Alexandrova, Giovanna Pellecchia, Guillermo Casallo, Tara Paton, Leanne E. Wybenga-Groot, Worrawat Engchuan, Bhooma Thiruvahindrapuram, Brett Trost, Jill de Rijke, Ashish Kadia, Fuzi Jin, Nelson Bautista Salazar, J. Javier Diaz-Mejia, Jeffrey R. MacDonald, Eric Deneault, P. Joel Ross, James Ellis, Carole Shum, John Georgiou, Olivia Rennie, Miriam S. Reuter, Ny Hoang, Ege Sarikaya, Thanuja Selvanayagam, Aeen Ebrahim Amini, Annabel Rutherford, Natalia Rivera-Alfaro, Christian R. Marshall, Marcello Scala, Cassandra K. Runke, Hutton M. Kearney, John Christodoulou, David I. Francis, Brian H. Y. Chung, Jill Pluciniczak, Alana Iaboni, Kristen M. Wigby, Christine W. Nordahl, David G. Amaral, Melissa L. Hudson, Calvin P. Sjaarda, Andrea Guerin, Mayada Elsabbagh, Rebecca Landa, Seema Mital, Robert Lesurf, Anjali Jain, Michael D. Wilson, Jacob Ellegood, Jason P. Lerch, Leo J. Lee, Brendan J. Frey, Michael W. Salter, Jacob A. S. Vorstman, Evdokia Anagnostou, Paul W. Frankland, Graham L. Collingridge & Stephen W. Scherer.
