Briefly, outcomes from microarray analysis were first uploaded into Qiagen's IPA system for core analysis and then overlaid with the global molecular network in the Ingenuity pathway knowledge base (IPKB). Int. In the current study, we made rat sciatic nerve transection, collected the distal nerve stump samples at different time points, re-analyzed previous obtained microarray data (Yao et al., 2012, 2013) by using the R software and the limma package and uploaded the massive microarray data into the IPA program for a systematic bioinformatic analysis. However, the up-regulation of MMP9 was largely compromised in mice with delayed Wallerian degeneration (Shubayev et al., 2006; Barrette et al., 2010). All these results highlight the central roles of the MMP family in nerve regeneration. An integrated global view of gene expression patterns during Wallerian degeneration was obtained by performing IPA core analysis, overlaying microarray data to IPKB, and then assigning differentially expressed genes to specific canonical pathways, diseases and biological functions, and networks. Chapter 3: histology of the peripheral nerve and changes occurring during nerve regeneration. For example, Gene Ontology analysis suggested that differentially expressed genes in the distal nerve stump could be mainly divided into functional groups with regulatory functions, including cell communication, cell transport, and transcriptional regulation (Bosse et al., 2006). Muscle Nerve Suppl. In the Canonical Pathways function of IPA, pathways were considered to be significantly dysregulated if they were associated with a right-tailed Fisher's exact p-value < 0.01. BMC Genomics. Immediately after peripheral nerve injury, the most significant pathways and cellular functions were found to be inflammatory and immune response, which remained to be activated until 4 weeks post nerve injury. Following sciatic nerve transection, a diverse array of biological processes, including stimulus detection and response, inflammatory and immune response, cell migration, cell proliferation, cell death, axonal regeneration and guidance, and myelination, were significantly activated in the proximal nerve stump (Li S. et al., 2013). In a few previous studies in our group, microarray was used to investigate the expression profiles in the distal nerve stump following peripheral nerve injury, and a number of up-regulated or down-regulated molecules were identified during Wallerian degeneration (Yao et al., 2012, 2013; Li M. et al., 2013; Li et al., 2014). Learn how to navigate through the Canonical Pathway results in a QIAGEN Ingenuity Pathway Analysis (IPA) Core Analysis. At 0.5, 1, 6, 12, and 24 h post nerve injury, top networks had scores of 21, 23, 23, 27, and 29, respectively. J. Neurol. Poor growth of Mammalian motor and sensory axons into intact proximal nerve stumps. From 4 days until 4 weeks post injury, less canonical pathways were activated. The IPA system (version 42012434, Ingenuity Systems; Qiagen China Co., Ltd.) was used for subsequent bioinformatics analysis, which included canonical pathway analysis, disease and function, regulator effects, upstream regulators and molecular networks. (2013). doi: 10.1016/j.aanat.2011.02.011, Dubový, P., Jancalek, R., and Kubek, T. (2013). Red color indicates up-regulation while green color indicates down-regulation. List of the gene networks at 0.5, 1, 6, 12, and 24 h, 4 days, and 1, 2, 3, and 4 weeks post sciatic nerve transection. doi: 10.1002/mus.24082, Li, S., Liu, Q., Wang, Y., Gu, Y., Liu, D., Wang, C., et al. 2016 Dec;65:321-329. doi: 10.1016/j.dci.2016.07.022. Oncol. Infection and RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection. The authors thank Professor Jie Liu for his help in manuscript preparation. The relative expression levels of (A) MMP9, (B) BDNF, (C) MAG, (D) MAL, (E) SHH, (F) SLC6A17, and (G) RET were calculated using comparative Ct with GAPDH as the reference gene. It may be because that at an early stage after nerve injury only non-myelinating Schwann cells, but not myelinating Schwann cells, enter into the cell cycle to avoid negative factors for nerve regeneration (Murinson et al., 2005), but later on myelinating Schwann cells start to proliferate and to form myelin sheaths (Liu et al., 1995; Vargas and Barres, 2007). Schwann cells, neurotrophic factors, and peripheral nerve regeneration. 