Gene expression in the brain reveals surprising similarities and differences
Autism is a very heterogeneous disorder. As the grand lady of neurology, Dr. Isabelle Rapin liked to emphasize when training new students “If you have seen one child with autism, you have seen one child with autism.” This heterogeneity has made understanding causes and designing effective treatments more challenging than it would be otherwise.
However, a new study published this week in Nature and supported by Autism Speaks’ Autism Tissue Program and Autism Genome Project reveals that the heterogeneity may not be as problematic as it initially seems. Differences in common molecular pathways appear to underlie the pathology in the brains of individuals with ASD.
Daniel Geschwind, M.D., Ph.D. (UCLA) launched an ambitious study to examine not just the variants of genes that may confer risk for autism, but the interaction with those genes and proteins working to support brain function. Looking for patterns of interaction in the brain, Dr. Geschwind and his colleagues sought to characterize the transcriptome – the set of fragments of instructions, called RNA, read from the gene DNA on the path to making functional proteins. Importantly, unlike the gene DNA that is relatively fixed for an individual’s life, the RNA transcriptome is modified through experience and interaction with the environment.
The authors analyzed patterns of expression of RNA for three areas of the post-mortem brain tissue from individuals with ASD or typically-developing individuals. Two areas of the late-developing cerebral cortex (prefrontal cortex and the superior temporal gyrus) and a region of the cerbellum known as the vermis were compared between the autism and typically developed brain tissue. The first big surprise was that although the cortex transcriptome revealed over 400 different genes with different expression between the autism and typical brain tissue samples, the similar comparison in the cerebellar transcriptome revealed exactly two differently expressed genes. Whatever differences exist in the brains of individuals with autism, these differences are greatest in the instructions that guide the structure and function of the cerebral cortex.
This, however, was just the beginning of what the research team found. Imagine the cerebral cortex of brain is like a bustling metropolis – one part of the city develops into a residential area and the other becomes a business district. Both neighborhoods have very distinctive features that make them unique due in part to the time and manner in which they developed and the people who inhabit them. So too for different regions of the typically-developing cerebral cortex. Different regions of the cortex develop at different times and with different inputs from the environment. The prefrontal cortex is one of the late-developing regions in the infant brain. Different regions also serve different functions, like integrating information from sight, sound and touch in the case of the superior temporal gyrus, and higher cognitive functions in the prefrontal cortex.
Importantly for Dr. Geschwind and his colleagues, these two cortical regions also have their own unique pattern of expression in brains from typically developed individuals. However, when looking for these unique signatures, the research team instead found surprisingly similar patterns of gene expression across the two regions in the brains of people with autism. Referring back to the metropolis analogy, in the autism brain samples, the residential and business districts are more alike than they ought to be.
There were also differences in expression of two gene networks between the autism and control brain samples. The first network of genes encodes synaptic function. This is reassuring because most of the autism risk genes identified through previous studies focused on synaptic function. The second network of differential gene expression was related to immune function and inflammation. This too harkens back to previous studies showing inflammation and immune system activation in the brains of individuals with autism. This gene network does not correlate with the results of large gene association studies like the synaptic network, indicating that secondary or environmental effects are involved in stimulating the observed inflammatory markers.
“This is the first study to show differences in the patterns of gene expression between brain regions, said Rob Ring, Ph.D., Autism Speaks vice president for translational research. “It’s those patterns of gene expression that enable the brain to function normally and to communicate properly with other regions of the brain.”
Taken together, these results have quite an impact on how we understand autism. The similarity of gene expression across different regions of cerebral cortex in the brains of individuals with autism tells us that we should look closely at very early brain development as these patterns in cerebral cortex emerge. The same goes for the network of synaptic genes that are differentially regulated in individuals with autism. However, the differences observed in immune and inflammation gene networks are more likely to be related to secondary or environmental effects. We must follow all the leads this research has provided if we are to make the next steps in developing supportive treatments and therapies for those living with autism spectrum disorders today.