Differentially expressed messenger RNAs and long noncoding RNAs after spinal cord injury
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PROVIDER: PRJNA698969 | ENA |
REPOSITORIES: ENA
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Project description:Spinal cord injury (SCI) is a severely disastrous event that occurs in the central nervous system (CNS) that is associated with high disability and mortality rates.To further explore the expression of mRNAs and lncRNAs and the potential roles of differentially expressed mRNAs and lncRNAs after SCI, we examined the expression of mRNAs and lncRNAs in a rat model at 2 hours, 2 days and 7 days after SCI and identified the differentially expressed lncRNAs (DE lncRNAs) and differentially expressed mRNAs (DE mRNAs) using microarray analysis. A total of 992 mRNAs were differentially expressed at 2 hours after SCI, among which 730 mRNAs were up-regulated and 262 mRNAs were down-regulated. A total of 4308 mRNAs were differentially expressed at 2 days after SCI, including 2229 mRNA with up-regulated expression and 2079 mRNAs with down-regulated expression. A total of 4113 mRNAs were differentially expressed at 7 days after SCI, including 2339 up-regulated and 1774 down-regulated mRNAs. After SCI, 772 lncRNAs were differentially expressed in the 2-hour group (528 were up-regulated, 244 were downregulated) , 3193 lncRNAs were differentially expressed in the 2-day group (1332 were up-regulated, 1861 were downregulated) ,3093 lncRNAs were differentially expressed in the 7-day group (1290 were up-regulated, 1803 were downregulated) .The current study on provides novel insights into how lncRNAs and mRNAs regulate the pathogenesis of the immediate phase after SCI.
2024-01-26 | GSE166009 | GEO
Project description:To systematically profile and characterize the noncoding RNA (ncRNA) expression pattern in the lesion epicenter of spinal tissues after traumatic spinal cord injury (TSCI). We used RNA-Seq to profle the expression and regulation patterns of noncoding RNAs and mRNAs of mice models after TSCI. A total of 498 circRNAs and 1203 mRNAs were identified in TSCI mice models to be differentially expressed. noncoding RNAs might play important roles via the competing endogenous RNA regulation pattern after TSCI, further findings arising from this study will not only expand the understanding of potential ncRNA biomarkers but also help guide therapeutic strategies for TSCI.
2021-10-27 | GSE158193 | GEO
Project description:Expression Profiles of Long Non-Coding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury
| PRJNA902314 | ENA
Project description:Spinal cord injury (SCI) is a serious disorder of the central nervous system with a high disability rate. Long noncoding RNAs (lncRNAs) are reported to mediate many biological processes. The aim of this study was to explore lncRNA and mRNA expression profiles and functional networks after SCI. Differentially expressed genes between SCI model rats and sham controls were identified by microarray assays and analyzed by functional enrichment. Key lncRNAs were identified using a support vector machine- (SVM-) recursive feature elimination (RFE) algorithm. A trans and cis regulation model was used to analyze the regulatory relationships between lncRNAs and their targets. An lncRNA-related ceRNA network was established. We identified 5465 differentially expressed lncRNAs (DE lncRNAs) and 8366 differentially expressed mRNAs (DE mRNAs) in the SCI group compared with the sham group (fold change > 2.0, p < 0.05). Four genes were confirmed by qRT-PCR which were consistent with the microarray data. GSEA analysis showed that most marked changes occurred in pathways related to immune inflammation and nerve cell function, including cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and GABAergic synapse. Enrichment analysis identified 30 signaling pathways, including those associated with immune inflammation response. A total of 40 key lncRNAs were identified using the SVM-RFE algorithm. A key lncRNA-mRNAs coexpression network was generated for 230 951 lncRNA-mRNA pairs with half showing positive correlations. Several key DE lncRNAs were predicted to have "cis"- or "trans"-regulated target genes. The transcription factors, Sp1, JUN, and SOX10, may regulate the interaction between XR_001837123.1 and ETS 1. In addition, five pairs of ceRNA regulatory sequences were constructed. Many mRNAs and lncRNAs were found to be dysregulated after SCI. Bioinformatic analysis showed that DE lncRNAs may play crucial roles in SCI. It is anticipated that these findings will provide new insights into the underlying mechanisms and potential therapeutic targets for SCI.
| S-EPMC9879695 | biostudies-literature
Project description:This study aimed to identify the crucial molecules and explore the function of noncoding RNAs and related pathways in IDD. We randomly selected 3 samples each from an IDD and a spinal cord injury group (control) for RNA-sequencing. We identified 463 differentially-expressed long noncoding RNAs (lncRNAs), 47 differentially-expressed microRNAs (miRNAs), and 1,334 differentially-expressed mRNAs in IDD. Three hundred fifty-eight lncRNAs as cis-regulators could potentially target 865 genes. Protein–protein interaction (PPI) network analysis confirmed that IL-6, VEGFA, IGF1, MMP9, CXCL8, FGF2, IL1B, CCND1, ITGAM, PTPRC, FOS and PTGS2 were hub genes. We built a competing endogenous RNA (ceRNA) network and identified lncRNA XIST–hsa-miR-4775–PLA2G7 and lncRNA XIST–hsa-miR-424-5p–AMOT/TGFBR3 ceRNA axes.
