Sheng Yi

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

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.

Regulation of Schwann cell proliferation and migration by miR-1 targeting brain-derived neurotrophic factor after peripheral nerve injury

Peripheral nerve injury is a global problem that causes disability and severe socioeconomic burden. Brain-derived neurotrophic factor (BDNF) benefits peripheral nerve regeneration and becomes a promising therapeutic molecule. In the current study, we found that microRNA-1 (miR-1) directly targeted BDNF by binding to its 3′-UTR and caused both mRNA degradation and translation suppression of BDNF. Moreover, miR-1 induced BDNF mRNA degradation primarily through binding to target site 3 rather than target site 1 or 2 of BDNF 3′-UTR. Following rat sciatic nerve injury, a rough inverse correlation was observed between temporal expression profiles of miR-1 and BDNF in the injured nerve. The overexpression or silencing of miR-1 in cultured Schwann cells (SCs) inhibited or enhanced BDNF secretion from the cells, respectively, and also suppressed or promoted SC proliferation and migration, respectively. Interestingly, BDNF knockdown could attenuate the enhancing effect of miR-1 inhibitor on SC proliferation and migration. These findings will contribute to the development of a novel therapeutic strategy for peripheral nerve injury, which overcomes the limitations of direct administration of exogenous BDNF by using miR-1 to regulate endogenous BDNF expression.

MiR-340 Regulates Fibrinolysis and Axon Regrowth Following Sciatic Nerve Injury

After peripheral nerve injury, the degenerative debris and inflammatory alterations at the injury site may block the elongation of regenerating axons to reach target organs. Tissue plasminogen activator (tPA), a serine protease, has a capability of degrading matrix molecules and cell adhesions. In this study, we found that either tPA or miR-340 was differentially expressed in the injured nerve after sciatic nerve injury, and that the expressions of tPA and miR-340 were negatively correlated to each other. Moreover, miR-340 and tPA were co-localized in sciatic nerve. miR-340 regulated tPA through direct targeting of the 3′-UTR of tPA. Functionally, over- or under-expression of miR-340 reduced or augmented the fibrinolytic activity and migration ability of cultured Schwann cells as well as tPA secretion from the cells, respectively. In rats with sciatic nerve crush injury, dysregulation of the miR-340 expression in the injury site affected the cell debris removal and axonal regrowth. Obviously, unlike many previous studies that investigate the functional impact of miRNAs on peripheral nerve regeneration in the perspective of miRNA regulation of neural cell behaviors, the present study focused on miRNA regulation of debris clearance, thus updating our understanding of the regulatory roles of miRNAs in peripheral nerve regeneration.

Microarray and qPCR Analyses of Wallerian Degeneration in Rat Sciatic Nerves

Wallerian degeneration occurs immediately following injury to mammal peripheral nerves. To better understand the molecular events occurring during Wallerian degeneration, a rat model of sciatic nerve transection was used to assess differentially expressed genes at 0.5, 1, 6, 12, 24 h, 4 days, 1, 2, 3, and 4 weeks post nerve injury (PNI). Hierarchical clustering, Euclidean distance matrix, and principal component analysis (PCA) collectively suggested three distinct phases within the post-injury period of 4 weeks. Gene ontology (GO) analysis suggested that phase I (0–6 h PNI), phase II (6–24 h PNI), and phase III (4 days to 4 weeks) were associated with acute response to injury, preformation of Wallerian degeneration, and complete execution of Wallerian degeneration, respectively. Critical signaling pathways and transcriptional factor networks responsible for the regulation of Wallerian degeneration were further identified and integrated using Kyoto Enrichment of Genes and Genomes (KEGG) pathway analysis and Ingenuity Pathway Analysis (IPA), respectively. Our results may help to elucidate some molecular mechanisms of gene regulation associated with Wallerian degeneration that occurs after traumatic injury to peripheral nerve axons in mammals.

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

Nerve injury is a common and difficult clinical problem worldwide with a high disability rate. Different from the central nervous system, the peripheral nervous system is able to regenerate after injury. Wallerian degeneration in the distal nerve stump contributes to the construction of a permissible microenvironment for peripheral nerve regeneration. To gain new molecular insights into Wallerian degeneration, this study aimed to identify differentially expressed genes and elucidate significantly involved pathways and cellular functions in the distal nerve stump following nerve injury. Microarray analysis showed that a few genes were differentially expressed at 0.5 and 1 h post nerve injury and later on a relatively larger number of genes were up-regulated or down-regulated. Ingenuity pathway analysis indicated that inflammation and immune response, cytokine signaling, cellular growth and movement, as well as tissue development and function were significantly activated following sciatic nerve injury. Notably, a cellular function highly related to nerve regeneration, which is called Nervous System Development and Function, was continuously activated from 4 days until 4 weeks post injury. Our results may provide further understanding of Wallerian degeneration from a genetic perspective, thus aiding the development of potential therapies for peripheral nerve injury.

miR-sc3, a Novel MicroRNA, Promotes Schwann Cell Proliferation and Migration by Targeting Astn1.

