Circular RNA expression alteration in rats after traumatic spinal cord injury (SCI)
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ABSTRACT:
PROVIDER: PRJNA471324 | ENA |
REPOSITORIES: ENA
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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
Project description:Circular RNA is implicated in numerous diseases and conditions, including traumatic injury to the central nervoussystem. However, we know little regarding their role in completely transected spinal cord injury (SCI). Our studyused high-throughput sequencing to analyze circular RNA expression in rats after experimental completetransection of spinal cord. We found differential expression in 400 circular RNAs after SCI, with 249 significantlyup-regulated and 151 significantly down-regulated. We then selected five circular RNAs for qRT-PCR validation,and the results were in agreement with RNA sequencing. Additionally, we predicted the function of circular RNAin SCI through GO and KEGG analyses, as well as the construction of circRNA/microRNA interaction networks.Furthermore, we identified circular RNA chr9:1829226-1834212 and mRNA Hdac11 as key molecules after SCI.In conclusion, this study is the first to characterize circular RNA function in rats after completely transected SCI,through identifying their differential expression. Our results provide insight into the mechanism and therapeutictargets of SCI.
2020-08-28 | GSE156999 | GEO
Project description:The goals of this study are to screen differential expression profiles of tRNA-Derived small RNAs (tsRNAs) in rats after traumatic spinal cord injury (SCI) using next-generation sequencing and qRT-PCR.As a result, in rat spinal cord 1 day after contusion, totally 297 tsRNAs differentially expressed were identified. 155 tsRNAs were significantly differentially expressed: 91 were significantly up-regulated, while 64 were significantly down-regulated after SCI (folding change>1.5; P<0.05).Next, four tsRNAs were selected to be verified by qRT-PCR. Taken together,this study explored, for the first time, the significant alteration of tsRNA expression profiles after traumatic SCI in rats and offered deep insights into many possible treatment targets of SCI by regulating tsRNAs.
2020-01-24 | GSE133157 | GEO
Project description:We conducted snRNAseq of mouse astrocytes after traumatic spinal cord injury (SCI). These data reveal transcriptomic similarities and differences among astrocytes in healthy spinal cord and after spinal cord injury.
2024-01-09 | GSE247844 | GEO
Project description:Individuals with SCI are severely affected by immune system changes, resulting in a SCI-induced immune deficiency syndrome (SCI-IDS). While recent data support that acute SCI-IDS symptoms differ from those present in the chronic phase, only limited data in humans is available. To characterize dynamic molecular and cellular immune phenotypes over the first year, we assess RNA (bulk-RNA sequencing), protein, and flow cytometry (FACS) profiles of blood samples from 12 individuals with SCI at 0-3 days and at 3, 6, and 12 months post injury (MPI) compared to 23 uninjured individuals (controls). We identified 967 differentially expressed (DE) genes in individuals with SCI (FDR<0.001) compared to controls. Within the first 6 MPI we detected a reduced expression of NK cell genes, consistent with reduced frequencies of CD56bright, CD56dim NK cells present at 12 MPI. Over 6MPI, we observed increased and prolonged expression of genes associated with inflammation (e.g. HMGB1, Toll-like receptor signaling) and expanded frequencies of monocytes acutely. Canonical T-cell related DE genes (e.g. FOXP3, TCF7, CD4) were upregulated during the first 6 MPI and increased frequencies of activated T cells at 3-12 MPI were observed. Neurological injury severity was reflected in distinct whole blood gene expression profiles at any time after SCI, indicating a persistent ‘neurogenic’ imprint. Overall, 2876 DE genes emerge when comparing profiles of motor complete to motor incomplete SCI (ANOVA, FDR<0.05), including genes related to neutrophils, inflammation, and infection. In summary, we identify dynamic SCI-IDS determinants in humans, including molecular and cellular profiles, which may provide potential targets to reduce inflammation, improve immunity, or serve as candidate biomarkers of injury severity.
