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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

Hierarchical cluster analysis showing partition clustering of genes most highly expressed in the distal nerve stumps after sciatic nerve injury. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.Based on the KEGG database, Fisher exact test and Chi square test were applied to the differential genes, significance analysis was performed with the pathways involving target genes, and the significant pathways were obtained by screening for P < 0.05.The heat map shows the intensity of expression as a function of color, with higher expression in red and lower expression in green or black.
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Figure 3: Hierarchical cluster analysis showing partition clustering of genes most highly expressed in the distal nerve stumps after sciatic nerve injury. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.Based on the KEGG database, Fisher exact test and Chi square test were applied to the differential genes, significance analysis was performed with the pathways involving target genes, and the significant pathways were obtained by screening for P < 0.05.The heat map shows the intensity of expression as a function of color, with higher expression in red and lower expression in green or black.

Mentions: Based on the GO database, Fisher's Exact Test and Chi Square tests were applied to the differentially-expressed genes, significance analysis was performed with the pathways involving target genes, and significant pathways were obtained by screening for P < 0.05. The KEGG Pathway database comprises information on networks of molecular interactions for numerous organisms, permitting functional classification. Pathway-based analysis provides insight into biological functions and interactions of genes. Based on a comparison against the GO database using BLAST with an E value cutoff of 10-5, 1 546 genes had significant matches in the database and were assigned to 70 KEGG pathways in early WD. KEGG pathway analysis identified numerous pathways, including those relating to B-cell receptor signaling, janus kinase and signal transducer and activator of transcription (Jak-STAT) signaling, apoptosis, cytokine-cytokine receptor interactions, toll-like receptor signaling, tight junctions, neuroactive ligand-receptor interactions, axon guidance, Wnt signaling, p53 signaling, T-cell receptor signaling, leukocyte transendothelial migration, vascular endothelial growth factor signaling, adherens junctions, cell adhesion molecules, ErbB signaling, gap junctions, transforming growth factor-β signaling, mitogen-activated protein kinase signaling, the extracellular matrix-receptor interactions, actin cytoskeleton regulation, calcium signaling and the cell cycle (Figure 3).


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)

Hierarchical cluster analysis showing partition clustering of genes most highly expressed in the distal nerve stumps after sciatic nerve injury. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.Based on the KEGG database, Fisher exact test and Chi square test were applied to the differential genes, significance analysis was performed with the pathways involving target genes, and the significant pathways were obtained by screening for P < 0.05.The heat map shows the intensity of expression as a function of color, with higher expression in red and lower expression in green or black.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Hierarchical cluster analysis showing partition clustering of genes most highly expressed in the distal nerve stumps after sciatic nerve injury. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of distal sciatic nerve stumps of rats at 0.5, 1, 6, 12 and 24 hours post-surgery.Based on the KEGG database, Fisher exact test and Chi square test were applied to the differential genes, significance analysis was performed with the pathways involving target genes, and the significant pathways were obtained by screening for P < 0.05.The heat map shows the intensity of expression as a function of color, with higher expression in red and lower expression in green or black.
Mentions: Based on the GO database, Fisher's Exact Test and Chi Square tests were applied to the differentially-expressed genes, significance analysis was performed with the pathways involving target genes, and significant pathways were obtained by screening for P < 0.05. The KEGG Pathway database comprises information on networks of molecular interactions for numerous organisms, permitting functional classification. Pathway-based analysis provides insight into biological functions and interactions of genes. Based on a comparison against the GO database using BLAST with an E value cutoff of 10-5, 1 546 genes had significant matches in the database and were assigned to 70 KEGG pathways in early WD. KEGG pathway analysis identified numerous pathways, including those relating to B-cell receptor signaling, janus kinase and signal transducer and activator of transcription (Jak-STAT) signaling, apoptosis, cytokine-cytokine receptor interactions, toll-like receptor signaling, tight junctions, neuroactive ligand-receptor interactions, axon guidance, Wnt signaling, p53 signaling, T-cell receptor signaling, leukocyte transendothelial migration, vascular endothelial growth factor signaling, adherens junctions, cell adhesion molecules, ErbB signaling, gap junctions, transforming growth factor-β signaling, mitogen-activated protein kinase signaling, the extracellular matrix-receptor interactions, actin cytoskeleton regulation, calcium signaling and the cell cycle (Figure 3).

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