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Gene Expression Study May Open Window on Brain Development

15 June 2009. A study of gene expression across the entire genome in developing human brains may lay the groundwork for an improved understanding of the origins of complex mental disorders. Nenad Sestan of Yale University in New Haven, Connecticut, and colleagues used advances in microarray processing to examine gene expression at the level of individual exons, the code-carrying parts of genes. In the May 28 issue of Neuron, the researchers report finding different patterns of expression, including alternative splicing, in different regions of the prenatal brain, even within the prefrontal cortex. The patterns differentiated themselves according to the regions’ functional roles.

The study’s first author, Matthew Johnson, of Yale University in New Haven, told SRF that the study sprang from the Sestan lab’s interest in how the cerebral cortex evolved to enable humans to do what other species cannot. He and his collaborators suspected that changes in gene expression (see SRF live discussion) might play a role in the development of humans’ advanced brain wiring. One way of changing gene expression involves alternative splicing, which makes different forms of messenger RNA from the same gene (see SRF related news story; SRF news story). The researchers wanted to know how much differential gene expression and alternative splicing occur during prenatal development in humans and whether various brain areas would differ in expression.

Expression shapes function?
Johnson and colleagues studied four apparently normal brains gathered at 18 to 23 weeks of gestation, a key time in the formation of neural circuits and structural asymmetry. Their study looked at gene expression and alternative splicing in 13 brain areas.

When they looked at the neocortex, hippocampus, striatum, thalamus, and cerebellum, the researchers found that 76 percent of genes were expressed in at least one brain region. Of these, 44 percent appeared to be regulated differently by brain region. In particular, they found differential expression of about 33 percent of the genes and signs of alternative splicing for 28 percent. Genes in the neocortex and hippocampus shared some similar expression patterns, while the cerebellum showed the most distinct ones.

Next, the researchers explored gene expression and splicing in nine neocortical areas. Those included the motor-somatosensory, parietal association, temporal auditory, temporal association, and occipital visual neocortex, as well as four prefrontal areas: specifically, the orbital, dorsolateral, medial, and ventrolateral. Following the notion that differential gene regulation molds brain development, they expected that fetal brains would show more differential gene expression than mature adult brains, which typically show the same expression across neocortical areas.

Functionally distinct areas of the prefrontal cortex showed similarities and differences that may offer a glimpse of the developmental process. For instance, the ventrolateral prefrontal cortex, which contains Broca’s speech area, correlated more strongly with the motor-somatosensory cortex than with other prefrontal areas. To the researchers, this means that these areas may resemble each other at the molecular level at this developmental stage.

The researchers further found enrichment of certain genes in the perisylvian cortical speech and language areas, which, despite being scattered across the lobes, share similar functions. They wondered whether differential gene expression could account for the emergence of between-hemisphere differences in the perisylvian areas that relate to handedness, speech, and language processing. However, they found no consistent asymmetry of gene regulation across all the brains.

The study did identify functionally defined gene clusters that were most enriched in particular areas. For instance, one group found in excess in the cerebral cortex fosters axon guidance. It includes, for instance, semaphorin 3A.

Taken together, the expression and splicing differences may explain how various parts of the brain develop their specialized roles. The findings also highlight the complexity of expression in the developing brain. As Johnson said, “There are genes expressed at this time that are critical for forming connections that are then not expressed later in the mature brain.”

“A lot of work previously—because it’s been technologically easier to do—has been focused on finding differences in the coding sequences, but not as much has been done looking at differences in the noncoding elements that control the spatial and temporal expression of genes,” Johnson said. These cis-regulatory elements reside near, but outside of, coding regions, and some are thought to have contributed to the evolution of the human brain. Consistent with that notion, Johnson and associates found that differentially expressed genes in the neocortex were twice as likely to appear near those elements that have shown faster evolution in humans than in other species.

The researchers also uncovered groups of co-regulated genes with similar connections. They suggested that genes with the most interconnections within a given network probably shape function in important ways. They hint that researchers might want to pay particular attention to these “hub genes.”

Although the study did not look at schizophrenia, the light it shines on the development of the nervous system someday may help set the stage for those who do. In their paper, Johnson and colleagues hint that differential gene expression may underlie the abnormal wiring seen in schizophrenia, especially in the prefrontal cortex. To date, only splice variation of the neuregulin 1 gene has received significant attention (see SRF related news story; SRF news story; SRF related news story).

Johnson says that these data can also help narrow the field of gene candidates that emerges from genomewide association studies. For example, he explains, if such a study implicates a stretch of DNA that holds 20 to 50 genes, “you can look at our data and see that only a handful, or only one, is highly expressed in the brain during development at the time that we think these circuits that are miswired in the disorder are being formed.” That kind of information “can start to give us a better handle on the actual processes that are going on in the human being during development and that go wrong in schizophrenia or other such disorders,” he adds.

In a commentary in the same issue of Neuron, Colette Dehay of the Stem Cell and Brain Research Institute in Bron, France, and Henry Kennedy of the Université de Lyon, France, likened the data set to the best gold mine. Fortunately, researchers enticed by these findings need not experience data envy. Rather, they can test their own ideas using the publicly available data (see Gene Expression Omnibus and USCS Genome Bioinformatics).—Victoria L. Wilcox.

Johnson MB, Kawasawa YI, Mason CE, Krsnik Z, Coppola G, Bogdanovic D, Geschwind DH, Mane SM, State MW, Sestan N. Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron. 2009 May 28; 62:494-509. Abstract

Dehay C, Kennedy H. Transcriptional regulation and alternative splicing make for better brains. Neuron. 2009 May 28; 62:455-457. Abstract

Comments on News and Primary Papers
Comment by:  Barbara Lipska
Submitted 15 June 2009 Posted 15 June 2009

In this very important and innovative study, Sestan and...  Read more

View all comments by Barbara Lipska

Comment by:  Karoly Mirnics, SRF Advisor
Submitted 15 June 2009 Posted 15 June 2009

This outstanding study reinforces how much we still do not...  Read more

View all comments by Karoly Mirnics
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