Long non-coding RNA and circular RNA and coding RNA profiling of plasma exosomes of osteosarcoma by RNA seq
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE218526 | GEO | 2023/05/27
REPOSITORIES: GEO
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2019-08-01 | GSE119256 | GEO
Project description:Objective: The diagnostic roles of long non-coding RNAs (lncRNAs) in clear cell renal cell carcinoma (ccRCC) are still not well defined. We aimed to identify differentially expressed lncRNAs and mRNAs in plasma of ccRCC patients and health controls systematically. Methods: Expression profile of lncRNAs and mRNAs in plasma from ccRCC patients and healthy controls was analyzed by microarray assay. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway based approaches were used to investigate biological functions and signaling pathways affected by the differentially expressed mRNAs. SOCS2-AS1 was selected for validation using Real-Time PCR. The differentially expressed genes were further compared with E-MTAB-1830 datasets by Venn and NetworkAnalyst website. The expression level and overall survival (OS) of differentially expressed mRNAs were analyzed in GEPIA and ULCAN website. Results: Compared with healthy controls, a total of 3,664 differentially expressed lncRNAs were revealed by heatmap and volcano-plot, including up-regulation in 1,511 and down-regulation in 2,153 (fold change ≥ 2 and P < 0.05), respectively. And differential expression was noticed in 2,268 mRNAs, including up-regulation in 932 mRNAs and down-regulation in 1,336 mRNAs, respectively (fold change ≥ 2 and P < 0.05). Pathways analysis based on deregulated mRNAs were mainly involved in melanogenesis and Hippo signaling pathway (P < 0.05). The expression of SOCS2-AS1 was down in ccRCC plasma and tissues, as well as in cell lines, which was the same as the results of lncRNA microarray. Compared with the E-MTAB-1830 gene expression profiles, we identified 18 lncRNAs, and 87 mRNAs were differently expressed in both plasma and neoplastic tissues of ccRCC. Ten mRNAs (EPB41L4B, CCND1, GGT1, CGNL1, CYSLTR1, PLAUR, UGT3A1, PROM2, MUC12, and PCK1) were correlated with the overall survival (OS) rate in ccRCC patients based on the GEPIA and ULCAN website.Conclusions: We first reported differentially expressed lncRNAs in ccRCC patient and healthy control systemically. Combined with the published dataset, we identified several differentially expressed lncRNAs and mRNAs which might to be diagnostic or prognostic markers. The biological functions of those lncRNAs and mRNAs should be further validated. Taken together, this study provided the basis for future treatment of ccRCC and novel insights into cancer biology.
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Project description:Purpose: The purpose of this study was to detect the expression profiles of circRNAs, lncRNAs and mRNAs in umbilical cord blood (UCB) exosomes from BPD infants. Methods:Microarray analysis was performed to compare the RNA profiles of UCB-derived exosomes from preterm newborn with and without BPD. Then, circRNA/lncRNA-miRNA-mRNA co-expression networks were built to determine their associations with BPD.Results:A total of 317 circRNAs, 104 lncRNAs, 135 mRNAs showed significant differential expression in UCB-derived exosomes from BPD preterm infants compared with the NBPD group. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for examining differentially expressed exosomal circRNAs, lncRNAs and mRNAs. Our results showed the GO terms and KEGG pathways mostly involving differentially expressed exosomal RNAs were closely associated with endothelial or epithelial cell development. In addition, two networks were identified, including circRNA-circ_0086018/miR-762/MEN1 and lncRNA-BASP1-AS1/miR-20a-5p/DNAJC22 networks, which may take part in BPD.
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Project description:Purpose: This study aimed to explore the differential expression profiles of exosomal lncRNAs and evaluated their potential utility in the accurate diagnosis of LAA stroke. Methods: LncRNA profiles of exosomes in large artery atherosclerosis stroke and controls were generated by high-throughput sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Hisat2, Trapnell, STAR. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: A total of 1020 differentially expressed lncRNAs were identified in LAA stroke patients. GO and KEGG pathway analyses indicated that their target genes are involved in atherosclerosis-related pathways, including inflammation, cell adhesion, and cell migration. 8 exosomal lncRNAs were confirmed with qRT–PCR.The result showed that the expression trend of differential expressed lncRNAs in validation was consistent with RNA-seq.Conclusion: Our study showed the differential expression of lncRNAs in plasma exosomes and presented related diagnostic potential for LAA stroke for the first time. The results suggested that exosomal lncRNA could be potential diagnostic tools in LAA stroke. Circular RNAs (circRNAs), novel endogenous noncoding RNAs, play diverse roles in ischemic stroke. Recently, the abundance and stability of circRNAs in exosomes have been identified. However, a comprehensive analysis of exosomal circRNAs in large artery atherosclerotic (LAA) stroke has not yet been reported. We performed RNA sequencing (RNA-Seq) to comprehensively identify differentially expressed exosomal circRNAs in five paired LAA and normal controls. RNA-Seq identified a total of 462 circRNAs in peripheral exosomes; there were 25 differentially expressed circRNAs among them. Additionally, circRNA competing endogenous RNA (ceRNA) network and translatable analysis revealed the potential functions of the exosomal circRNAs in LAA progression. Two ceRNA pathways involving 5 circRNAs, 2 miRNAs, and 3 mRNAs were confirmed by qRT-PCR. In the validation cohort, receiver operating characteristic (ROC) curve analysis identified two circRNAs as possible novel biomarkers, and a logistic model combining two and four circRNAs increased the area under the curve compared with the individual circRNAs.
