Hsa_circ_0001583 a novel biomarker for breast cancer related to immune response
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE165884 | GEO | 2021/02/02
REPOSITORIES: GEO
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Project description:Objective: As one kind of novel non-coding RNA with high stability and conservatism, circular RNAs (circRNAs) are involved in different biological processes. Although growing evidence has supported the important role of circRNAs in renal diseases, the specific mechanism still remains unknown in neonatal acute kidney injury (AKI). Methods: High throughput sequencing analysis was applied to investigate the expression patterns of circRNAs in the comparison between hypoxia induced AKI neonates and controls. Then, bioinformatics analysis was conducted to predict the function of differentially expressed circRNAs and construct the network of circRNA-miRNA interaction. Results: (1) We identified 296 differentially expressed circRNAs (circRNAs with Fold change > 2 and P value < 0.05). Of them, 184 circRNAs were markedly up-regulated and 112 were significantly down-regulated in the AKI group. (2) Bioinformatics analysis indicated that the parental genes of the differentially expressed circRNAs were predominantly implicated in the cell and cell part, cellular process and cancer pathways. Conclusion: This study could contribute to future research of circRNAs in the pathogenesis of neonatal AKI and facilitate the identification of novel therapeutic targets of circRNAs.
2023-01-11 | GSE222578 | GEO
Project description:To determine the expression profile and clinical significance of circular RNAs (circRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with primary gout and healthy control subjects. Human circRNA microarrays were used to identify the differentially expressed circRNAs in primary gout (Gout, n = 5) and healthy subjects (HC, n = 3). Bioinformatics analyses were performed to predict the roles of differently expressed circRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results in 90 gout patients, and 60 healthy control subjects (HC). Microarray analysis indicated that 238 circRNAs were up-regulated and 41 circRNAs were down-regulated in the Gout group (Fold change>1.5, p-value<0.05). Bioinformatics analysis showed that differentially expressed circRNAs were involved in the pathogenesis of gout through a variety of different pathways. Significant association was observed between these circRNAs and lipid metabolism indicators. Our results provide novel insight into the mechanisms of primary gout, and reveal that hsa_circRNA_103657 could effectively discriminate the gout group and the healthy control groups.
2021-06-25 | GSE178825 | GEO
Project description:Aims: Exosomes exist in almost all body fluid and contain diverse biological contents which may be reflective of disease state. Circular RNAs (CircRNAs) are stable in structure and have a long half-life in exosomes without degradation, thus making them reliable biomarkers. However, the potential of exosomal circRNAs as biomarkers of coronary artery disease (CAD) remains to be established. Here we aimed to investigate the expression levels and the potential use of exosomal circRNAs as diagnostic biomarkers of CAD. Main methods: CircRNAs expression levels in exosomes obtained from three plasma samples from CAD patients and three paired controls were analyzed using RNA sequencing. Exosomal circRNAs obtained in the profiling phase were then verified in two-center validation cohorts. Finally, the ability of exosomal circRNAs, adjusting for Framingham Heart Study (FHS) risk factors, was determined to discriminate between CAD patients and non-CAD controls. Key findings: 355 circRNAs were differentially expressed between these two groups: 164 were upregulated, and 191 were downregulated. Here we selected potential circRNAs (fold change > 4, P < 0.05) as candidate biomarkers for further validation. Our data showed that only hsa_circ_0005540 was significantly associated with CAD (P < 0.0001). After adjustment for risk factors, hsa_circ_0005540 showed a high discriminatory power for CAD in ROC analyses (AUC = 0.853; 95% confidence interval [CI] = 0.799 - 0.906, P < 0.001). Significance: Our results suggest that plasma exosomal hsa_circ_0005540 can be used as a promising diagnostic biomarker of CAD.
2020-07-20 | GSE152498 | GEO
Project description:Here, we established a rat sciatic nerve injury model and investigated the circRNA expression profiles by Next-generation sequencing. In all, 7222 distinct circRNA candidates were found in these tissues and 4942 of these circRNAs contained at least two unique back-spliced reads. On the basis of expression of circRNA analysis, we found 131 circRNAs to be significantly (p-value<=0.05, Fold-change>=2) differently expressed in injured sciatic nerve tissues compared with matched normal tissues. All these circRNAs are derived from 21 rat chromosomes.
2020-01-01 | GSE115315 | GEO
Project description:Increasing evidence has demonstrated that circular RNA exerts important function in the pathogenesis of some diseases. While, the contributions of circRNAs to aseptic lossening after total hip arthroplasty remain largely unknown. Our research is to explore the differently expressed circRNAs and elucidate complex regulated mechanism of circRNAs in aseptic lossening. The differently expressed circRNAs were identified by RNA sequencing analysis. Reverse transcription-quantitative polymerase chain reaction was adopted to corroborate these differently expressed circRNAs. The potential function of circRNAs in aseptic lossening tissue was identified by competing endogenous RNA analysis. Enrichment analysis were performed for target mRNAs and host genes of the differently expressed circRNAs by Gene Oncology and Kyoto Encyclopedia of Genes and Genomes. 257 differently expressed circRNAs were obtained from RNA-seq results. Then, circRNA–miRNA–mRNA network was established based on the validated circRNAs. The result of Gene Oncology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that the circRNAs were related with some biological functions and pathways of aseptic lossening. A novel pathogenesis and treatment strategy about aseptic lossening after total hip arthroplasty was revealed from our study of circRNA–miRNA–mRNA network.
