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Gene expression profiling of the rat sciatic nerve in early Wallerian degeneration after injury.

Yao D, Li M, Shen D, Ding F, Lu S, Zhao Q, Gu X - Neural Regen Res (2012)

Bottom Line: Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed components involved in the Jak-STAT, ErbB, transforming growth factor-β, T cell receptor and calcium signaling pathways.Key factors included interleukin-6, interleukin-1, integrin, c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine (C-C motif) ligand, matrix metalloproteinase, BH3 interacting domain death agonist, baculoviral IAP repeat-containing 3 and Rac.The data were validated with real-time quantitative PCR.

View Article: PubMed Central - PubMed

Affiliation: Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong 226019, Jiangsu Province, China ; School of Life Sciences, Nantong University, Nantong 226019, Jiangsu Province, China.

ABSTRACT
Wallerian degeneration is an important area of research in modern neuroscience. A large number of genes are differentially regulated in the various stages of Wallerian degeneration, especially during the early response. In this study, we analyzed gene expression in early Wallerian degeneration of the distal nerve stump at 0, 0.5, 1, 6, 12 and 24 hours after rat sciatic nerve injury using gene chip microarrays. We screened for differentially-expressed genes and gene expression patterns. We examined the data for Gene Ontology, and explored the Kyoto Encyclopedia of Genes and Genomes Pathway. This allowed us to identify key regulatory factors and recurrent network motifs. We identified 1 546 differentially-expressed genes and 21 distinct patterns of gene expression in early Wallerian degeneration, and an enrichment of genes associated with the immune response, acute inflammation, apoptosis, cell adhesion, ion transport and the extracellular matrix. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed components involved in the Jak-STAT, ErbB, transforming growth factor-β, T cell receptor and calcium signaling pathways. Key factors included interleukin-6, interleukin-1, integrin, c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine (C-C motif) ligand, matrix metalloproteinase, BH3 interacting domain death agonist, baculoviral IAP repeat-containing 3 and Rac. The data were validated with real-time quantitative PCR. This study provides a global view of gene expression profiles in early Wallerian degeneration of the rat sciatic nerve. Our findings provide insight into the molecular mechanisms underlying early Wallerian degeneration, and the regulation of nerve degeneration and regeneration.

No MeSH data available.


Related in: MedlinePlus

Key network analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.The gene expression data were used as the input file for the generation of biological networks using the analyze network algorithm with default settings.The networks are prioritized based on the number of fragments of canonical pathways. Thick cyan lines indicate the fragments of canonical pathways.Up-regulated genes are marked with red circles; down-regulated genes with blue circles. The checker board pattern indicates mixed expression for the gene between files or between multiple tags for the same gene.
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Figure 4: Key network analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.The gene expression data were used as the input file for the generation of biological networks using the analyze network algorithm with default settings.The networks are prioritized based on the number of fragments of canonical pathways. Thick cyan lines indicate the fragments of canonical pathways.Up-regulated genes are marked with red circles; down-regulated genes with blue circles. The checker board pattern indicates mixed expression for the gene between files or between multiple tags for the same gene.

Mentions: Key networks were constructed from active experiments. The gene expression data was used as the input for the generation of biological networks, using the analyze network algorithm with default settings. This is a variant of the shortest paths algorithm with main parameters of relative enrichment and relative saturation of networks with canonical pathways. Genes encoding signal transducers or factors involved in processes such as cell death, the immune response, transport and transcriptional regulation showed injury-specific gene expression. The expression of numerous genes is required for regeneration[222324]. In this study, we used CTRNN to dynamically model GO processes for gene regulatory networks. A number of key networks were identified, including those comprising interleukin-6, interleukin-1, integrin (ITG), c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine (C-C motif) ligand, matrix metalloproteinase, BH3 interacting domain death agonist (BID), baculoviral IAP repeat-containing 3 (BIRC3) and Rac (a subfamily of the Rho family of GTPases) (Figure 4). These key networks cover the most important pathways and play important roles in regulating gene expression profiles through mainly biological GO processes during WD of the sciatic nerve. The data obtained here are consistent with published data and support the conclusion that genetic programs of regenerating and developing peripheral nerves exhibit relevant differences. The data revealed that signaling molecules significantly regulated in the lesioned distal stump after sciatic nerve injury were steadily up and down-regulated. All of these molecules were significantly regulated after sciatic nerve injury and are known to modulate signaling pathways composing the key networks[1525262728]. The data also suggest that the functional group of transcriptional regulators identified by the gene expressional changes may be an essential prerequisite for nerve degeneration and/or regeneration/development[293031].


