Expression profiles of long non-coding RNAs in neurogenic bladder of spinal cord injured rats: A transcriptomic analysis
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ABSTRACT:
PROVIDER: PRJNA810864 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18158486_1.fastq.gz | Fastqsanger.gz | |||
| SRR18158486_2.fastq.gz | Fastqsanger.gz | |||
| SRR18158487_1.fastq.gz | Fastqsanger.gz | |||
| SRR18158487_2.fastq.gz | Fastqsanger.gz | |||
| SRR18158488_1.fastq.gz | Fastqsanger.gz |
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Project description:Neurogenic detrusor overactivity (NDO) is a frequent complication of spinal cord injury (SCI), often accompanied by profound structural and functional changes in the bladder. While inosine has previously been shown to improve bladder function in SCI models, its molecular effects on the bladder remain largely unexplored. In this study, we performed transcriptomic profiling of bladder tissues from SCI rats treated with inosine or vehicle. Bladder compartments were microdissected into detrusor and mucosa to capture compartment-specific changes. SCI induced widespread transcriptional alterations in both compartments, with inosine treatment partially restoring gene expression patterns toward those observed in non-injured controls. Unsupervised clustering and principal component analyses confirmed distinct transcriptional profiles associated with injury and treatment. Notably, inosine influenced a set of genes consistently altered by SCI, suggesting a protective or regulatory role at the molecular level. These findings reveal a compartment-specific transcriptomic response to spinal cord injury and provide insight into the mechanisms by which inosine may exert its therapeutic effects on the injured bladder.
2025-07-09 | GSE294930 | GEO
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
Project description:Spinal cord injury (SCI) evokes profound dysfunction in hollow organs such as the urinary bladder and gut. Current treatments are limited by a lack of molecular data to inform novel therapeutic avenues. Previously, we showed systemic treatment with the neuroprotective agent inosine improved bladder function following SCI in rats. This RNA-seq dataset captures global transcriptomic changes in the rat bladder at multiple time points following spinal cord injury (SCI). Full-thickness bladder tissues were collected from male Sprague Dawley rats at 2, 8, and 16 weeks post-complete T8 spinal cord transection, alongside non-injured controls.
2025-07-09 | GSE294927 | GEO
Project description:Purpose: The goal of this study was to determine the gene expression changes that occur over 7 days in parralyzed muscle in response to isometric contraction elicited by electrical stimulation initiated 4 months after spinal cord injury and to compare such changes to those observed in a normal muscle subjected to overload. Methods: Electrical stimulation of the soleus and plantaris muscle was stimulated in female rats with complete transection of the spinal cord at the interspace between the 9th and 10th thoracic vertebrae. Stimulation was begun 16 weeks after spinal cord transection and produced near-isometric contraction of soleus, plantaris and tibialis anterior. Muscle was analyzed at 1, 2 and 7 days after starting exercise with electrical stimulation. To provide a baseline reference for gene expression at 16 weeks after spinal cord injury, muscle was also analysed from an additional group of spinal cord transected animals. One additional group of animals with a sham-spinal cord injury was included to provide information about gene expression in neurologically intact animals of similar age. In parallel studies, rats underwent bilateral gastrocnemius ablation to overload soleus and plantaris, or a sham ablation as a control. Muscle was analyzed at 1, 3 and 7 days after gastrocnemius ablation or sham-ablation. Gene expression was determined using Affymetrix Rat Exon microarrays. For each group of animals, microarray analysis was performed for soleus muscle for each of 3 separate animals, using one array per animal. Control sammples for the spinal cord injured groups included a group of animals with a Sham-spinal cord injury, and a group of spinal cord injured animals that did not get electrical stimulation. The comparator for determining fold-change expression values was the spinal cord injured group that did not receive electrical stimulation. For each day after gastrocnemius ablation, a control was included that received all procedures needed for this ablation except cutting the distal insertion of the gastrocnemius into the Achilles tendon to control for effects of the surgery on gene expression.
