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Patterns of gene Expression during the Spinal cord Injury/Regeneration

ABSTRACT: Spinal cord injury (SCI) induces a sequence of endogenous autodestructive changes known as secondary injury, as well as reactive biochemical changes that are neuroprotective and/or promote recovery. All these responses to SCI are, in part reﬂected in changes in gene expression. In order to assess changes in gene expression involved in the regeneration process,microarrays were performed as a function of time after SCI for the various treatments.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE29488 | GEO | 2012/01/01

SECONDARY ACCESSION(S): PRJNA141649

REPOSITORIES: GEO

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Patterns of gene Expression during the Spinal cord Injury/Regeneration

Project description:Spinal cord injury (SCI) induces a sequence of endogenous autodestructive changes known as secondary injury, as well as reactive biochemical changes that are neuroprotective and/or promote recovery. All these responses to SCI are, in part re?ected in changes in gene expression. In order to assess changes in gene expression involved in the regeneration process,microarrays were performed as a function of time after SCI for the various treatments. Three groups rats(i.e.NT-3-chitosan tube group, tube alone group and lesion control group) used to interrogate Affymetrix (SantaClara,CA) GeneChips were sacrificed by intraperitoneally over dose injecting 6% chloral hydrate at 1, 3, 10, 20, 30, and 90 d after the operation. The spinal cords were surgically re-exposed and spinal tissue including dura and meninges was dissected into three blocks, i.e. 5 mm long segments in the lesioned area (M), rostral to the lesioned area (R), and caudal to the lesioned areas (C) were sampled under RNAase-free conditions. The samples were quick frozen and kept in liquid nitrogen.

2012-01-01 | E-GEOD-29488 | biostudies-arrayexpress

Effect of inhibition of oxidative stress on transcriptome profiles in rats with spinal cord injury.

Project description:The occurrence and development of secondary injury after spinal cord injury (SCI) is a key role affecting SCI recovery, and oxidative stress plays an important role in secondary injury. α-lipoic acid (ALA) is recognized as a powerful antioxidant that mitigates secondary damage and exerts neuroprotective effects. However, the mechanism by which ALA provides antioxidant role remains unknown. The application of ALA to rats after SCI was used to explore the effect of ALA on local gene transcription and expression after SCI and its role in SCI recovery.

2024-04-29 | GSE242507 | GEO

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

Project description:Spinal cord injury (SCI) is a devastating neurological condition for which there are currently no effective treatment options to restore function. A major obstacle to the development of new therapies is our fragmentary understanding of the coordinated pathophysiological processeses triggered by damage to the human spinal cord. An additional challenge to translation of preclinical therapies is the reliance of clinical trials on standardized neurological assessments to enrol and stratify patients, rather than objective injury biomarkers. Here, we describe a systems biology approach to integrate decades of small-scale experiments with unbiased, genome-wide gene expression from the human spinal cord, revealing a gene regulatory network signature of the pathophysiological response to SCI. Our integrative analyses converge on an evolutionarily conserved gene subnetwork enriched for genes associated with the response to SCI by small-scale experiments, and whose expression is upregulated in a severity-dependent manner following injury and downregulated in functional recovery. We validate the severity-dependent upregulation of this subnetwork in prospective transcriptomic and proteomic studies. Our analysis provides a systems-level view of the coordinated molecular processes activated in response to SCI. Further, our results nominate quantitative biomarkers of injury severity and functional recovery, with the potential to facilitate development and translation of novel therapies.

2018-09-25 | PXD010192 | Pride

Proteomics analysis of zebrafish spinal cord regeneration

Project description:Label-free mass spectrometry-based quantitative proteomics was applied to a larval zebrafish spinal cord injury model, which allows axon regeneration and functional recovery within two days (days post lesion; dpl) after a spinal cord transection in 3 day-old larvae (dpf). Proteomic profiling of the lesion site was performed at 1 dpl and 2 dpl as well as corresponding age-matched unlesioned control tissue (4 dpf as control for 1 dpl; 5 dpf as control for 2 dpl).

2023-09-06 | PXD037590 | Pride

Transcription profiling time series analyzing the molecular events in rat spinal cord sections following mechanical injury

Project description:Summary: Spinal cord injury (SCI) is a damage to the spinal cord induced by trauma or disease resulting in a loss of mobility or feeling. SCI is characterized by a primary mechanical injury followed by a secondary injury in which several molecular events are altered in the spinal cord often resulting in loss of neuronal function. Hypothesis: Spinal cord injury (SCI) induces a cascade of molecular events including the activation of genes associated with transcription factors, inflammation, oxidative stress, ionic imbalance, apoptosis and neuroregeneration which suggests the existance of endogenous reparative attempts. However, not all mechanisms following SCI are well known. Specific Aim: The goal of this project is to analyze the molecular events following spinal cord injury 1 cm above, below, and at the site of injury (T9), aiming at finding potential new targets to improve recovery and therapy.