2022-02-08 | GSE167199 | GEO
Project description:Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our High-throughput Annotation of Modified Ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base-pairing at three different levels of the human and Arabidopsis thaliana transcriptomes (polyadenylated, small, and degrading RNAs). We find modifications primarily within actively degrading mRNAs and lncRNAs, suggesting they can act as a potent signal for RNA turnover. Additionally, modifications within stable mRNAs mark alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis of RNA modification across multiple RNA classes yields new functional insights into these covalent RNA additions. polyA-selected RNA-seq, smRNA-seq, and polyA-selected global mapping of uncapped transcripts (GMUCT) in Arabidopsis thaliana; smRNA-seq in HEK293T and HeLa human cell lines.
2015-10-31 | E-GEOD-66224 | biostudies-arrayexpress
Project description:Analysis of long noncoding RNAs expression profiles explores mechanisms of hyperbaric oxygen treatment promoting spinal cord injury recovery
| PRJNA818173 | ENA
Project description:BackgroundSepsis is the primary cause of mortality in the intensive care unit (ICU), mainly due to sepsis-induced dysfunction of essential organs such as the heart and lungs. This study investigated the myocardium's epigenetic characterization from septic mice to identify potential treatment targets for septic myocardial dysfunction.MethodsCecal ligation and puncture (CLP) was used to induce sepsis in male C57BL/6 mice. Hearts were collected 24 h after surgery to determine the expression profiles of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray. To validate the reliability of microarray results, we randomly chose six differentially expressed lncRNAs for qRT-PCR. Functional mapping of differentially expressed mRNAs was annotated with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses; lncRNA-mRNA co-expression network was constructed to reveal connections between lncRNAs and mRNAs.ResultsMicroarray analysis indicated that 1,568 lncRNAs and 2,166 mRNAs were differentially expressed in the myocardium from septic mice, which was further confirmed by qRT-PCR. KEGG pathway analysis showed that numerous differentially expressed mRNAs were relevant to tumor necrosis factor (TNF) and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathways. Moreover, according to the lncRNA-mRNA co-expression network constructed by the above six lncRNAs and their interacting mRNAs, the co-expression network profiles had 57 network nodes and 134 connections, including 76 positive interactions and 58 negative interactions.ConclusionsIn mouse hearts, sepsis resulted in differential expression of lncRNAs and mRNAs related to TNF and PI3K-Akt signaling pathways, suggesting that lncRNAs and their interacting mRNAs may participate in the pathogenesis of septic myocardial dysfunction by regulating TNF and PI3K-Akt signaling pathways.
| S-EPMC7940873 | biostudies-literature
Project description:Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our High-throughput Annotation of Modified Ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base-pairing at three different levels of the human and Arabidopsis thaliana transcriptomes (polyadenylated, small, and degrading RNAs). We find modifications primarily within actively degrading mRNAs and lncRNAs, suggesting they can act as a potent signal for RNA turnover. Additionally, modifications within stable mRNAs mark alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis of RNA modification across multiple RNA classes yields new functional insights into these covalent RNA additions.
2015-10-31 | GSE66224 | GEO
Project description:Spinal cord injury (SCI) is a serious disorder of the central nervous system with a high disability rate. Long non-coding RNAs (lncRNAs) are reported to mediate many biological processes. The aim of this study was to explore lncRNA and mRNA expression profiles and functional networks after SCI.We identified 5465 differentially expressed lncRNAs (DE lncRNAs) and 8366 differentially expressed mRNAs (DE mRNAs) in the SCI group compared with the sham group (fold change >2.0, P<0.05). Four genes were confirmed by real-time PCR which were consistent with the microarray data. GSEA analysis showed that most marked changes occurred in pathways related to immune inflammation and nerve cell function, including cytokine-cytokine receptor interaction (rno04060), TNF signaling pathway (rno04668), neuroactive ligand-receptor interaction (rno04080)，and GABAergic synapse (rno04727). Enrichment analysis identified 30 signaling pathways, including those associated with inflammation and the immune response. A total of 40 key lncRNAs were identified using the SVM-RFE algorithm. A key lncRNA-mRNAs co-expression network was generated for 230 951 lncRNA-mRNA pairs with half showing positive correlations. Several key DE lncRNAs were predicted to have “cis” or “trans”-regulated target genes. The transcription factors, Sp1, JUN, and SOX10, may regulate the interaction between XR_001837123.1 and ETS 1. In addition, five pairs of ceRNA regulatory sequences were identified.
2023-01-01 | GSE218088 | GEO