Gene expression profiling of the rat sciatic nerve in early Wallerian degeneration after injury.

Yao D, Li M, Shen D, Ding F, Lu S, Zhao Q, Gu X - Neural Regen Res (2012)

Key network analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.The gene expression data were used as the input file for the generation of biological networks using the analyze network algorithm with default settings.The networks are prioritized based on the number of fragments of canonical pathways. Thick cyan lines indicate the fragments of canonical pathways.Up-regulated genes are marked with red circles; down-regulated genes with blue circles. The checker board pattern indicates mixed expression for the gene between files or between multiple tags for the same gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4308797&req=5

Figure 4: Key network analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.The gene expression data were used as the input file for the generation of biological networks using the analyze network algorithm with default settings.The networks are prioritized based on the number of fragments of canonical pathways. Thick cyan lines indicate the fragments of canonical pathways.Up-regulated genes are marked with red circles; down-regulated genes with blue circles. The checker board pattern indicates mixed expression for the gene between files or between multiple tags for the same gene.
Mentions: Key networks were constructed from active experiments. The gene expression data was used as the input for the generation of biological networks, using the analyze network algorithm with default settings. This is a variant of the shortest paths algorithm with main parameters of relative enrichment and relative saturation of networks with canonical pathways. Genes encoding signal transducers or factors involved in processes such as cell death, the immune response, transport and transcriptional regulation showed injury-specific gene expression. The expression of numerous genes is required for regeneration[222324]. In this study, we used CTRNN to dynamically model GO processes for gene regulatory networks. A number of key networks were identified, including those comprising interleukin-6, interleukin-1, integrin (ITG), c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine (C-C motif) ligand, matrix metalloproteinase, BH3 interacting domain death agonist (BID), baculoviral IAP repeat-containing 3 (BIRC3) and Rac (a subfamily of the Rho family of GTPases) (Figure 4). These key networks cover the most important pathways and play important roles in regulating gene expression profiles through mainly biological GO processes during WD of the sciatic nerve. The data obtained here are consistent with published data and support the conclusion that genetic programs of regenerating and developing peripheral nerves exhibit relevant differences. The data revealed that signaling molecules significantly regulated in the lesioned distal stump after sciatic nerve injury were steadily up and down-regulated. All of these molecules were significantly regulated after sciatic nerve injury and are known to modulate signaling pathways composing the key networks[1525262728]. The data also suggest that the functional group of transcriptional regulators identified by the gene expressional changes may be an essential prerequisite for nerve degeneration and/or regeneration/development[293031].

Bottom Line: Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed components involved in the Jak-STAT, ErbB, transforming growth factor-β, T cell receptor and calcium signaling pathways.Key factors included interleukin-6, interleukin-1, integrin, c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine (C-C motif) ligand, matrix metalloproteinase, BH3 interacting domain death agonist, baculoviral IAP repeat-containing 3 and Rac.The data were validated with real-time quantitative PCR.

View Article: PubMed Central - PubMed

Affiliation: Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong 226019, Jiangsu Province, China ; School of Life Sciences, Nantong University, Nantong 226019, Jiangsu Province, China.

ABSTRACT
Wallerian degeneration is an important area of research in modern neuroscience. A large number of genes are differentially regulated in the various stages of Wallerian degeneration, especially during the early response. In this study, we analyzed gene expression in early Wallerian degeneration of the distal nerve stump at 0, 0.5, 1, 6, 12 and 24 hours after rat sciatic nerve injury using gene chip microarrays. We screened for differentially-expressed genes and gene expression patterns. We examined the data for Gene Ontology, and explored the Kyoto Encyclopedia of Genes and Genomes Pathway. This allowed us to identify key regulatory factors and recurrent network motifs. We identified 1 546 differentially-expressed genes and 21 distinct patterns of gene expression in early Wallerian degeneration, and an enrichment of genes associated with the immune response, acute inflammation, apoptosis, cell adhesion, ion transport and the extracellular matrix. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed components involved in the Jak-STAT, ErbB, transforming growth factor-β, T cell receptor and calcium signaling pathways. Key factors included interleukin-6, interleukin-1, integrin, c-sarcoma, carcinoembryonic antigen-related cell adhesion molecules, chemokine (C-C motif) ligand, matrix metalloproteinase, BH3 interacting domain death agonist, baculoviral IAP repeat-containing 3 and Rac. The data were validated with real-time quantitative PCR. This study provides a global view of gene expression profiles in early Wallerian degeneration of the rat sciatic nerve. Our findings provide insight into the molecular mechanisms underlying early Wallerian degeneration, and the regulation of nerve degeneration and regeneration.

No MeSH data available.


Related in: MedlinePlus