2007-09-04 | E-GEOD-464 | biostudies-arrayexpress

Activity-induced changes in the liver transcriptome after chronic spinal cord injury

Project description:Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Disorders, such as lung injury, cardiovascular disease, liver damage, kidney and urinary tract dysfunction, alterations in gut microbiome, neuropathic pain, depression and altered immune responses are common in SCI patients. Such whole body, systemic responses hinder the functional recovery and can be life-threatening in SCI population. Investigations of organ specific gene expression analyses can provide a better understanding of the injury response and identify molecular targets. Consequently, this can be used to develop treatment for SCI, promoting functional recovery and overall quality of life.

2019-04-29 | GSE124819 | GEO

Transcriptional changes in soleus muscle for rats exposed to different activities after contusion injury to the spinal cord and transcriptional changes in soleus muscle with complete spinal cord transection injury

2020-04-07 | GSE129694 | GEO

Gene expression profiles in the spinal cord below the lesion level and influence of treadmill locomotor training

Project description:Traumatic spinal cord injury (SCI) often leads to loss of locomotor function. Neuroplasticity of spinal circuitry underlies some functional recovery and therefore represents a therapeutic target to improve locomotor function following SCI. However, the cellular and molecular mechanisms mediating neuroplasticity below the lesion level are not fully understood. The present study performed a gene expression profiling in the rat lumbar spinal cord at 1 and 3 weeks after contusive SCI at T9 compared to control rat that received sham injury (laminectomy). The below-level gene expression profiles were compared with those of animals that were subjected to treadmill locomotor training. Rat lumbar spinal cords were taken for the microarray analysis at 1 and 3 weeks after contusive spinal cord injury at the T9 level. Another group of rats received treadmill locomotor training for 3 weeks, and theirs spinal cords were harvested for the microarray. The changes in gene expression after spinal cord injury were analyzed at the two time points. The influence of treadmill locomotor training was evaluated by comparing gene expression profiles between animals with or without treadmill training.

2013-11-27 | E-GEOD-52763 | biostudies-arrayexpress

RNA-Seq analysis after spinal cord injury in lamprey reveals distinct transcriptional responses during functional recovery in spinal cord and brain

Project description:The lamprey is a vertebrate that, unlike mammals, achieves spontaneous recovery after spinal cord transection. Despite anatomical, physiological, and behavioral data on spinal cord regeneration in lamprey, the molecular mechanisms underlying this capacity are largely unknown. To address this, we used RNA-Seq to obtain transcriptional profiles from uninjured animals and at 10 time points ranging from 6 hours to 12 weeks post injury. Overall, 4208 (spinal cord) and 3788 (brain) transcripts are differentially expressed (DE). Complex intraspinal and supraspinal responses were induced acutely and occurred even at chronic phases of recovery. Leveraging functional data for mammalian homologs of DE genes (via Enrichr) permitted identification of enriched conserved genes and pathways. These included genes and pathways induced after mammalian peripheral nerve injury, such as those associated with regeneration, immune function, cell growth, proliferation and cell death. For example, ATF3, a transcription factor implicated in mammalian peripheral nerve regeneration, is highly expressed and enriched in lamprey spinal cord and brain after SCI. Other homologs of regeneration-associated genes that are differentially expressed after SCI include members of the WNT, HDAC, SOX, SMAD, KLF, and JUN families. This study provides the first comprehensive view of transcriptional responses during successful anatomical and functional recovery from spinal cord injury in lamprey, and reveals unexpectedly large changes in transcription in the brain, which is quite distant from the spinal lesion site. Gene expression patterns associated with functional recovery in lamprey may be useful in guiding studies aimed at modulating mammalian responses to SCI.

2018-03-03 | GSE95686 | GEO

The effects of scar resection in chronic complete spinal cord injury(SCI) and the effects of scar resection combined with decellularized hydrogel (scaffold)

Project description:This study examines the molecular effects of surgical scar resection in　complete chronic spinal cord injury (SCI) through RNA sequencing. Results show that scar resection alters gene expression, with downregulation of axonal growth inhibitors and upregulation of neuroprotective genes. Additionally, the application of a decellularized extracellular matrix (dECM) hydrogel as a scaffold promoted angiogenesis. Gene Ontology analysis indicated enrichment of immune-related processes, suggesting that scar resection improves the spinal cord microenvironment for neural repair. These findings indicate the potential of combining scar resection with scaffolding to support recovery after chronic complete SCI.

2024-10-08 | GSE278491 | GEO

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