2023-05-26 | GSE226238 | GEO
Project description:Traumatic spinal cord injury (SCI) may induce irreversible damage leading to severe incapacity. Molecular mechanisms underlying SCI are not fully understood, preventing the development of novel therapeutic resources. Tamoxifen has demonstrated to be a promising therapy. Our aim was to elucidate the molecular mechanisms involved in the beneficial effect of TMX administered after SCI. We use a rat model of SCI, Tamoxifen was administred intraperitoneal 30 min after injury. Four groups were organized, 1) Non-injured without TMX (Sham/TMX-), 2) Non-injured with TMX (Sham/TMX+), 3) Injured without TMX (SCI/TMX-), and 4) Injured with TMX (SCI/TMX+). From the comparison between Sham/TMX- and SCI/TMX-, 708 genes showed differential expression. Among the relevant genes Anxa1 was upregulated, this gene’s product is a promising marker of injury severity. Enriched pathways were the spinal cord injury pathway and pathways related to inflammatory response. When comparing SCI/TMX- versus SCI/TMX+, only 30 genes showed differential expression. Our results reinforce the key role of inflammatory response in SCI and Tamoxifen seem to be able to regulate this response by suppressing changes in gene expression. Our data also support the potential of previously described severity markers.
2023-09-14 | GSE229618 | GEO
Project description:The decellularized spinal cord matrix (DSCM) provides the advantage in the translational potential for microenvironment replacement therapies to repair spinal cord injury (SCI) However, the cell type alteration in the SCI repairing niche is undefined. Using single cell transcriptome and bulk RNA-seq analysis, we showed that DSCM regulated cell fate changes in niches related to the multicellular model. This work opens the door for understanding the SCI repairing from a tissue niche perspective.
2022-12-31 | GSE202731 | GEO
Project description:Spinal cord injury (SCI) is mostly caused by trauma. As primary mechanical injury is unavoidable in SCI, a focus on the pathophysiology and underlying molecular mechanisms of SCI-induced secondary injury is necessary to develop promising treatments for SCI patients. Circular RNAs (circRNAs) are associated with various diseases. Nevertheless, studies to date have not yet determined the functional roles of circRNAs in traumatic SCI. We examined circRNA expression profiles in the contused spinal cords of rats using microarray and quantitative reverse transcription-PCR (qRT-PCR) then predict their potential roles in post-SCI pathophysiology with bioinformatics. We found a total of 1676 differentially expressed circRNAs (fold change ? 2.0; P < 0.05) in spinal cord 3 days after contusion using circRNA microarray; 1261 circRNAs were significantly downregulated, whereas the remaining 415 were significantly upregulated. Then, five selected circRNAs, namely, rno_circRNA_005342, rno_circRNA_015513, rno_circRNA_002948, rno_circRNA_006096, and rno_circRNA_013017 were all significantly downregulated in the SCI group after verification by qRT-PCR, demonstrating a similar expression pattern in both microarray and PCR data. The next section of the study was concerned with the prediction of circRNA/miRNA/mRNA interactions using bioinformatics analysis. In the final part of the study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses indicated carbohydrate metabolic process was one of the most significant enrichments and meaningful terms after GO analysis, and the top two signaling pathways affected by the circRNAs-miRNAs axes were the AMP-activated protein kinase signaling pathway and the peroxisome related pathway. In summary, this study showed an altered circRNA expression pattern that may be involved in physiological and pathological processes in rats after traumatic SCI, providing deep insights into numerous possibilities for SCI treatment targets by regulating circRNAs.
| S-EPMC6339904 | biostudies-literature
Project description:Traumatic spinal cord injury (SCI) initiates a complex series of pathophysiological secondary responses that lead to tissue loss and functional deficits.This study represents a comprehensive database of temporal changes in gene expression that underlie the secondary injury response that occurs in a well-defined mouse model of contusion injury. Keywords: Time-Series
2006-07-12 | GSE5296 | GEO
Project description:Injured axons in the CNS do not spontaneously regenerate leading to paralysis. Neurons can transport RNA and ribosomes to the site of injury where de novo translation has been known to occur, facilitating repair. Yet the tools available for studying axonal specific RNA are limited. We came up with a simple modification using Cold Active Proteases that enabled us to enrich for axonal RNA from rats with spinal cord injury (SCI) compared to non-injured. Our enriched axonal prep was then analyzed by bulk RNA-seq, where we looked at total RNA and we found differentially expressed genes (DEGs). Analyzing our bulk RNA-seq by Gene Ontology, we found the second most significant pathway for all DEGs was for axonogenesis, with markedly low glial cell contamination. From our DEGs we detected Rims2, which is reported to be predominately a circular RNA (circRNA) in the rodent CNS. Upon further annotation, we found over 200 putative circRNAs. circRNAs are abundant and well conserved in the brain, they are thought to be transcriptional regulators by functioning as microRNA (miR) sponges or binding to RNA-binding proteins (RBPs). By computational analysis using Circular RNA Interactome, we are able to predict which miRs or RBPs could bind to circRims2.
2023-07-25 | GSE230066 | GEO