Injured CNS axons do not demonstrate any significant regeneration, whereas axotomy of PNS axons can lead to functional recovery (for review ). The underlying molecular mechanisms are only partially understood. Peripheral nerve injury induces changes in the molecular program of the injured neurons which include up-regulation of the immediate early genes (e.g. c-Jun) followed by regeneration-associated genes such as GAP-43 (for review ). Some similar reactions have also been observed in axotomized CNS neurons, but this response is rather "short-lived" and does not lead to any functional regeneration [2, 24, 31].
In our present study, we have investigated the gene expression pattern of regenerating facial nucleus neurons and non-regenerating red and Clarke's nucleus neurons after axotomy using the DD-PCR method. This allows the identification of similarities and differences in the molecular reactions of the lesioned PNS and CNS neurons. The lesion paradigms chosen for the present investigation are widely acknowledged and popular models of PNS and CNS injuries. Since a large number of molecules are known to be differentially expressed at approximately 7 days after injury [1, 13, 16, 17, 24, 31, 37], we have chosen this time point for our DD-PCR analysis. Subsequent ISH analysis has been applied to prove the differential expression of these genes in vivo, revealing the anatomical and cellular localization. Since the identification of the cellular localization of the gene of interest facilitates the interpretation of its functional role, ISH represents the ideal tool for the verification of differential expression.
Sixty nine gene fragments showed high homologies to known gene sequences. Most of the identified genes could be divided into different groups belonging to transcription factors, homeobox-genes, genes involved in signaling pathways or metabolism, receptors and cytoskeletal molecules (Table 2). The group of miscellenous genes encoded for a variety of proteins with specific functions. The high number of different genes related to different groups associated with the process of regeneration reflects the complexity of this issue. In a similar, very extensive study, using micro array analysis, Costigan and co-workers identified a vast number of differentially expressed genes within axotomized sensory neurons after sciatic nerve transection . Similar to our results, these genes encode for different classes of proteins.
However, we were surprised not having detected genes encoding for neuropeptides or transmitters. It is likely that this is simply due to chance. The screening was halted when we had obtained 180 differentially expressed mRNAs. We believe that, had we performed an even more extensive screen, we would indeed have identified mRNAs corresponding to neuropeptides or transmitters.
We have identified several transcriptions factors in this investigation. This is not a major surprise, because the protein synthesis is largely regulated by gene transcription. Transcription factors are proteins which may recognize specific binding sites of a number of genes, regulating their activation . A number of studies have already demonstrated that transcription factors such as c-jun or STAT-3 play a significant role for the processes of regeneration and degeneration [3, 16, 39–41]. In our investigations, c-maf and Oct-2 are induced in axotomized facial nucleus neurons. The transcription factor Oct-2 is belonging to the POU family and is induced in sensory neurons after sciatic nerve transection . It is known that the expression of Oct-2 is influenced by the nerve growth factor (NGF) and might therefore be affected by the removal of target derived NGF following axotomy. This up-regulation of Oct-2 has been suggested to induce the phenotypic changes involved in the neuronal response to injury . C-maf is known to be expressed during embryogenesis and is involved in cell differentiation. No data are available for an involvement in the process of regeneration. However, it is known that post-traumatic regenerative events in the nervous system often recapitulate some of the molecular systems that were employed during development . In this context, the differential expression of homeobox-genes such as Hox-9 might recapitulate their role during embryonic ontogenesis. Homeobox-genes are important for the establishment of the specific identity of a cell and its topographic organization [44, 45]. Previous investigations have revealed that the homeobox-gene, Islet-1, is down-regulated in axotomized facial nucleus neurons. Islet-1 is a key marker for motoneurons during development and this down-regulation might reflect a loss of neuronal identity or some form of de-differentiation. This might be an important prerequisite for neuronal regeneration .
We have also identified genes involved in signal transduction pathways and metabolism. These classes of molecules have also been identified by others using similar experimental approaches [46, 47]. Specific signal transduction pathways are involved in almost every cellular process . They are rapidly activated and may play key roles in the regulation of differential gene expression . It is very likely that the identification of genes involved in metabolism rather reflects the functional stage of the cells than being key elements for the process of regeneration. However, ISH demonstrated the differential expression of several genes influencing protein translation, which might reflect an interesting aspect of the process of regeneration which has, to date, been poorly appreciated. In the axotomized facial nucleus, genes encoding for proteins of the small (S3 and S6) and large (L7) ribosomal subunits were up-regulated in glial cells. In axotomized neurons, a gene fragment homologue to the mouse elongation factor-2 (eEF2) showed enhanced neuronal expression. The difference to the published sequence for rat eEF2 suggests an unknown isoform. It could be hypothesized that the balance of these molecules might control the rate of protein translation leading to selective production of specific mRNA species.
