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MicroRNA Dysregulation in the Spinal Cord following Traumatic Injury

Yunta, Mónica, Nieto-Díaz, Manuel, Esteban, Francisco J., Caballero-López, Marcos, Navarro-Ruíz, Rosa, Reigada, David, Pita-Thomas, D. Wolfgang, Águila, Ángela del, Muñoz-Galdeano, Teresa, Maza, Rodrigo M.·2012·PLoS ONE
DOI 10.1371/journal.pone.0034534PMC PMC3325277
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Figure 1 Functional and morphological outcomes after injury. Recovery of locomotor function as represented by BBB scores (A) and subscores (B) after moderate injury and sham surgical procedure. Open circles represent sham animals and closed circles represent injured animals. (C) Representative histological images of eriochrome/cyanine-stained spinal cords from the different experimental groups. Tissue samples show the site of impact and 0.5 cm rostral and caudal sections with a separation of 200 µm between each image.
Figure 1 Functional and morphological outcomes after injury. Recovery of locomotor function as represented by BBB scores (A) and subscores (B) after moderate injury and sham surgical procedure. Open circles represent sham animals and closed circles represent injured animals. (C) Representative histological images of eriochrome/cyanine-stained spinal cords from the different experimental groups. Tissue samples show the site of impact and 0.5 cm rostral and caudal sections with a separation of 200 µm between each image.CC BY · PubMed Central
Figure 2 MicroRNA expression profiles after spinal cord injury. (A) Hierarchical cluster analysis and heat map, Euclidean distance and average linkage clustering of data from individual replicates. This analysis provides a visual ordination of the samples and genes according to their overall similarity. The colors of the heat map indicate microRNA upregulation (red) and downregulation (green). (B) PCA and scatterplot of the first two components, showing the separation of the LS7 individuals. (C) Scatterplot of the first and third components of the PCA, showing a group of LS3 samples. All analyses were based on data from the 463 microRNAs showing variable expression (IQR>0.5). PC1, PC2, and PC3 correspond to the axis determined by the first, second and third principal components of the PCA, respectively. These components are lineal combinations of the expression values for each gene optimized to capture the maximum variation of the matrix. Each consecutive component is orthonormal to the previous ones and absorbes the maximum amount of the remaining gene expression variation (AV, absorbed variation). Ls7, Ls3, Ls1, Sh1, Sh3 and Ct indicate sample type and correspond to Lesion (Ls), Sham (Sh) and control, while the numbers 1, 3, 7 indicate the sampling time after surgery.
Figure 2 MicroRNA expression profiles after spinal cord injury. (A) Hierarchical cluster analysis and heat map, Euclidean distance and average linkage clustering of data from individual replicates. This analysis provides a visual ordination of the samples and genes according to their overall similarity. The colors of the heat map indicate microRNA upregulation (red) and downregulation (green). (B) PCA and scatterplot of the first two components, showing the separation of the LS7 individuals. (C) Scatterplot of the first and third components of the PCA, showing a group of LS3 samples. All analyses were based on data from the 463 microRNAs showing variable expression (IQR>0.5). PC1, PC2, and PC3 correspond to the axis determined by the first, second and third principal components of the PCA, respectively. These components are lineal combinations of the expression values for each gene optimized to capture the maximum variation of the matrix. Each consecutive component is orthonormal to the previous ones and absorbes the maximum amount of the remaining gene expression variation (AV, absorbed variation). Ls7, Ls3, Ls1, Sh1, Sh3 and Ct indicate sample type and correspond to Lesion (Ls), Sham (Sh) and control, while the numbers 1, 3, 7 indicate the sampling time after surgery.CC BY · PubMed Central
Figure 3 Number of microRNA expression changes following spinal cord injury. (A) Table showing the number of expression changes detected for the different pair comparisons performed. For each comparison, the first number (in bold type) corresponds to the number of significant changes according to t-test analyses after FDR adjustment; the second number (in regular type) corresponds to the number of significant changes according to the non-parametric Rank Product test; the third number (between brackets) corresponds to the changes found to be significant by both tests. (B) Scatterplot illustrating the changes in microRNA expression after SCI. The y-axis indicates the number of up-regulated (positive axis) and down-regulated (negative axis) microRNAs. Values were derived from the t-test analyses comparing microRNA expression levels at different times after SCI to the corresponding sham or control data.
Figure 3 Number of microRNA expression changes following spinal cord injury. (A) Table showing the number of expression changes detected for the different pair comparisons performed. For each comparison, the first number (in bold type) corresponds to the number of significant changes according to t-test analyses after FDR adjustment; the second number (in regular type) corresponds to the number of significant changes according to the non-parametric Rank Product test; the third number (between brackets) corresponds to the changes found to be significant by both tests. (B) Scatterplot illustrating the changes in microRNA expression after SCI. The y-axis indicates the number of up-regulated (positive axis) and down-regulated (negative axis) microRNAs. Values were derived from the t-test analyses comparing microRNA expression levels at different times after SCI to the corresponding sham or control data.CC BY · PubMed Central