2013-03-30 | E-GEOD-37476 | biostudies-arrayexpress
Project description:Background: Neurogenic bladder (NB) after suprasacral spinal cord injury (SSCI) is an interstitial disease with structural remodeling of bladder tissue and matrix over-deposition. Circular RNAs (circRNAs), which have extensive post-transcriptional regulatory functions, widely participate in the pathogenesis of fibrotic diseases and may be promising new biomarkers and potential therapeutic targets. However, the expression profiles and possible roles of circRNAs in bladder fibrosis and NB after SSCI still remain elusive. Methods: Spinal cord transection at the T10–T11 level was used to construct the NB after SSCI model in rats. The bladders were collected in rats without (sham) and with (SSCI 1-3 groups) NB status. Morphological observation was performed to detect the severity of bladder fibrosis. The expression profiles of mRNAs and circRNAs were detected by transcriptome high-through-put sequencing. The dynamic changes of differentially expressed mRNAs (DEMs) and circRNAs (DECs) in different time periods of SSCI were further analyzed. Moreover, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed to investigate the potential functions. In addition, the co-expression network (circRNA–miRNA–mRNA) was constructed to understand the internal regulating relationships of these DEMs and DECs. The top ten common expressed DECs in each NB stage were subjected to Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to verify their expression. Results: Bladder weight, smooth muscle cells hypertrophy, and extracellular matrix gradually increased over time after SSCI. Compared with the normal control (NC) group, 3255 DEMs and 1339 DECs, 3449 DEMs and 1324 DECs, 884 DEMs and 1151 DECs were detected in the SSCI 1-3 groups, respectively. Specifically, circRNA3621, circRNA5775, circRNA3111, and circRNA0586 were significant DECs common to SSCI 1–3 compared with NC group. Moreover, GO enrichment suggested that “inflammatory response”, “inflammatory response” and “chronic inflammatory response” were the key events in NB progression. The KEGG pathway related to “Chemokine signaling pathway”, “IL-17 signaling pathway”, and “TGF-beta signaling pathway” were enriched, implying potential roles in regulatory process. Conclusion: This study provides a systematic perspective on the potential functions of these DEMs and DECs during bladder fibrosis process and NB after SSCI, and could help pave the way for effective therapeutics for this devastating and complex disease.
2023-08-18 | GSE227447 | GEO
Project description:This study investigates the molecular changes in the bladder following spinal cord injury (SCI) in rats and the impact of inosine treatment using a multi-omics approach. We discovered the activation of PARP (Poly(ADP-ribose) polymerase) in response to SCI, a previously unrecognized phenomenon, and its attenuation with inosine treatment. SCI triggered significant DNA damage and oxidative stress pathways, whereas inosine treatment prevents DNA damage and inhibits PARP activation, offering a potential therapeutic avenue. The integrated analysis of transcriptomics and proteomics data revealed concordant regulation of multiple pathways following SCI, including EIF2 signaling and NRF2-mediated oxidative stress response, which are ameliorated by inosine treatment. These findings have relevance to human neurogenic bladder pathobiology. Pathway inhibition by inosine in the setting of SCI suggests its potential for neuroprotection in the bladder. Despite limitations, such as the focus on male rats and a lack of proteomics data from separated detrusor and mucosa, this study provides valuable insights into the molecular mechanisms underlying bladder dysfunction following SCI. It also suggests the repurposing of FDA-approved PARP inhibitors for the treatment of bladder dysfunction following spinal injury.
2025-07-14 | PXD046096 | Pride
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
Project description:To better understand which genes/pathways are activated in injured muscles following a spinal cord injury (SCI) and how these promote the development of neurogenic heterotopic ossification (NHO), we performed gene expression profiling by microarray of muscles in the early phase following muscle injury.
2021-12-01 | GSE165062 | GEO
Project description:Transcriptomic Remodeling of the Spinal Cord-Injured Bladder and Its Modulation by Inosine Treatment
| PRJNA1252057 | ENA
Project description:Neurogenic bladder (NB)-induced fibrosis is the major cause of irreversible bladder dysfunction, yet the underlying mechanisms remain undefined. Here, we performed single-cell RNA sequencing on bladder tissues collected from rats following bilateral pelvic nerve injury, and characterized the alterations in the bladder microenvironment post-injury.
2025-12-23 | GSE305964 | GEO