Abstract
BackgroundThe different physiological repertoire of CA3 and CA1 neurons in the hippocampus, as well as their differing behaviour after noxious stimuli are ultimately based upon differences in the expressed genome. We have compared CA3 and CA1 gene expression in the uninjured brain, and after cerebral ischemia using laser microdissection (LMD), RNA amplification, and array hybridization.ResultsProfiling in CA1 vs. CA3 under normoxic conditions detected more than 1000 differentially expressed genes that belong to different, physiologically relevant gene ontology groups in both cell types. The comparison of each region under normoxic and ischemic conditions revealed more than 5000 ischemia-regulated genes for each individual cell type. Surprisingly, there was a high co-regulation in both regions. In the ischemic state, only about 100 genes were found to be differentially expressed in CA3 and CA1. The majority of these genes were also different in the native state. A minority of interesting genes (e.g. inhibinbetaA) displayed divergent expression preference under native and ischemic conditions with partially opposing directions of regulation in both cell types.ConclusionThe differences found in two morphologically very similar cell types situated next to each other in the CNS are large providing a rational basis for physiological differences. Unexpectedly, the genomic response to ischemia is highly similar in these two neuron types, leading to a substantial attenuation of functional genomic differences in these two cell types. Also, the majority of changes that exist in the ischemic state are not generated de novo by the ischemic stimulus, but are preexistant from the genomic repertoire in the native situation. This unexpected influence of a strong noxious stimulus on cell-specific gene expression differences can be explained by the activation of a cell-type independent conserved gene-expression program. Our data generate both novel insights into the relation of the quiescent and stimulus-induced transcriptome in different cells, and provide a large dataset to the research community, both for mapping purposes, as well as for physiological and pathophysiological research.
Highlights
The different physiological repertoire of CA3 and CA1 neurons in the hippocampus, as well as their differing behaviour after noxious stimuli are based upon differences in the expressed genome
We dissected CA3 and CA1 hippocampal subfields by laser microdissection from Thionin-stained cryosections, and amplified the RNA
We identified the nephroblastoma-overexpressed gene (Nov) in our gene lists as an CA1-enriched gene (CA1/CA1 sham ratio 2.29) which was verified by Lein et al using in-situ hybridization
Summary
The different physiological repertoire of CA3 and CA1 neurons in the hippocampus, as well as their differing behaviour after noxious stimuli are based upon differences in the expressed genome. The brain harbours a large variety of neuron types and sub-types, besides a large number of glial cells These neurons can differ strongly in their physiological tasks and capacities, and can be very specialized. Different neuron types display a quite specialized response to pathophysiological influences This is exemplified in neurodegenerative disorders, where often mutations in broadly expressed genes only cause pathology in one type of neurons (e.g. SOD1 mutations only affect motoneurons in ALS, Parkin mutations only affect dopaminergic neurons of the substantia nigra in PD). Or complementarily, systematic generation of mice expressing marker proteins under control of large genomic elements may be used [5] These strategies approach the problem on a gene-by-gene basis, and will not allow to explore functional genomic differences between two cell types on a statistical level
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