Recent research published in nature A specific gene sequence that does not produce a protein has been suggested to play an important role in the core behavioral features of autism in men. By examining the genetics of genetically modified mice and humans, scientists discovered that this missing piece of genetic material leads to social difficulties and repetitive behaviors without affecting general intelligence. These findings provide evidence that targeting specific brain circuits may ultimately help people with autism.
Autism spectrum disorders exhibit key characteristics such as differences in social communication and repetitive behaviors. Approximately 1 in 50 children and youth in Canada has this condition. Despite the diversity in how people experience autism, changes in social interactions and repetitive behaviors are common across the spectrum. Many people with autism also experience additional symptoms, such as intellectual disability and attention problems.
Separating the biology of the core traits of autism from these other symptoms remains a significant challenge in genetics. Most of the known genetic variants associated with autism encode proteins and tend to affect a wide range of brain development, making it difficult to determine what causes specific social and repetitive behaviors. A large international research team led by scientists from Toronto’s Hospital for Sick Children (SickKids) initiated this project to study a specific genetic region on the X chromosome known as PTCHD1-AS.
This gene region produces long non-coding ribonucleic acids commonly known as RNA. Unlike typical genes, which provide instructions for making proteins, long non-coding RNA molecules act as functional regulators within cells. By interacting with other genes and cellular machinery, they help control when and how other gene instructions are turned on or off. The researchers targeted PTCHD1-AS because it is located in a region close to other protein-coding genes that have been linked to autism and intellectual disability.
“PTCHD1-AS provides us with a new entry point to study the biology of ASD and deepens our understanding of how specific biological pathways are linked to key traits of autism,” said Stephen Scherer, senior scientist in genetics and genome biology, SickKids principal investigator, and director of the McLaughlin Center at the University of Toronto. “This is essential because new treatments in clinical trials are not designed to modulate the key features of ASD.”
To begin the study, scientists analyzed whole-genome sequence data from more than 9,300 individuals in a global database. They identified 27 autistic men from 23 unrelated families who were missing a small DNA fragment of the PTCHD1-AS gene. Scientists focused on men because this gene is on the X chromosome, and women have a backup X chromosome that provides protection. Statistical analysis showed that these gaps increased the odds of being diagnosed with autism by more than 2.5 times.
Notably, the clinical records of these particular individuals show fewer instances of intellectual disability and attention problems compared to the general autism population. When the researchers expanded their focus to a broader group of 118 people with neurodevelopmental disorders, they found that those with the PTCHD1-AS deletion primarily displayed core autistic features. This clinical profile provided evidence that the PTCHD1-AS region may differentially govern core social and repetitive features of autism.
To understand how this gene deletion functions in the brain, scientists created two different genetically modified mouse models. In both models, we used gene editing tools to delete a specific segment in the mouse that corresponds to the PTCHD1-AS gene. These male mice and genetically typical control mice were then subjected to a variety of behavioral and physiological tests.
Behavioral evaluations revealed that the genetically modified mice had significantly less social interaction. In a standard test using a three-chamber enclosure, these mice showed similar interest in inanimate objects as they did in another living mouse. They also spent significantly more time doing repetitive grooming compared to control mice.
The scientists also tested how mice responded to social scents, which rodents rely heavily on for communication. A typical mouse will intensely sniff a new odor, such as another mouse’s urine, but lose interest over time. Genetically modified mice showed little interest in new social odors, were unable to adapt to them, and showed limited social responses.
To assess communication, the researchers recorded the high-frequency sounds the mice made to each other. Mice lacking the gene segment had fewer distinct vocalizations and were less communicative. At the same time, the researchers tested the mice’s memory and complex learning tasks. The genetically modified mice performed as well as control mice on tasks such as navigating puzzle boxes and remembering spatial cues.
“Our findings suggest that a different biology is involved in our PTCHD1-AS model compared to other ASD protein-coding models,” said Lisa Bradley, first author and research scientist in the Center for Applied Genomics at SickKids. This behavioral profile in mice perfectly mirrored the human data. This suggests that the PTCHD1-AS gene influences social and repetitive behaviors independently of learning and memory.
To see whether the brains of these mice developed differently, the researchers repeatedly scanned 50 mice from early birth until adulthood. They observed subtle developmental differences in specific brain structures, such as the anterior cingulate cortex, and nerve fiber tracts associated with sensory processing. To find out what was going on 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 reward processing, motor control, and habit regulation.
“When we looked at gene and protein expression in this region, we found changes in genes and proteins involved in synaptic plasticity and the regulation of myelination, the process that allows electrical signals to travel faster between neurons,” Bradley says. “This provides molecular patterns that can be used for future studies on the biological effects of this non-coding gene in the brain.”
