The acute pain following a single injection of carrageenan disappears within a few days; however, the enhanced sensitivity to a new noxious challenge may persist for a prolonged time [5–7]. The enhanced sensitivity may contribute to posttraumatic and postsurgical persistent pain. In experiments with repeated carrageenan injections in response to the first injection into a rat's hind paw, the induced hyperalgesia was profound on the side of injection and minimal or absent in the contralateral hind paw. However, repeated injection of carrageenan into the previously noninjected hind paw resulted in pronounced hyperalgesia in the other paw. The difference between distant hyperalgesia after the initial and repeated-crossover injection of carrageenan was used as a measure of the hyperalgesia-related memory. The enhanced hyperalgesia is present even 28 days after the initial injection .
In this study we found alterations of gene expression that lasted at least 28d and were quite different from transitory changes observed 24h after injection. The genes altered at 24h include those involved in immune reaction and protein synthesis (Table 2), whereas long-lasting changes observed 28 days after injection indicate different pathways, most notably those responsible for new synapse formation (Table 3).
The observed short-term upregulation of the immune response genes concurs with earlier reports that IL-6 [20, 21] and TNF-a (tumor necrosis factor-a)  play an important role in inflammatory pain. The upregulation of these genes had previously been associated with the development of neuropathic pain as well . A similar result has been found following nerve injury and spinal cord injury (SCI). SCI induces a robust and significant increase in mRNAs of inflammatory cytokines such as TNF-a, interleukin-1β (IL-1β), and IL-6 at 1, 3, and 24 h post-injury [23–25]. We do not know whether the changes in gene expression are mediated by inflammation, pain, possible injury to the nerve, or a combination thereof.
We observed significant changes in expression of several key enzymes (3-alpha-hydroxysteroid dehydrogenase, phospholipase a2, prostaglandin d2 synthase, and COX2) involved in eicosanoid biosynthesis (Table 4, Arachidonic acid cascade and mediators of inflammation). This cascade is usually initiated by the activation of phospholipase A2 and the release of arachidonic acid (AA) . The AA is subsequently transformed by cyclooxygenase (COX) and lipoxygenase pathways to prostaglandins, thromboxane, and leukotrienes, collectively termed eicosanoids. Eicosanoid production is considerably increased during inflammation and inflammation-induced pain, and COX is the major target for nonsteroidal antiinflammatory drugs (NSAIDs). It is possible that activation of eicosanoids by inflammation/pain causes lasting changes in gene expression. NMDA receptors, which are prominently involved in activity-dependent synaptic plasticity and tonic pain , could mediate the upregulation of inflammatory factors. Inflammation-induced NMDAR activation involves phosphorylation of the NR1 and NR2B subunits in the spinal dorsal horn by fyn proto-oncogene . The downstream changes in Egr1, MAPK, and AC expression (see Table 4) can be also induced by activation of the NMDA receptor. As an alternative, activation of the neurotensin receptor can stimulate Egr1 expression and MAP kinase pathways .
We do not know whether activation of eicosanoids and MAP kinases is part of one inflammatory/pain pathway or the former is the result of inflammation and the latter is pain-induced. In any case, long-lasting changes in gene expression are unlikely to be induced by ongoing inflammation, since the majority of genes known to be involved directly in the inflammatory response have a profile with maximum changes at 24h and returning to control levels 28d following injection. No detectable changes of inflammatory cytokine genes, including those described above, were found 28d after injection. However, initial inflammatory response may contribute to long-term changes in gene expression and pain memory. A number of genes altered in the 28d group are involved in inflammation-induced potentiation of pain sensitivity. For example, dynorphin [30, 31], neuropeptide Y (NPY), and NPY (Y1) receptor  are induced in the spinal cord by peripheral inflammation. However, it is unknown whether activation of nociceptors is required.
Based on our expression data, carrageenan injection affected at least two signal transduction pathways, MAPK and cAMP/adenylyl cyclase (AC), known to regulate nociceptive signal perception and transmission. Several isoforms of MAPK are involved in regulation of acute and chronic pain both in neuron and glial cells [33, 34]. cAMP mediates many aspects of pain transmission within neuronal cells. In particular, AC isoform 8 (AC8) that couples NMDA receptor activation to cAMP signaling pathways in neurons are important in the development of persistent pain . Activation of MAPK cascade might be mediated by neurotensin receptor via Egr1, which is known to be upregulated in response to persistent inflammatory pain  and stimulates Erk1/2 phosphorylation . It is likely that an interaction between the glutamate pathway and cAMP signaling is mediated by modulation of metabotropic glutamate receptor by RGS2 and RGS4 [37, 38], which were downregulated 24h after carrageenan injection (Table 4). Based solely on our data, we cannot tell whether the trigger for long-term changes in gene expression is the initial inflammation or pain or their combination. It is also unlikely that all changes in gene expression observed in the 28d group are related to formation and maintenance of nociceptive memory. However, the prominent group (Table 3) of differentially expressed genes controls neuronal connectivity, synaptogenesis, and neurogenesis. It is known that long-term memory and plasticity in CNS depend on formation of new synapses that require synthesis of proteins responsible for cell-to-cell interaction–in particular cadherin-like protein. There is also evidence that formation of new neurons is important for memory formation and plasticity .
There is similarity in the development of long-term potentiation (LTP), long-term memory, and pain. Research indicates that central sensitization in the spinal cord has the identical mechanism to LTP . We have found that a number of genes altered at 28d were also altered in the hippocampus during LTP: brain-derived neurotrophic factor (BDNF), early growth response 1 (EGR1), CD9 antigen (CD9), neuropeptide Y receptor Y5 (NPY5R), and neuropeptide Y receptor (NPY1R) . Genes such as BDNF [13, 42], NtrkB (BDNF receptor), Egr1 , neuropeptide Y receptor, and neuregulin1 are also known to be involved in inflammation-induced pain. For example, BDNF, a known modulator of memory, was found to be altered in rat pups one day after peripheral inflammation induced by injection of Freund's complete adjuvant . We do not believe, however, that pain memory and LTP are identical phenomena but rather share some basic mechanisms. They have different anatomical substrates, and most alterations found in our study were not observed in the hippocampus following memory formation. Based on our data, pain or inflammation or a combination thereof induces dramatic changes in gene expression. Most of these changes in gene expression subside when inflammation disappears, while some of them persist and even increase 28d later. Thus, part of the pain- and inflammation-induced changes in gene expression belong to pathway(s) that remain activated long after inflammation and acute pain disappear. We can only speculate which genes whose expression increased much more at 28d than at 24h belong to these pathways. Additional experiments are needed to narrow down the list of affected pathways. Based on the results of GO analysis, proteins involved in synaptogenesis, cell-cell interaction, and the formation of new neurons are overrepresented among differentially expressed genes at 28d after carrageenan injection. Thus, we propose that pathways related to synapse formation between newly generated neurons are particularly important for "pain memory." The tentative nature of this conclusion depends on the exploratory nature of our microarray data and analysis. The selection of genes is based on a limited number of replicates and multiple comparisons, which implies that a number of genes may be false positives. We confirmed the differential expression for a few selected genes by PCR, but more research is needed to complete verification of the microarray data.