29, 321–332. Adult male Sprague-Dawley (SD) rats, body weight 180–200 g, were purchased from the Experimental Animal Center of Nantong University and housed in temperature- and humidity-controlled large cages with sawdust bedding and given access to tap water and food ad libitum. IPA results provided us with some new insights into Wallerian degeneration. Inflammation and its role in neuroprotection, axonal regeneration and functional recovery after spinal cord injury. The quality and quantity of isolated RNA were checked by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA) and NanoDrop ND-1000 spectrophotometer (Infinigen Biotechnology Inc., City of Industry, CA), respectively. 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. doi: 10.1146/annurev.neuro.30.051606.094354, Venezie, R. D., Toews, A. D., and Morell, P. (1995). To obtain an elementary investigation of the molecular mechanisms underlying Wallerian degeneration, microarray data were submitted to IPA core analysis. The involvement of Nervous System Development and Function at different time points. Keywords: Bioinformatic analysis was performed to analysis differentially expressed genes at 0.5, 1, 6, 12, and 24 h, 4 days, and 1, 2, 3, and 4 weeks post sciatic nerve transection. Expression changes and bioinformatic analysis of Wallerian degeneration after sciatic nerve injury in rat. Different from the central nervous system, the peripheral nervous system is able to regenerate after injury. Different from the central nervous syst… Therefore, genes involved in this function category were further analyzed. doi: 10.1111/j.1460-9568.1991.tb00069.x, Brown, M. C., Lunn, E. R., and Perry, V. H. (1992). Contributed reagents/materials/analysis tools: JY and SY. Pathway/Tox List 搜尋 IPA內建有 Ingenuity Canonical Pathways 與 Toxicity Lists Library資料。例如可以找到Hepatic Cholestasis相關的毒物以及Signaling Pathway資料。此搜尋是針對該內建資料庫，您需要輸入 pathway的名稱作為關鍵字搜尋。 IV. The expression levels of genes were indicated by the color bar (attached to the raster plot). These top networks are generally associated with cellular morphology, assembly, organization, and organ development. List of primer pairs for real-time quantitative qPCR. Why were not the myelin-related genes up-regulated until a relatively later stage post injury? The heapmap suggested that nearly 2/3 of genes involved in this cellular function were firstly up-regulated and then down-regulated while a little bit less than 1/3 of differentially genes were first down-regulated and then up-regulated. Neural Regenerat. 125, 2675–2683. J. Neuropathol. Supplementary Table 4. Differentially expressed genes involved in Nervous System Development and Function at 0.5, 1, 6, 12, and 24 h, 4 days, and 1, 2, and 3 weeks post sciatic nerve transection. The differentially expressed genes were categorized to related canonical pathways based on IPKB. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Table 2. 54, 487–496. Bull. Microarray data analysis was performed by the R software platform (v.2.13.0) and the limma (linear regression model) package (Ritchie et al., 2015; Xu and Sun, 2015). 24, 577–583. (2014). Exp. J. Mol. Supplementary Table 1. Mol. Why is Wallerian degeneration in the CNS so slow? 96, 1441–1457. Limited knowledge exists on pathways, networks and transcriptional factors regulated within epithelial cells by diverse Mycobacterium tuberculosis genotypes. Only a signaling pathway, called Agranulocyte Adhesion and Diapedesis, was activated during nearly whole post-injury period. (2016). 6, 391–407. Compared with the expressed genes at 0 h post injury, only a small number of genes were differentially expressed at 0.5 and 1 h after nerve injury. Different from the central nervous system that can hardly regenerate by itself, the peripheral nervous system has a certain ability to regenerate on its own (Raimondo et al., 2011; Gu et al., 2014). Laminin overrides the inhibitory effects of peripheral nervous system and central nervous system myelin-derived inhibitors of neurite growth. Clin. Ingenuity Pathways Analysis (IPA) IPA is a web-based bioinformatics application that allows researchers to upload data analysis results from high-throughput experiments such as microarray and next generation sequencing for functional analyze, integration, and further understanding.
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