Open Access Research article

Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model

Mahmood Chamankhah1, Eftekhar Eftekharpour2, Soheila Karimi-Abdolrezaee3, Paul C Boutros456, Serban San-Marina7 and Michael G Fehlings189*

Author Affiliations

1 Krembil Neuroscience Center, Division of Cell and Molecular Biology, Toronto Western Hospital, Toronto, ON, Canada

2 Regenerative medicine and Spinal Cord Research Centre, Department of Physiology, University of Manitoba, Winnipeg, MB, Canada

3 Physiology and Regenerative Medicine Program, University of Manitoba, Winnipeg, MB, Canada

4 Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada

5 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada

6 Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada

7 Biostatistix Drug Discovery/Bioinformatics, Toronto, ON, Canada

8 Department of Surgery, Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada

9 Division of Neurosurgery and Neuroscience Program, University of Toronto, Toronto, ON, Canada

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BMC Genomics 2013, 14:583  doi:10.1186/1471-2164-14-583

Published: 28 August 2013



The aneurysm clip impact-compression model of spinal cord injury (SCI) is a standard injury model in animals that closely mimics the primary mechanism of most human injuries: acute impact and persisting compression. Its histo-pathological and behavioural outcomes are extensively similar to human SCI. To understand the distinct molecular events underlying this injury model we analyzed global mRNA abundance changes during the acute, subacute and chronic stages of a moderate to severe injury to the rat spinal cord.


Time-series expression analyses resulted in clustering of the majority of deregulated transcripts into eight statistically significant expression profiles. Systematic application of Gene Ontology (GO) enrichment pathway analysis allowed inference of biological processes participating in SCI pathology. Temporal analysis identified events specific to and common between acute, subacute and chronic time-points. Processes common to all phases of injury include blood coagulation, cellular extravasation, leukocyte cell-cell adhesion, the integrin-mediated signaling pathway, cytokine production and secretion, neutrophil chemotaxis, phagocytosis, response to hypoxia and reactive oxygen species, angiogenesis, apoptosis, inflammatory processes and ossification. Importantly, various elements of adaptive and induced innate immune responses span, not only the acute and subacute phases, but also persist throughout the chronic phase of SCI. Induced innate responses, such as Toll-like receptor signaling, are more active during the acute phase but persist throughout the chronic phase. However, adaptive immune response processes such as B and T cell activation, proliferation, and migration, T cell differentiation, B and T cell receptor-mediated signaling, and B cell- and immunoglobulin-mediated immune response become more significant during the chronic phase.


This analysis showed that, surprisingly, the diverse series of molecular events that occur in the acute and subacute stages persist into the chronic stage of SCI. The strong agreement between our results and previous findings suggest that our analytical approach will be useful in revealing other biological processes and genes contributing to SCI pathology.

Spinal cord injury; Microarray; Pathway analysis; GO enrichment