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Gene Expression Study Points to Common Transcription Shifts in Autistic Brains

By Andrea Anderson

NEW YORK (GenomeWeb News) – Autism may be associated with shared gene expression patterns in the brain despite its diverse genetic underpinnings, according to a study appearing online today in Nature.

Researchers from the US, UK, and Canada did microarray analyses and RNA sequencing of post-mortem brain tissue donated by dozens of individuals with or without autism. Although autism spectrum disorders are known to stem from a range of genetic glitches, findings from the new transcriptomic analyses point to some shared shifts in expression patterns in certain parts of the brain in those with ASD.

Along with sets of genes that have elevated and muted expression levels in the autistic brains, for instance, the researchers also found changes in spatial expression patterns in the frontal cortex and temporal cortex.

"On the one hand, the transcriptome is more variable than the genome, because it's also influenced by the environment," lead author Irina Voineagu, a post-doctoral researcher in Daniel Geschwind's University of California at Los Angeles neurology and human genetics lab, told GenomeWeb Daily News.

"But on the other hand," she explained, "although autism cases have very heterogeneous genetic causes, ultimately they do have the same phenotype — the same behavioral changes. So it's reasonable to expect that perhaps there are common molecular changes."
Past research has uncovered an assortment of genetic changes that can contribute to the ASD, though a complete picture of the genetic and environmental factors involved in the neurodevelopmental condition remains elusive.

"[A] fundamental question is whether autism represents an aetiologically heterogeneous disorder in which the myriad genetic or environmental risk factors perturb common underlying molecular pathways in the brain," the authors of the new study wrote.

To address this possibility, the researchers used Illumina Ref8v3 arrays to profile gene expression patterns in post-mortem brain tissue from 19 individuals with ASD and 17 unaffected individuals. Samples for the study were obtained through the Autism Tissue Project and Harvard Brain Bank.

The team focused on three brain regions: the superior temporal gyrus and prefrontal cortex, both in the cortex, as well as the cerebellar vermis in the cerebellum.

"It's these regions that have been previously implicated in various manifestations of autism," Voineagu explained, noting cerebellum has been shown to have pathological changes in autism, while the temporal and prefrontal regions of the cerebral cortex are thought to contribute to language and social behavior, respectively.

When they looked at quality filtered array data for samples from the cortex and cerebellum, researchers found the most ASD-associated expression differences in the cerebral cortex, a brain region associated with everything from creativity and emotion to language and hearing. Some 444 genes showed significant expression differences in cortex samples of those with ASD versus controls, compared to just two in the cerebellum, they reported.

"Probably the most striking finding for the differentially expressed genes is the fact that they could group the majority of autism samples together," Voineagu said.

For instance, the team detected elevated expression of inflammation and immune system related genes in brain samples from the ASD group compared to those in control brains. On the other hand, brain samples from those with autism had markedly lower expression of genes from synapse function and neuronal communication pathways.

In general, the expression modules found in the ASD brains matched those of control brains when the group did analysis looking at groups of genes that tend to be co-expressed together.

But some differences turned up in this co-expression network analysis as well. While expression levels for hundreds of genes varied between frontal and temporal lobes of the cerebral cortex in unaffected volunteers, researchers found almost identical gene expression patterns in the two lobes when they assessed samples from individuals with ASD.

"These data suggest that typical regional differences, many of which are observed during fetal development, are attenuated in frontal and temporal lobe in autism brain, pointing to abnormal developmental patterning as a potential pathophysiological driver in ASD," the authors wrote.

Network analyses also identified gene expression modules that distinguished the ASD from control brains. Again, genes involved in inflammatory and immune processes cropped up in an expression module that was up-regulated in ASD, while a module containing genes implicated in neuronal processes and synaptic function — including several genes identified through past genome-wide association studies of ASD — was down-regulated in the ASD cases.

"We did not see a statistically significant enrichment for autism susceptibility genes for the differentially expressed genes," Voineagu explained. "But then when we moved on and did the network analysis, the neuronal module was enriched in autism susceptibility genes. So that was basically saying that we get more powerful results with the network approach."

At the hub of this neuronal module, researchers found the neuronal splicing factor gene A2BP1, also called FOX1, a previously identified autism susceptibility gene.

In an effort to determine the consequences of dialing back the expression of this splicing factor, Voineagu explained, the team used the Illumina GAIIx to do RNA sequencing of brain samples from three individuals with ASD who had particularly low A2BP1 expression levels.

Indeed, they found, lower A2BP1 expression coincided with changes in the way several genes found in the neuronal expression module were spliced in the autistic brain, hinting that some of these genes are regulated by the splicing factor.

"Collectively, our results provide strong evidence for convergent molecular abnormalities in ASD," the team wrote, "and implicate transcriptional and slicing dysregulation as underlying mechanisms of neuronal dysfunction in this disorder."

Voineagu said she and her colleagues will likely do RNA sequencing and other analyses of additional brain regions in the future to explore these and other transcription patterns in autistic brains in more detail.