Two large-scale studies provide new data on genes, inherited variations, and de novo mutations associated with autism spectrum disorder (ASD). Some of them are also associated with other neurological conditions, like developmental delay (DD), or schizophrenia.

In the biggest analysis to date, involving 150,000 people, scientists identified 252 genes, 72 strongly linked to ASD. In a parallel study of 42,600 ASD cases, researchers found 60 significant genes and 5 new risk genes. These results were reported in two simultaneous articles published in the August 18, 2022, issue of Nature Genetics.

The large number of genes found in the first study and their overlap with intellectual disability is not a surprise. It reinforces the idea that autism and DD syndromes be included in a single biological pathway.

"Like in other medical disciplines, psychiatry will need to adopt a precision medicine approach, a treatment that is specifically tailored to the biology in each individual," co-senior author Joseph Buxbaum told BioWorld Science. Buxbaum is the director of the Seaver Autism Center for Research and Treatment and professor at the Icahn School of Medicine at Mount Sinai.

Genetic studies of ASD are based on whole exome sequencing (WES), whole genome sequencing (WGS) or genome-wide genotyping association techniques. In 2020, the MSSNG project conducted the largest WES study, analyzing the exome of 35,584 people (11,986 with ASD). They identified 102 risk genes. Previously, the Simons Foundation Powering Autism Research for Knowledge (SPARK) reported 26 ASD risk genes in a 2019 study with 27,615 individuals (genome-wide genotyping and WES) and 457 families (WGS).

Many of these genes were previously known, but their rare variants, or those that could explain the enormous variety of phenotypes associated with ASD, were not. To discover those, scientists needed precise methods and larger samples.

The necessary resolution to identify altered genes came from the analysis of protein-truncating variants, missense variants, and copy number variants. The large sample came from different consortia.

While DD genes are expressed in immature neurons, ASD genes are strongly expressed in mature excitatory neurons. The earlier and more widely one of these genes is expressed in these cells, "the more likely is there to be extensive impact on behavior and, broadly on development," Buxbaum explained.

Many of these genes affect more than one organ. "On average, genes that impact multiple aspects of brain and body development and function are going to be expressed earlier and more broadly and not just in mature or maturing neurons," he said. These differences will help to understand the social communication challenges and repetitive behaviors of autism.

In the inheritance of ASD, each common variant adds a small effect and explains 50% of cases. Rare or de novo variants represent 10% of high-risk factors. ASD severity and gender are associated with carrying certain mutations, as this study showed.

The thin line between ASD, DD and schizophrenia genes

Of the 72 ASD genes the team identified, 61 were related to DD and 8 to schizophrenia. However, only 3 of the 82 predominant genes in DD are associated with schizophrenia.

A subset of ASD risk genes may overlap with DD, while a different subset overlaps with schizophrenia. Scientists must now delve into these genes since different mutations of the same gene could lead to a different clinical outcome.

While other laboratories analyzed the 72 genes, researchers at the Seaver Autism Center studied the ARID1B gene in human stem cells. They found that certain ARID1B mutations are associated with ASD and others increase the risk of intellectual disability and DD.

Their project opens three paths for future research. Buxbaum furthers knowledge of the ADNP, DDX3X, FOXP1 and SHANK3 gene mutations with clinical and mouse studies. He also uses human neurons from patient-derived and CRISPR-engineered stem cells. "These studies are providing insights into these rare genetic conditions and are also paving a way for therapies specifically targeting deficits caused by mutations in these genes," he commented.

The second line would focus on the convergent genetic pathways in ASD applying high-throughput CRISPR gene editing techniques to reduce the number of pathways. This could simplify the approaches to treatment.

The third line could aim to discover more genes by integrating noncoding changes and their risk for ASD, already shown in this study for the plexin A1 gene (PLXNA1).

"Another area of immediate focus is on chromosome X. Because of its unique nature, there are many boys with autism and/or intellectual disability and/or DD that inherit the genetic variant that contributes to risk. Mutations that are inherited are going to be harder to detect", Buxbaum added. This issue could be addressed with the high sample sizes now being evaluated.

SPARK identifies five new moderate ASD genes

The second study provided new WES data from the SPARK project to determine inherited and de novo variants. It was led by Wendy Chung, director of Clinical Genetics and professor of Pediatrics and Medicine at Columbia University. Her team cites 60 genes and includes five new risk genes (NAV3, ITSN1, MARK2, SCAF1 and HNRNPUL2).

"For the first time, we systematically identified autism genes (at exome-wide significance) with inherited variants of moderate risk," Chung said. "These variants are rare in the population but are present in people with autism at levels higher than would be expected by chance. These variants do not always lead to autism; hence we refer to them as variants of moderate risk."

Chung described six archetypes that represent important biological processes in autism (neurotransmission, chromatin modification, RNA processing, vesicle-mediated transport, MAPK signaling and migration, and cytoskeleton and mitosis).

The NAV3 gene, expressed in the inner cortical plate of the developing cortex, is associated with the cytoskeleton and mitosis archetype. ITSN1, to the vesicle-mediated transport. SCAF1, MARK2 and HNRNPUL2 are mixtures of the identified archetypes, suggesting that these genes may function in potentially novel processes in autism.

These genes represent rare hereditary loss-of-function (LoF) variants that provide a moderate effect, with less cognitive impairment compared to autistic individuals with LoF variants in highly penetrant genes.

Rare, LoF inherited variants of moderate risk contribute to at least a similar amount of autism cases as de novo variants of strong effect, Chung said. This means that there are inherited variants and genes that harbor LoF inherited variants of moderate risk left to be discovered.

To discover new moderate-risk genes and understand the high heritability of ASD, Chung believes that SPARK needs at least a sample of 100,000 people with ASD. The recruitment has already started, including Afro-American, Asian-American and Pacific Islander communities