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Analysis of long noncoding RNAs expression profiles explores mechanisms of hyperbaric oxygen treatment promoting spinal cord injury recovery

ABSTRACT: Aims: To better understand the potential mechanisms of hyperbaric oxygen (HBO) treatment alleviating spinal cord injury (SCI). Materials and methods: The SCI model was firstly built in mice, which were randomly divided into three groups: Sham (SH), SCI and HBO groups, followed by hind limb motor function evaluation. Then the spinal cord tissue samples were harvested for genome-wide transcriptional analysis at 1 week after injury. Finally, some highly expressed lnc-rna were selected for functional analysis. Results: the present study uncovered the lncRNAs expression profile of spinal cord following HBO treatment, and identified 577 DE lncRNAs in spinal cord sample among the SH, SCI and HBO groups. The key biological process and pathways were also identified and may be important mechanisms by which HBO treatment alleviating SCI Conclusions: Moreover, this study indicated that lncRNAs NONMMUT 092674.1 and NONMMUT042986.2 may be involved in the process of HBO treatment promoting the recovery of neurological function after SCI.

ORGANISM(S): Mus musculus

PROVIDER: GSE199043 | GEO | 2022/03/24

REPOSITORIES: GEO

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Next Generation Sequencing facilitates quantitative analysis of spinal cord tissue to explore the mechanisms of hyperbaric oxygen treatment alleviating the spinal cord inury

Project description:Aims: To better understand the potential mechanisms of hyperbaric oxygen (HBO) treatment alleviating spinal cord injury (SCI). Materials and methods: The SCI model was firstly built in mice, which were randomly divided into three groups: Sham (SH), SCI and HBO groups, followed by hind limb motor function evaluation. Then the spinal cord tissue samples were harvested for histological evaluation and genome-wide transcriptional analysis at 1 week after injury. Finally, some oxidative stress and cell death related differently expressed genes were selected to be analyzed followed by the functional analysis. Results: HBO treatment significantly improved the recovery of hind limb motor function and decreased the histology score compared to the SCI group. In the genome-wide transcriptional analysis, a total of 76 common differently expressed gene among the three groups were obtained at 1 week after injury, which were enriched in functional pathway such as ferroptosis, calcium signaling pathway, serotonergic synapse, etc. Trends in expression of the six genes were consistent with transcriptional analysis. Conclusions: Identified differentially expressed genes and related signaling pathways may be associated with HBO treatment alleviating second spinal cord injury. These results contribute to elucidate the mechanism of HBO in the treatment of SCI.

2021-10-08 | GSE185301 | GEO

Hyperbaric oxygen therapy after mid-cervical spinal contusion injury

Project description:Hyperbaric oxygen (HBO) therapy is frequently used to treat peripheral wounds or decompression sickness. Evidence suggests that HBO therapy can provide neuroprotection and has an anti-inflammatory impact after neurologic injury including spinal cord injury (SCI). Our primary purpose was to conduct an unbiased, genome-wide screening of mRNA expression changes in the injured spinal cord after HBO therapy. A mRNA gene array was used to evaluate samples taken from the contused region of the spinal cord following a lateralized mid-cervical contusion injury in adult female rats. HBO therapy consisted of daily, 1-hour sessions (3.0 ATA, 100% O2) initiated on the day of SCI. Gene set enrichment analyses indicated that HBO upregulated genes in pathways associated with electron transport, mitochondrial function, and oxidative phosphorylation, and downregulation genes in pathways associated with inflammation (including cytokines and NF-B) and apoptotic signaling. In a separate cohort, spinal cord histology was performed to verify whether the HBO treatment impacted neuronal cell counts or inflammatory markers. Compared to untreated rats, there was increased NeuN positive cells in the spinal cord of HBO treated rats (p=0.007). Further, staining for anti-ionized calcium binding adaptor protein (Iba-1, a microglial marker) was reduced after HBO (p=0.028). We conclude that HBO therapy, initiated shortly after SCI and continued for 10-days, can alter the molecular signature of the lesioned spinal cord in a manner consistent with an anti-inflammatory and neuroprotective impact.