MicroRNAs (miRNAs, miRs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level. We have previously identified a group of novel miRNAs in proximal sciatic nerve after sciatic nerve transection by Solexa sequencing, and miR-sc3 is a member of the group. In this study, we aimed to investigate the effects of miR-sc3 on phenotypic modulation of Schwann cells (SCs). miR-sc3 was highly expressed in the injured nerve after sciatic nerve transection. An increased and decreased expression of miR-sc3 promoted and reduced the proliferation and migration of primary SCs, respectively. miR-sc3 directly targeted astrotactin 1 (Astn1) and led to translational suppression of Astn1. There was an inverse association between the time-dependent expressions of miR-sc3 and Astn1 in proximal sciatic nerve after sciatic nerve transection. Overall, miR-sc3 affected SC proliferation and migration by targeting Astn1, thus playing the regulatory role in peripheral nerve regeneration.

miR-sc8 Inhibits Schwann Cell Proliferation and Migration by Targeting Egfr

MicroRNAs (miRNAs) negatively regulate the expression of target genes at the post-transcriptional level in diverse biological processes. We have previously identified a group of novel miRNAs in proximal nerve following rat sciatic nerve transection by Solexa sequencing. In this study, the biological function and action mode of miR-sc8, one of the above identified miRNAs, were investigated. An increased expression of miR-sc8 inhibited cell proliferation and migration of Schwann cells (SCs), and inversely, silencing of the miR-sc8 expression promoted cell proliferation and migration of SCs. The epidermal growth factor receptor (Egfr) was identified as the target gene of miR-sc8, which exerted negative regulation of Egfr by translational suppression. The temporal change profile of the miR-sc8 expression was negatively correlated with that of the Egfr expression in proximal nerve following sciatic nerve transection. Moreover, Knockdown of Egfr attenuated the promoting effects of miR-sc8 inhibitor on SC proliferation and migration. Overall, our data indicate that miR-sc8 affects phenotype modulation of SCs by targeting Egfr, providing further insights into the regulatory role of miRNAs in peripheral nerve regeneration.

Differential temporal expression of matrix metalloproteinases following sciatic nerve crush

We previously performed transcriptome sequencing and found that genes for matrix metalloproteinases (MMPs), such as MMP7 and 12, seem to be highly upregulated following peripheral nerve injury, and may be involved in nerve repair. In the present study, we systematically determined the expression levels of MMPs and their regulators at 1, 4, 7 and 14 days after sciatic nerve crush injury. The number of differentially expressed genes was elevated at 4 and 7 days after injury, but decreased at 14 days after injury. Among the differentially expressed genes, those most up-regulated showed fold changes of more than 214, while those most down-regulated exhibited fold changes of more than 2−10. Gene sequencing showed that, at all time points after injury, a variety of MMP genes in the “Inhibition of MMPs” pathway were up-regulated, and their inhibitor genes were down-regulated. Expression of key up- and down-regulated genes was verified by quantitative real-time polymerase chain reaction analysis and found to be consistent with transcriptome sequencing. These results suggest that MMP-related genes are strongly involved in the process of peripheral nerve regeneration.

Transcriptional Profiling at High Temporal Resolution Reveals Robust Immune/Inflammatory Responses during Rat Sciatic Nerve Recovery

After peripheral nerve injury, immune/inflammatory responses are triggered, which are critical for nerve regeneration. Despite their importance, the underlying molecular changes in immune/inflammatory responses remain largely unknown. In this study, we systematically analyzed differentially expressed genes in immune/inflammatory-related pathways at high temporal resolution and experimentally validated gene expression changes with RT-PCR following sciatic nerve crush in rats. We found that immune/inflammatory reactions not only occur in the acute injury but also remained activated over two weeks after injury. Detailed bioinformatic studies suggested that multiple immune/inflammatory pathways, including agranulocyte adhesion and diapedesis, granulocyte adhesion and diapedesis, IL-6 signaling, and IL-10 signaling, were sustained activated during nerve degeneration and regeneration. Our current study expands our understanding of the molecular basis of altered immune/inflammatory-related pathways following injury and thus might offer the possibility of targeting related molecules as therapeutic intervention for peripheral nerve regeneration.

Critical signaling pathways during Wallerian degeneration of peripheral nerve

Wallerian degeneration is a critical biological process that occurs in distal nerve stumps after nerve injury. To systematically investigate molecular changes underlying Wallerian degeneration, we used a rat sciatic nerve transection model to examine microarray analysis outcomes and investigate significantly involved Kyoto Enrichment of Genes and Genomes (KEGG) pathways in injured distal nerve stumps at 0, 0.5, 1, 6, 12, and 24 hours, 4 days, 1, 2, 3, and 4 weeks after peripheral nerve injury. Bioinformatic analysis showed that only one KEGG pathway (cytokine-cytokine receptor interaction) was significantly enriched at an early time point (1 hour post-sciatic nerve transection). At later time points, the number of enriched KEGG pathways initially increased and then decreased. Three KEGG pathways were studied in further detail: cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and axon guidance. Moreover, temporal expression patterns of representative differentially expressed genes in these KEGG pathways were validated by real time-polymerase chain reaction. Taken together, the above three signaling pathways are important after sciatic nerve injury, and may increase our understanding of the molecular mechanisms underlying Wallerian degeneration