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Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [miRNA]

ABSTRACT: We explored the whole expression profiles of transcriptome included miRNA, circRNA, lncRNA and mRNA in 5 pairs of LSCC and matched non-LSCC tissues by microarray The LSCC-related competing endogenous RNA (ceRNA) networks were constructed based on these microarray data.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE116994 | GEO | 2020/07/10

REPOSITORIES: GEO

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Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [circRNA]

Project description:We explored the whole expression profiles of transcriptome included miRNA, circRNA, lncRNA and mRNA in 5 pairs of LSCC and matched non-LSCC tissues by microarray The LSCC-related competing endogenous RNA (ceRNA) networks were constructed based on these microarray data.

2020-07-10 | GSE117001 | GEO

2020-07-10 | GSE117005 | GEO

Comprehensive circRNA expression profile and construction of circRNAs-related ceRNA network in a mouse model of autism

Project description:Purpose: We aimed to detected the circRNA expression profile and constructed a circRNA-based competing endogenous RNA (ceRNA) network in autism. Methods:Valproate acid was used to establish an in vivo model of autism in mice. circRNAs in autism group was identified by RNA sequencing. The expression of circRNAs were detected by real-time PCR. Module analysis was conducted followed by GO and KEGG pathway enrichment analysis. Results: A total of 1059 differentially expressed circRNAs (477 upregulated and 582 downregulated) in autism group. The expression of novel_circ_015779 and novel_circ_035247 were detected by real-time PCR. A ceRNA network based on altered circRNAs was established, with 9715 nodes and 150408 edges. The top three modules were all correlated with autism-related pathways involving ‘TGF-beta signaling pathway’, ‘Notch signaling pathway’, ‘MAPK signaling pathway’, ‘long term depression’, ‘thyroid hormone signaling pathway’, etc. Conclusions: The present study reveals a novel circRNA involved mechanisms in the pathogenesis of autism.

2020-12-29 | GSE163904 | GEO

Whole-transcriptomic analysis of circRNA-miRNA-mRNA ceRNA network in 4-month APP/PS1 mouse hippocampus

Project description:Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, and the molecular mechanisms of AD remain unclear. Accumulating evidence indicates the involvement of non-coding RNAs in AD pathogenesis. Here, we applied RNA-seq to explore the expression changes of circRNA, miRNA, and mRNA simultaneously, and investigate competing endogenous RNA (ceRNA) networks in hippocampus of 4-month APP/PS1 and wild-type mice.

2022-07-27 | GSE166393 | GEO

Comprehensive Analysis of ceRNA Network Composed of circRNA, miRNA, and mRNA in septic acute kidney injury patients based on RNA-seq

Project description:Sepsis is a complex, life-threatening clinical syndrome that can cause other related diseases, such as acute kidney injury (AKI). Circular RNA (circRNA) is a type of non-coding RNA with a diverse range of functions, and it plays essential roles in miRNA sponge. CircRNA plays a huge part in the development of various diseases. CircRNA and the competing endogenous RNA (ceRNA) regulatory network are unknown factors in the onset and progression of septic AKI (SAKI). This study aimed to clarify the complex circRNA-associated regulatory mechanism of circRNAs in SAKI.

2023-09-14 | GSE242059 | GEO

Comprehensive Analysis of ceRNA Network Composed of circRNA, miRNA, and mRNA in septic acute kidney injury patients based on RNA-seq

2023-09-14 | GSE232404 | GEO

Comprehensive analysis of circRNA expression profiles and circRNA associated competing endogenous RNA networks in IgA nephropathy

Project description:Purpose: Immunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide, the exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA, microRNA (miRNA), and messenger RNA (mRNA) ceRNA network in peripheral blood mononuclear cells (PBMCs) of IgAN. Methods: CircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls. A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN. Results: A total of 145 circRNAs were differentially expressed in IgAN compared with controls (|log2 (FC)|>1 and P-value <0.05). Combined with the data from GSE73953 and GSE25590 in GEO database, a ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs). Conclusion: Our study identified a novel circRNA-mediated ceRNA regulatory network mechanisms in the pathogenesis of IgAN.

2020-11-08 | GSE154046 | GEO

The angiogenic role of circRNA-007371 in liver fibrosis [circRNA Microarray]

Project description:Objective Circular RNAs (circRNAs) are covalently closed, endogenous non-coding RNAs. CircRNAs play a vital role in liver diseases, acting as microRNA (miRNA) sponges. However, the angiogenic role of circRNA remains unknown in liver fibrosis and is the focus of this study. Methods Liver fibrosis was induced by thioacetamide (TAA), or carbon tetrachloride (CCl4) in mice. CircRNA-microarray, AGO2-RNA immunoprecipitation (RIP), and RNA-seq were utilized to explore the hepatic circRNAs profile. The qPCR and PCR-gel electrophoresis analysis were used to investigate the characterization of circRNA-007371. Liver tissues and EMOA murine endothelial cells were used to verify the angiogenic mechanism of circRNA-007371. Results The increased collagen deposition, pseudolobule formation, and angiogenesis were observed in murine liver induced by TAA and CCl4. CircRNA-microarray in TAA-induced fibrotic murine liver indicated that the expression of circRNA-007371 was up-regulated. Moreover, AGO2-RIP and PCR analysis showed that circRNA-007371 had the characterization of circRNAs and played a role as competing endogenous RNAs (ceRNA) sponging miR-200a. In vitro, circRNA-007371 promoted the ability of migration, growth, and blood vessel formation in EMOA murine endothelial cells using wound healing and tube formation assay. The AGO2-RIP and RNA-sequencing analysis in overexpression circRNA-007371 EMOA murine endothelial cells demonstrated that circRNA-007371 upregulates the stromal antigen 1 (Stag1) via spouse of miR-200a and HIF-1 signaling pathway might participate in the angiogenesis. Conclusions This study discovers that circRNA-007371, a novel ceRNA, is up-regulated, and enhances the angiogenesis via angiocrine role to regulate the STAG1-miR-200a-5p signaling pathway in liver fibrosis.

2023-06-28 | GSE218574 | GEO

Identification of specific ceRNA signatures in prostate cancer (PCa)

Project description:In order to develop novel biomarkers in prostate cancer, we applied a competing endogenous RNA (ceRNA) microarray to identify differentially expressed mRNAs, circRNAs and lncRNAs in PCa tissue.

2019-11-26 | GSE140927 | GEO

Whole transcriptome sequencing of 50 laryngeal squamous cell carcinoma and paired adjacent normal tissues

Project description:Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout transcriptome sequencing to identify lncRNA, mRNA, and circRNA that associated with LSCC progression.Transcriptome sequencing were performed on a cohort of LSCC tissues (50 samples) and paired adjacent normal mucosa tissues (50 samples).

2023-05-24 | GSE130605 | GEO

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