Adaptive changes in gene expression patterns in the somatosensory cortex after deletion of ephrinA5

The role of wiring molecules in circuit assembly is tested directly in genetically engineered animals, in which the corresponding gene has been selectively mutated. Minor alterations in neuronal circuits in these mutant animals are explained by redundancy and/or adaptive changes of other genes relevant for brain development. There is very little known, however, about the extent and nature of the compensatory molecular mechanisms. Using gene microarrays, we compared gene expression patterns in the somatosensory cortex of wild type and ephrinA5 deficient mice, which exhibit subtle, but highly reproducible alterations of thalamocortical projections and intrinsic cortical circuits. We found that between 2.2%–5.7% of all transcripts (140–373 targets) detected in the somatosensory cortex are differentially expressed in comparing wild type and ephrinA5 mutants. A gene group analysis of the annotated transcripts revealed that a high proportion of the dysregulated genes encode proteins relevant for circuit development. Finer grain analysis by in situ hybridization and quantitative RT-PCR revealed that 20% of the Eph/ephrin family genes expressed in the somatosensory cortex are up-regulated in the mutant. One of these genes, EphB6, was up-regulated in all cortical layers, where it is normally expressed. However, the ephrinA2 and EphA5 were up-regulated only in selected layers in the cortex of the mutant; expression levels in other layers did not change. These findings indicate that there is specificity of adaptive and compensative changes in gene expression after the mutation of a single gene relevant for cortical development. Our results also point to the complexity of interpreting phenotypes of gene knock-out animals.