Figure 4 Negative correlation between microRNA and mRNA expression changes. Graph illustrating the relationship between the changes in microRNA and mRNA expression 7 days after injury. It clearly shows that mRNA upregulation parallels decreased microRNA expression. Numbers of upregulated and downregulated microRNA data according to the t-tests comparing the injured and sham animals at 7 days after SCI. The mRNA data correspond to the equivalent comparisons (mild plus moderately injured vs. sham at 7 dpo) from DeBiase et al. [7].
Figure 4 Negative correlation between microRNA and mRNA expression changes. Graph illustrating the relationship between the changes in microRNA and mRNA expression 7 days after injury. It clearly shows that mRNA upregulation parallels decreased microRNA expression. Numbers of upregulated and downregulated microRNA data according to the t-tests comparing the injured and sham animals at 7 days after SCI. The mRNA data correspond to the equivalent comparisons (mild plus moderately injured vs. sham at 7 dpo) from DeBiase et al. [7].CC BY · PubMed Central
Figure 5 Temporal expression profiles of selected microRNAs. The expression levels of selected microRNAs were assessed using quantitative PCR (left columns) and compared with the corresponding microarray data (right columns) using a correlation analysis (c.c: correlation coefficient). The fold changes in the sham and injured experimental groups are with respect to the control group. The Q-PCR data were analyzed using a one-way ANOVA followed by a Tukey post-test. * = p<0.05; ** = p<0.01; *** = p<0.001.
Figure 5 Temporal expression profiles of selected microRNAs. The expression levels of selected microRNAs were assessed using quantitative PCR (left columns) and compared with the corresponding microarray data (right columns) using a correlation analysis (c.c: correlation coefficient). The fold changes in the sham and injured experimental groups are with respect to the control group. The Q-PCR data were analyzed using a one-way ANOVA followed by a Tukey post-test. * = p<0.05; ** = p<0.01; *** = p<0.001.CC BY · PubMed Central
Figure 6 Functional involvement of microRNAs with expression changes. A heat map of unsupervised hierarchical clustering of all Gene Ontology (GO) categories obtained from an enrichment analysis of the microRNAs with significant changes among groups according to the t-test analyses. The GSEA values were obtained using DAVID (http://david.abcc.ncifcrf.gov) algorithms. The gradient represents the percentage of microRNAs targeting each category in each comparison. The GO terms included in each cluster (A to M) are detailed in file S5.
Figure 6 Functional involvement of microRNAs with expression changes. A heat map of unsupervised hierarchical clustering of all Gene Ontology (GO) categories obtained from an enrichment analysis of the microRNAs with significant changes among groups according to the t-test analyses. The GSEA values were obtained using DAVID (http://david.abcc.ncifcrf.gov) algorithms. The gradient represents the percentage of microRNAs targeting each category in each comparison. The GO terms included in each cluster (A to M) are detailed in file S5.CC BY · PubMed Central
Figure 7 Selected networks affected by microRNA expression changes according to Ingenuity Pathway Analysis (IPA). Each node represents molecules (microRNAs, gene) and the biological relationship between two nodes is represented as a line. These networks include microRNAs with expression changes obtained by comparison of the injury 7dpo group (LS7) with respectively non-injured control group (CT)(network 1 and 2), Sham 7dpo group (SH7)(network3) and injury 1dpo (LS1) (network4). The top four functions associated with networks are (A) Inflammatory Disease, Cell Morphology, Cellular Assembly and Organization, (B) Organismal Injury and Abnormalities, Cardiac Damage, Cardiovascular Disease, (C) Nervous System Development and Function, Tissue Morphology, Cellular Development and (D) Cell Death, Nervous System Development and Function, Cellular Function and Maintenance.
Figure 7 Selected networks affected by microRNA expression changes according to Ingenuity Pathway Analysis (IPA). Each node represents molecules (microRNAs, gene) and the biological relationship between two nodes is represented as a line. These networks include microRNAs with expression changes obtained by comparison of the injury 7dpo group (LS7) with respectively non-injured control group (CT)(network 1 and 2), Sham 7dpo group (SH7)(network3) and injury 1dpo (LS1) (network4). The top four functions associated with networks are (A) Inflammatory Disease, Cell Morphology, Cellular Assembly and Organization, (B) Organismal Injury and Abnormalities, Cardiac Damage, Cardiovascular Disease, (C) Nervous System Development and Function, Tissue Morphology, Cellular Development and (D) Cell Death, Nervous System Development and Function, Cellular Function and Maintenance.CC BY · PubMed Central

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Metadata

Authors
Yunta, M., Nieto-Díaz, M., Esteban, F. J., Caballero-López, M., Navarro-Ruíz, R., Reigada, D., Pita-Thomas, D. W., Águila, Á. D., Muñoz-Galdeano, T., & Maza, R. M.
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-04-12
Volume
7
Issue
4
Pages
e34534
ISSN
1932-6203
DOI
10.1371/journal.pone.0034534
PMC
PMC3325277
Cited by
122
References
10
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

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