2021-01-19 | GSE149315 | GEO
Project description:Circular RNAs (circRNAs) are a kind of novel non-coding RNAs. Recent evidence has known that circRNAs play important roles in various diseases; however, few circRNAs have been well characterized in lung cancer. Understanding the expression profile of circRNAs and protein-coding genes is critical to discover the pathogenesis of lung cancer.
2017-07-19 | GSE101586 | GEO
Project description:Aberrant expression of circular RNAs (circRNAs) has been reported in a variety of cancers. CircRNAs may serve as candidate biomarkers and have implications for cancer diagnosis and treatment. RNA-sequencing (RNA-seq) was applied to detect circRNA expression in five CRC and paired normal tissues. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to measure circRNA expression, and the receiver operating characteristic curve was used to assess the diagnostic value of circRNA as a biomarker in 50 patients. A total of 1602 circRNAs were differentially expressed, including 743 upregulated and 859 downregulated circRNAs in CRC. CircST7L (hsa_circ_0110464) has a high diagnostic value for CRC. The expression of circST7L was closely associated with tumor size (P=0.024), grade (P=0.017), depth of invasion (P=0.034) and lymph node metastasis (P=0.001). In addition, prediction of circRNA-miRNA interactions identified miR-6821-5p, miR-1908-3p, and miR-6748-5p as pivotal targets of differentially expressed circRNAs. Finally, we predicted 7 miRNAs that may bind to circST7L and 13 target genes for these miRNAs. This study demonstrated that circRNAs were differentially expressed between CRC and normal tissues, and suggested that circST7L might be a promising diagnostic biomarker for CRC.
2023-09-01 | GSE235850 | GEO
Project description:Circular RNAs (circRNAs) have been increasingly indicated to be important participants in the development and progression of various malignant tumors. Our previous studies found that hundreds of circRNAs were aberrantly expressed in bladder cancer (BC) by high-throughput sequencing and we have confirmed that the downregulated circRNAs circHIPK3, BCRC3 and circNR3C1 played inhibitory roles in BC progression. However, the role of these upregulated circRNAs remain to be clarified. In this study, we analyzed circRNA high-throughout sequencing from human tissues and focused on the upregulated circRNAs and identified a novel circular RNA, hsa_circ_0001361 (also named bladder cancer upregulated circRNA-1, BCUC-1), as a new candidate circRNA derived from FNDC3B gene. The expression levels of circRNA and miRNAs in BC tissues and cells were detected by qRT-PCR. Transwell migration, Matrigel invasion, CCK-8, EdU, cell cycle and in vivo tumor metastasis assays were preformed to evaluate the effects of circ0001361 on BC cells. Transcriptome analysis was performed to find the potential genes that could be regulated by BCUC-1. Luciferase reporter, RNA pull-down and fluorescence in situ hybridization (FISH) assays were applied to verify the interaction between BCUC-1 and miR-491-5p.
2019-09-06 | GSE136919 | GEO
Project description:In order to identify circRNAs involved in HCC tumorigenesis, we performed circular RNA microarray analysis on three pairs of total RNA from HCC patient plasma and healthy controls. A total of 5122 differentially expressed circRNAs were identified (FC ≥ 2 or FC ≤ -2, P-value ≤ 0.05) . Among them, 4162 circRNAs were significantly up-regulated, and 960 circRNAs were significantly down-regulated.
2021-02-13 | GSE166678 | GEO
Project description:Background: Circular RNAs (circRNAs) have attracted increasing attention in recent years for their potential application as disease biomarkers due to their high abundance and stability. In this study, we attempted to screen circRNAs that can be used to predict postoperative recurrence and survival in patients with gastric cancer (GC). Methods: High-throughput RNA sequencing was used to identify differentially expressed circRNAs in GC patients with different prognoses. The expression level of circRNAs in the training set (n=136) and validation set (n=167) was detected by quantitative real-time PCR (qRT-PCR). Kaplan–Meier estimator, receiver operating characteristic (ROC) curve and cox regression analysis were used to evaluate the prognostic value of circRNAs on recurrence-free survival (RFS) and overall survival (OS) in GC patients. CeRNA network prediction, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for the circRNAs with prognostic significance. Results: A total of 259 differentially expressed circRNAs were identified in GC patients with different RFS. We found two circRNAs (hsa_circ_0005092 and hsa_circ_0002647) that highly expressed in GC patients with good prognoses, and subsequently established a predictive model for postoperative recurrence and prognosis evaluation, named circPanel. Patients with circPanellow might have shorter recurrence-free survival (RFS) and overall survival (OS). We also performed circRNA-miRNA-mRNA network prediction and functional analysis for hsa_circ_0005092 and hsa_circ_0002647. Conclusions: CircPanel has the potential to be a prognostic biomarker in GC patients with greater accuracy than a single circRNA and certain traditional tumor markers (e.g., CEA, CA19-9 and CA724).
2021-08-12 | GSE181769 | GEO