Deep Sequencing and Bioinformatic Analysis of Lesioned Sciatic Nerves after Crush Injury

Abstract

The peripheral nerve system has an intrinsic regenerative capacity in response to traumatic injury. To better understand the molecular events occurring after peripheral nerve injury, in the current study, a rat model of sciatic nerve crush injury was used. Injured nerves harvested at 0, 1, 4, 7, and 14 days post injury were subjected to deep RNA sequencing for examining global gene expression changes. According to the temporally differential expression patterns of a huge number of genes, 3 distinct phases were defined within the post-injury period of 14 days: the acute, sub-acute, and post-acute stages. Each stage showed its own characteristics of gene expression, which were associated with different categories of diseases and biological functions and canonical pathways. Ingenuity pathway analysis revealed that genes involved in inflammation and immune response were significantly up-regulated in the acute phase, and genes involved in cellular movement, development, and morphology were up-regulated in the sub-acute stage, while the up-regulated genes in the post-acute phase were mainly involved in lipid metabolism, cytoskeleton reorganization, and nerve regeneration. All the data obtained in the current study may help to elucidate the molecular mechanisms underlying peripheral nerve regeneration from the perspective of gene regulation, and to identify potential therapeutic targets for the treatment of peripheral nerve injury.

Ingenuity Pathway Analysis of Gene Expression Profiles in Distal Nerve Stump following Nerve Injury: Insights into Wallerian Degeneration

“…Our study, from the genetic aspect, confirmed the critical roles of macrophages during Wallerian degeneration. Moreover, our finding that inflammation and immune response was continuously activated is consistent with previous observation in a model of sciatic nerve crush injury (Yi et al, 2015). …”

Gene expression analysis at multiple time-points identifies key genes for nerve regeneration

“…Curiously, olfactory transduction was the most enriched process among DE mRNAs in our study, which differs from the findings by Yi et al . in their RNA sequencing study . Furthermore, Olfr was involved in the response to stimulus, consistent with previous studies .…”

“…Because axon regeneration–specific genetic pathways governing metabolism and cell proliferation generally involve cytokine–cytokine receptor interaction pathways and cell cycle pathways, it is not surprising that these 2 pathways were significantly enriched among DE mRNAs. Intriguingly, in a parallel comparative analysis with RNA sequencing, the axon guidance pathway was consistently enriched among DE mRNAs in the early stages postinjury . Moreover, the early upregulated expression pattern of related mRNAs verified by PCR (Fig.…”

Proteomic expression profile of injured rat peripheral nerves revealed biological networks and processes associated with nerve regeneration

“…Interestingly, two of the enriched pathways, LXR/RXR, and acute phase response signaling, are involved in the regulation of immune responses. These findings are in agreement with the immunohistochemical staining of FFPE nerves tissues, that revealed the presence of immune cells at the injured site, and further extend at proteomic level previous observations that identified by gene expression analysis both pathways as significantly up‐regulated after nerve crush injury (Yi et al, ). At the level of protein synthesis, we found a highly significant enrichment of EIF2 signaling, suggesting an elevated rate of protein synthesis.…”

“…Moreover, immunohistochemical analysis for monocyte/macrophage markers (CD11b, CD68), leukocyte marker (CD45), and T cell marker (CD3) showed markedly infiltrations of both monocyte and macrophages in the injured nerves (Figure c, uninjured vs. injured panels). This confirms other studies that described the presence of multiple cell types at the injured site, creating a cellular microenvironment that can improve the regenerative process (Yi et al, ).…”