Single-cell Analysis Opens Doors for Targeted Treatment in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a developmental disorder characterized by neurodevelopmental abnormalities that typically begin in early childhood. The 5th edition of the diagnostic and statistical manual of mental disorders (DSM-5) is the gold-standard diagnostic tool in ASD. The DSM-5 outlines impaired social communication and behavioral problems, such as fixated interests and repetitive behaviors, as major manifestations of ASD.

Recent statistics from The Centers for Disease Control and Prevention (CDC) suggest that ASD now affects 1 in 59 children in the US, a 15 % increase in prevalence compared to the previous report.

Currently there is no medical cure for ASD, with treatment approaches being purely symptomatic based on our limited understanding of the disorder's molecular pathophysiology. In recent years, research has exploited the technological advances made in the "post-genomic era" to investigate the impact inherited genes may have on ASD susceptibility.

"Autism has a large genetic component, and based on twin studies, the heritability index of autism is around 60 %. Therefore, to understand causes and pathology of autism, genetic studies are important. There are also several genetic conditions where autism is a primary component of the clinical symptoms." says Dmitry Velmeshev, post-doctoral researcher in regenerative medicine at the University of California, San Francisco.  

A single-cell approach

In a study published today in Science , Velmeshev has adopted a single-cell analysis approach to studying the molecular underpinnings of ASD. "Previously, studies looked at bulk gene expression changes in the brain of autism patients using whole-tissue RNA sequencing and microarray," comments Velmeshev.

Unlike these studies, the research group have performed unbiased single-nucleus RNA sequencing of snap-frozen post-mortem brain tissue to analyze the transcriptomes of single brain cells, including neurons and glia.

"Since in the mature brain different cell types and neuronal subtypes have very specific functions and form orderly connections and neuronal circuits, understanding what genes are dysregulated in each cell type is important to both to understand the mechanism of autism and design specific therapies targeting most affected cell types," adds Velmeshev.

The cell nuclei were obtained by lysing thick sections of human cortical tissue that were then isolated by ultracentrifugation. For single-nucleus RNA sequencing, the 10x Genomics platform was adopted. "Single-cell profiling allows for pinpointing of the dysregulation of expression of specific genes to specific cell types and neuronal subtypes, something bulk tissue RNA-seq cannot do." 

A role for cell signaling and neuronal plasticity?

Velmeshev et al generated more than 100,000 single-nuclei gene expression profiles through the analysis, from which they found that the pathways most affected by ASD were those regulating synaptic function, neuronal migration and outgrowth. Particularly, genetic dysregulation of genes expressed in upper-layer projection neurons was discovered, aligning with the behavioral traits observed in ASD patients.

"We saw that synaptic signaling of upper-layer cortical projection neurons was especially affected," Velmeshev says. "These neurons function in the processing of social information, something that is disturbed in ASD." The authors note that trying to normalize synaptic signaling here could be a potential aim of future therapies. 

Aberrant neural plasticity, the brain's ability to change and adapt throughout an organism's life, can lead to a breakdown of the structural connections required for normal cognition and behavior. "We saw dysregulation of genes required for neuronal migration and neural outgrowth, suggesting dysfunctional development of specific neuronal cell types," Velshemev adds. "These genes may be implicated in neuronal plasticity in the adult brain, suggesting that plasticity of specific neuronal subtypes, such as upper cortical-layer neurons, is affected in autism." 

Targeted treatment avenues for ASD

The researchers hope that targeting cellular pathways in specific cell types could lead to improvement of symptoms in a wide variety of ASD patients. "Restoring normal synaptic function of upper-layer neurons by targeting small molecule inhibitors or genetic vectors to these neurons could be a potential targeted treatment," Velmeshev notes.

They also emphasize that it is first important to conduct further research into the convergence of autism pathology in specific cell types, and to analyze genes and cellular pathways affected across heterogenous populations of ASD patients. 

Nonetheless, single-cell analysis certainly looks to be a promising tool for gaining deeper insight into the pathophysiology of disorders for the development of targeted treatments. "There are some recent advances with using viral vectors that cross blood-brain barrier, and those can be potentially modified to also target specific cell types," Velmeshev concludes.

Velmeshev et al. provide their dataset describing transcriptomic and ASD-associated gene expression changes across neuronal and glial cell types in an interactive web browser: https://cells.ucsc.edu/dev/?ds=autism.