2022-05-18 | GSE185600 | GEO

Expression data from ICR mouse spinal cords - normal or injured spinal cord

Project description:LncRNAs played a crucial role in the cell growth, development and some diseases relating to central nerve system.This study suggest that with regulating the LncRNAs expression level we might design novel therapy for spinalcord injury. In this dataset, we profiled the expression pattern of LncRNAs by microarray method after spinal cord injury (SCI). Through Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis seek LncRNAs potential function in the repair of spinal cord injury. Fifteen samples were analyzed. In these sample, we divided into five groups (sham operation, 1 day post-injured, 3 days post-injured, 1 week post-injued and 3 weeks post-injured) and each group contained three mice.After RNA extraction,RNA form mice in the same group were mixed by equal mass for the preparation of microarray.Compared with spinal cord without injury, the differential expression level of LncRNAs had a few changes at 1day post-injury, reached the peak at 1 week after SCI, and subsequently declined until 3 weeks post-injury. Genes with an FDR≤0.05 and a fold-change ≥2 were selected. Subsequently we analysis the significant differential expression genes.

2015-09-01 | E-GEOD-67515 | biostudies-arrayexpress

Expression data from ICR mouse spinal cords - normal or injured spinal cord

2015-09-01 | GSE67515 | GEO

Expression profiles of long non-coding RNAs in neurogenic bladder of spinal cord injured rats: A transcriptomic analysis

Project description:Purpose: In this study, the expression profiles of lncRNAs and mRNAs were explored in the bladder tissue of SCI rats using next-generation sequencing. Methods:Twenty female Wistar rats were randomly divided into SCI 1-3 and normal control (NC) groups. The spinal cord was completely transected at the T9-T10 level to establish the SCI model. Bladder tissues were collected on days 7, 14, and 28 after the operation. The expression profiles of lncRNAs were detected by NGS. Differentially expressed lncRNAs (DELs) were chosen for qRT-PCR verification to validate the RNA sequencing results. Results: Compared with the NC group, the SCI 1-3 groups had 468, 117, and 408 DELs (fold change (FC) > 2), including 282, 38, and 201 up-regulated and 186, 79, and 207 down-regulated lncRNAs, respectively. Likewise, 6654, 2133, and 5706 mRNAs (FC > 2) were differentially expressed between SCI 1-3 and NC rats, of which 4821, 1195, and 3695 were up-regulated, and 1833, 938, and 2011 were down-regulated, respectively. Conclusions: The results revealed the expression profiles and possible roles of lncRNAs in SCI rat NB.

2022-03-02 | GSE197544 | GEO

Circular RNA expression alteration in rats after traumatic spinal cord injury (SCI)

Project description:To determine whether the expression levels of circular RNAs were altered and lay a foundation for future work, we used high-throughput microarray analysis to screen circular RNAs expression patterns in the spinal cord of adult rats after traumatic spinal cord injury (SCI), finally to evaluate the potential rat models as a platform for the development of novel therapeutic targets for spinal cord injury in future clinical studies. Overall six rats at 3 days post-SCI in two groups were used to perform the microarray.

2018-05-15 | GSE114426 | GEO

PROTEOMIC IDENTIFICATION OF SYSTEMIC BIOMARKERS IN RAT MODELS OF SPINAL CORD INJURY

Project description:Biomarkers to more accurately determine severity and prognosis following spinal cord injury (SCI) are needed to ensure that patients are assigned to the most suitable treatment and rehabilitation regimes. This study aimed to characterise the blood proteome following SCI in clinical rat injury models to identify novel candidate biomarkers and altered biological pathways.

2022-05-19 | PXD021137 | Pride

Transcription profiling time series of Rattus norvegicus raphe magnus and sensorimotor cortex samples following moderate spinal cord 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. Analysis of the areas directly (spinal cord) and indirectly (raphe and sensorimotor cortex) affected by injury will help understanding mechanisms of SCI. Hypothesis: Areas of the brain primarily affected by spinal cord injury are the Raphe and the Sensorimotor cortex thus gene expression profiling these two areas might contribute understanding the mechanisms of spinal cord injury. Specific Aim: The project aims at finding significantly altered genes in the Raphe and Sensorimotor cortex following an induced moderate spinal cord injury in T9.

2007-10-08 | E-GEOD-2270 | biostudies-arrayexpress

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

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

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