2021-06-08 | GSE173719 | GEO
Project description:Gallbladder cancer (GBC) is the most common biliary tract malignancy worldwide. Although a growing number of studies have been devoted to the mechanism’s exploration of GBC, few molecules can be utilized as a specific biomarker for GBC early diagnosis and therapeutic treatment. Recent studies have shown that exosomes not only participate in the progression of tumors, but also carry the specific information which can define multiple cancer types. The present study was carried out to investigate the expression profile of coding and non-coding RNAs (lncRNAs and circRNAs) in the plasma-derived exosomes from GBC patients. By using high-throughput RNA sequencing and subsequently bioinformatic analysis, we identified a number of differentially expressed (DE) mRNAs, lncRNAs and circRNAs in GBC-exosomes comparing to xantho-granulomatous cholecystitis (XGC)-exosomes. Then we applied Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analysis to investigate the potential function of these DE RNAs. Furthermore, we explored the interaction networks and competing endogenous RNA networks of these DE RNAs and their targeted genes, which revealed a complex regulatory network among coding and non-coding RNAs. In summary, this study will give evidence on the diagnostic worth of plasma-derived exosomes in GBC and provide a new perspective on the novel mechanism of GBC.
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Project description:This study aimed to develop a short-read RNA-Seq protocol to detect mRNAs, lncRNAs and circRNAs (including putative novel lncRNAs) in human plasma. This protocol was applied to plasma from patients with established stable CAD (samples collected ~4 months after an acute coronary event) and healthy controls to screen for candidate mRNA, lncRNA and circRNA biomarkers associated with the presence of coronary artery disease and the progression from CAD to HF. We hypothesised that circulating levels of non-coding RNAs in patients with stable CAD may relect progression of atherosclerotic disease or adverse myocardial remodeling, and may help identify patients at risk of future cardiovascular events. Here we demonstrate that mRNAs, lncRNAs and circRNAs can be reliably detected in human plasma by deep RNA-Seq and report novel candidate biomarkers for the presence of CAD.
2022-11-02 | GSE208194 | GEO
Project description:Idiopathic short stature is diagnosed by a standing height of less than two standard deviation scores in a specific population adjusted for age and gender and the exclusion of identifiable diseases. A series of studies have confirmed that noncoding RNAs can regulate the chondrocyte proliferation, hypertrophy, and endochondral ossification in the growth plate. In order to analyze and find differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs in peripheral blood exosomes of idiopathic short stature and healthy controls, we aimed to explore whether differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes of idiopathic short stature. Three pairs of peripheral blood exosomes samples were subjected to microarray analysis using the SBC human ceRNA Microarray.
2023-01-31 | GSE193994 | GEO
Project description:Aims Osteoarthritis (OA) is a common degenerative disease that is pathologically characterized by destruction of the joint matrix and reduction of articular chondrocytes, resulting in joint deformity and motor dysfunction. However, the molecular mechanisms governing this pathology have not been fully elucidated to date. Methods In this study, we determined the expression levels of lncRNAs, circRNAs, and mRNAs extracted from synovial exosomes of OA and control patients. A network of circRNA/lncRNA–miRNA–mRNA interactions was established using MiRanda and TargetScan software to explore OA pathogenesis. The exosomal lncRNA, circRNA and mRNA expression profiles of the OA and control groups were analysed using LC human competing endogenous RNA (ceRNA) microarrays. The differentially expressed genes were identified to determine their potential roles in the pathogenesis of OA by bioinformatic analysis. Results Compared with the control group, 11 mRNAs, 52 lncRNAs, and 30 circRNAs were upregulated, while 41 mRNAs, 144 lncRNAs, and 68 circRNAs were downregulated in osteoarthritis synovial exosomes. The final ceRNA network of lncRNAs and circRNAs exhibited a complex interaction between ncRNA and mRNA related to OA pathological mechanisms. An intersection analysis of the ceRNA network showed that 22 miRNAs, 45 lncRNAs, and 34 circRNAs in the PI3K/Akt and autophagy pathways correlated with 7 enriched mRNAs and may play important roles in OA pathological mechanisms. Conclusion Our work analysed mRNA/lncRNA/circRNA expression and displayed the ceRNA network of lncRNAs and circRNAs to profile the pathogenesis of OA in synovial exosomes. The results of this study may help to elucidate the pathogenesis of OA and may provide important references for further research attempting to identify more effective targets for the diagnosis and therapy of OA.
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Project description:Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs circRNAs and miRNAs. We identified that the expression of 501 lncRNAs, 1789 mRNAs, 2038 circRNAs and 143 miRNAs were often altered between glioblastoma and matched normal brain tissue. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on these differentially expressed mRNAs and miRNA-mediated target genes of lncRNAs and circRNAs. Furthermore, we used a multi-step computational framework and several bioinformatics methods to construct a ceRNA network combining mRNAs, miRNAs, lncRNAs and circRNA, based on co-expression analysis between the differentially expressed RNAs. We identified that plenty of lncRNAs, CircRNAs and their downstream target genes in the ceRNA network are related to glutamatergic synapse, suggesting that glutamate metabolism is involved in glioma biological functions. Our results will accelerate the understanding of tumorigenesis, cancer progression and even therapeutic targeting in glioblastoma. We hope to inspire researchers to study the role of non-coding RNAs in glioblastoma.
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Project description:We report the application of RNA sequencing technology for high-throughput profiling of transcriptomes in plasma exosomes from early-stage ESCC and esophagitis. By analyzing over 95G of clean reads (depleted rRNA), we found that expression features of exosomal lncRNAs were distinct from that of exosomal mRNAs. We identified differentially expressed exosomal lncRNAs and mRNAs for ESCC, and esophagitis. We further analyzed the biological functions of differentially expressed lncRNAs using GO, KEGG, as well as knockdown assay with siRNAs. This study provides information for identifying cancer and non-malignant disease relevant exosomal lncRNAs through integrative analyses of RNA sequencing data.
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