Differential gene expression after complete spinal cord transection in adult rats: an analysis focused on a subchronic post-injury stage

In an attempt to characterize changes in transcription after a sub-chronic spinal cord injury (SCI), we investigated gene expression profiles using cDNA microarray. Among 7523 genes and expressed sequence tags (ESTs) examined, 444 transcripts, including 218 genes and 226 ESTs, were identified to be either up-regulated (373 of 444) or down-regulated (71 of 444) greater than 2.0-fold in the spinal cord at 14 days after a complete spinal transection at the 11th thoracic level in adult rats. Based on their potential function, these differentially expressed genes were categorized into seven classes which include cell division-related protein, channels and receptors, cytoskeletal elements, extracellular matrix proteins, metalloproteinases and inhibitors, growth-associated molecules, metabolism, intracellular transducers and transcription factors, as well as others. Strong expressional changes were found in all classes revealing the complexity and diversity of gene expression profiles following SCI. We verified array results with RT-PCR for eight genes, Northern blotting for nine genes, and in situ hybridization for one gene and immunohistochemistry for four genes. These analyses confirmed, to a large extent, that the array results have accurately reflected the molecular changes occurring at 14 days post-SCI. Importantly, the current study has identified a number of genes, including annexins, heparin-binding growth-associated protein (HB-GAM), P9ka (S100A4), matrix metalloproteinases, and lysozyme, that may shed new light on SCI-related inflammation, neuroprotection, neurite-outgrowth, synaptogenesis, and astrogliosis. In conclusion, the identification of molecular changes using the large-scale microarray analysis may lead to a better understanding of underlying mechanisms, thus, the development of new repair strategies for SCI.