One interesting molecule identified in the present investigation might be the enzyme stearoyl-CoA desaturase (SCD-1), which is dramatically up-regulated in axotomized facial nucleus neurons. One of the preferred substrates, stearoyl-CoA, is desaturated into oleoyl-CoA, which is further converted into its corresponding fatty acid: oleate. Beside its function as an energy store in the form of triacylglycerides, oleate is part of biological cell membranes and is believed to be involved in protein kinase C (PKC) dependent second messenger cascades, thereby influencing, for example, the activation of regeneration-associated genes such as GAP-43 [50, 51]. By using comparative studies, we have demonstrated that SCD-1 is not induced in non-regenerating rubrospinal or Clarke's nucleus neurons suggesting a significant role for successful neuronal regeneration (Breuer et al., submitted for publication).
Furthermore, we have identified receptors and cytoskeletal molecules. The role of the transferrin and B-cell receptors being differentially expressed in the axotomized facial nucleus  or red nucleus respectively, remains unclear. However, it could be demonstrated that the lack of functional B and T lymphocytes led to a significant loss of axotomized facial nucleus neurons [52, 53]. These results highlight that the immune system is heavily involved in regulating neuronal survival after peripheral nerve injury [54–56]. Cytoskeletal elements such as GFAP or vimentin are well known to be up-regulated in glial cells when they respond to different types of injury which reflects a typical feature of accompanying glial reactions [57, 58].
Among the group of miscellenous genes, differential expression of connexin-43, ferritin light chain and the β-1 subunit of the Na/K-ATPase were identified. Connexin-43 (Cx-43) has already been reported to be up-regulated in glial cells surrounding axotomized facial nucleus neurons. The role of the induction of ferritin light chain within axotomized facial nucleus neurons remains to be elucidated. Very little is known about the involvement of iron metabolism in the axonal regeneration. However, ferritin is known to be the major iron storage protein and is a key component in protecting the brain from iron induced oxidative damage . The β1-subunit of Na/K-ATPase was down-regulated in axotomized Clarke's nucleus neurons. It has been already demonstrated that the alpha 3 subunit mRNA is reduced in ventral horn neurons after spinal cord transection. This reduction could be reversed by dexamethasone, indicating that the expression of Na/K-ATPase may constitute an important mechanism by which glucocorticoids help to re-establish neuronal function after injury . Furthermore, the alpha 2 and beta isoforms of Na/K-ATPase are down-regulated after sciatic nerve injury. This reduction took place in the distal segments owing to Wallerian degeneration and returned to baseline during nerve regeneration . These data suggest a functional role for the process of regeneration which has to be proven by further studies.
Furthermore, 66 gene fragments did not show homologies to known sequences of the rat genome. Since the rat and mouse genomes are known to be very similar, we compared our "unknown" sequences obtained from rat RNAs with the mouse genome, which was recently published. As anticipated, we found many homologies to the mouse genome. Sixty gene fragments showed homologies to different regions on different mouse chromosomes (Table 4). It is likely that these gene fragments are related to the corresponding sequences on the rat genome, which have not yet been identified. ISH demonstrated that 3 of those genes were up-regulated in axotomized facial nucleus neurons. One gene was up-regulated in axotomized rubrospinal neurons and one gene was down-regulated in axotomized Clarke's nucleus neurons.
Although the DD-PCR technique leads to the rapid identification of a number of differentially expressed genes, a major problem lies in the selection of genes for further studies. It has to be considered, that the elucidation of the functional role of defined genes and their products is very time consuming. In the past, several other techniques such as subtractive suppression hybridization (SSH) or serial analysis of gene expression (SAGE) have been developed to analyze differentially expressed genes. Recently, even more advanced methods such as arrays and DNA chip analysis have been introduced. However, all of these techniques lead to the identification of a high number of differentially expressed genes and this leads to the limitations of what can be quantitatively and qualitatively analyzed by one research group. All new techniques do not solve the problem of identifying which genes have to be selected for further detailed analysis. Therefore, other strategies are necessary to facilitate this selection. In our studies we have decided to performed comparative studies using different lesion paradigms. Genes which have been identified by DD-PCR and have been proven to be differentially expressed using ISH will be analyzed in our different lesion paradigms. The comparison of data from regenerating and non-regenerating models facilitates the identification of those genes that are regulated in a „model-specific" manner and those that may be of general importance for the process of regeneration. By these comparative analyses, we will select genes for further investigation which are exclusively regulated in a regenerating or non-regenerating lesion paradigm or show different regulation pattern.
So far, we have compared the gene expression pattern of a few selected genes identified by the DD-PCR in all our lesion models. By this means, we have demonstrated that 4 gene fragments showing homologies to the mouse genome are exclusively regulated in one lesion paradigm. In contrast, mRNA up-regulation of one of those gene fragments could also be detected in non-regenerating neurons of the red and Clarke's nucleus, but not in regenerating facial nucleus neurons. Such molecular differences between regenerating and non-regenerating neurons could be observed for the stearoyl-CoA-desaturase. SCD-1 is induced in regenerating facial nucleus neurons, but not in non-regenerating neurons of red and Clarke's nucleus. Thus, these genes fulfill the criteria of being exclusively regulated in only one lesion paradigm, indicating the importance of the functional role in the process of regeneration. These examples will provide the impetus for detailed functional analysis (e.g. antisense or gene transfer studies) of these genes.