Scientists used advanced sequencing techniques to examine RNA from individual brain cells, allowing them to see exactly which cellular pathways had changed. They found that the absence of PTCHD1-AS prevents the production of molecules involved in myelin production. The scientists also found changes in supporting cells called astrocytes, suggesting a low-grade brain inflammation specific to the striatum.
The scientists also used mass spectrometry to analyze thousands of proteins in brain tissue. They discovered changes in proteins involved in synaptic plasticity. Synapses are tiny gaps where nerve cells communicate with each other, 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 electrical activity in slices of the striatum and hippocampus. In the hippocampus, which deals with memory, electrical activity and plasticity were completely normal. But in the striatum, a particular type of synaptic inhibition, a process that weakens connections between neurons, was significantly enhanced in genetically modified mice.
“Through a multidisciplinary approach combining human genetics, mouse models, multi-omics and electrophysiology, we linked non-coding genes to measurable changes in brain function,” said study co-author Graham Collingridge. He is a senior researcher at the Lunenfeld-Tannenbaum Research Institute in the Sinai Health Region, director of the Tanz Neurodegenerative Disease Research Center, and professor in the Department of Physiology at the Temerty Faculty of Medicine. University of Toronto.
“Our study helps reveal how unique changes in synaptic plasticity are related to core features of autism,” Collingridge added.
A particular family of enzymes known as classical protein kinase C was markedly reduced in these brain regions. The researchers determined that these changes were a decrease in enzyme activity in specific brain circuits that connect the cortex and striatum. When researchers chemically blocked these enzymes in normal mice, their brain tissue behaved exactly like tissue from genetically engineered mice. This confirms that the gene deletion actively changes the way striatal neurons communicate.
Although these findings are very detailed, it is important not to misinterpret the results as a universal explanation for autism. PTCHD1-AS deletions account for only a small portion of autism cases worldwide. Additionally, animal models cannot fully reproduce the complexity of human neurodevelopment or human social experience. This study focused only on male individuals and male mice, meaning the exact role of this genetic region in females remains unresolved.
The research team notes that by linking specific genes and biological pathways to social and repetitive behaviors, these findings may be relevant to all autism diagnoses, regardless of clinical complexity. Future studies should investigate how these striatal circuits interact with other brain regions early in development. The researchers’ next steps include a deeper investigation of the molecular, cellular, and circuit-level pathways affected by PTCHD1-AS. By identifying potential targets that promote the core features of autism, scientists hope to offer future precision treatments to those seeking them.
Professor Scherer, who is also a professor in the Department of Molecular Genetics at the University of Toronto’s Temerty School of Medicine, points out the broader implications of this finding. “This study not only significantly advances our understanding of autism as a human disease, but also shows how small changes in DNA can influence complex human behavior,” says Professor Scherer. “It’s amazing to me that so much of our temperament is genetically ‘hardwired’, even in the traits that shape the way we connect and interact. ”
A scientific effort of this scale requires extensive support from public and private institutions. The research was funded by multiple organizations, including Autism Speaks, Autism Science Foundation, Canada Foundation for Innovation, Canadian Institutes of Health Research, Genome Canada, Ontario Genomics, the Government of Ontario, Ontario Brain Institute, Ontario Neurodevelopmental Disorders Network, Simons Foundation Autism Research Initiative, University of Toronto McLaughlin Center, and Sick Kids Foundation.
The authors of the study, “X-linked long noncoding RNA, PTCHD1-AS, and core features of autism,” are Clarissa 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, Rumiana Alexandrova, and Giovanna Pellecchia, Guillermo Casaro, Tara Payton, Leanne E. Wibenga Groot, Worawat Entuan, Bhuma Thiruvahindrapuram, Brett Trost, Jill de Rijke, Ashish Kadia, Fuji Jin, Nelson Bautista Salazar, J. Javier Diaz Mejia, Jeffrey R. McDonald, Eric Denault, P. Joel Ross, James Ellis, Carol Shum, John Georgiou, Olivia Rennie, Miriam S. Reuter, Ni Hoang, Ege Sarikaya, Tanuja Selvanayagam, Aeen Ebrahim Amini, Annabelle Rutherford, Natalia Rivera Alf Aro, Christian R. Marshall, Marcello Scala, Cassandra K. Runke, Hutton M. Carney, John Christodoulou, David I. Francis, Brian HY Chan, Jill Prusinichak, Alana Iaboni, Kristen M. Wigbee, Christine W. Nordahl, David G. Amaral, Melissa L. Hudson, Calvin P. Sharda, Andrea Guerin, Mayada Elsabberg, Rebecca Landa, Seema Mittal, Robert Rusaf, Anjali Jain, Michael D. Wilson, Jay Iacob Elgood, Jason P. Lerch, Leo J. Lee, Brendan J. Fry, Michael W. Salter, Jacob A.S. Forstmann, Evdokia Anagnostou, Paul W. Frankland, Graham L. Collingridge, Stephen W. Scherer.
