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CircRNA microarray profile analysis in esophageal squamous cell carcinoma(ESCC) and adjacent normal tissues

ABSTRACT: The circRNA expression profile related to ESCC in high-incidence areas of China was successfully constructed, and differentially expressed circRNAs were screened out and their functions were predicted.The circRNA expression in ESCC tissues was significantly different from that in adjacent normal tissues.GO and Pathway analysis showed that differentially expressed circRNAs were mainly involved in biological functions such as cellular process, metabolic process, biological regulation, binding and catalytic activity, and involved in multiple regulatory pathways including extracellular matrix receptor interaction, adhesion spot, protein digestion and absorption.Then their circRNA-miRNA network was constructed to better understand the related mechanism of circRNAs and provide ideas for exploring the biology functions of circRNAs in ESCC, revealing that the differentially expressed circRNAs were closely related to ESCC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE157803 | GEO | 2023/09/10

REPOSITORIES: GEO

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microRNA microarray profile analysis in esophageal squamous cell carcinoma(ESCC) and adjacent normal tissues

Project description:The miRNA expression profile related to ESCC in high-incidence areas of China was successfully constructed, and differentially expressed miRNAs were screened out and their functions were predicted.The miRNA expression in ESCC tissues was significantly different from that in adjacent normal tissues.GO and Pathway analysis showed that differentially expressed miRNAs were mainly involved in biological functions such as cellular process, metabolic process, biological regulation, binding and catalytic activity, and involved in multiple regulatory pathways including extracellular matrix receptor interaction, adhesion spot, protein digestion and absorption.Then their circRNA-miRNA network was constructed to better understand the related mechanism of miRNAs and provide ideas for exploring the biology functions of miRNAs in ESCC, revealing that the differentially expressed miRNAs were closely related to ESCC.

2023-09-10 | GSE157805 | GEO

DNA methylation analysis in esophageal squamous cell carcinoma(ESCC) and adjacent normal tissues

Project description:DNA methylation related to ESCC in high-incidence areas of China was successfully constructed, and differentially DNA methylation were screened out and their functions were predicted.The DNA methylation in ESCC tissues was significantly different from that in adjacent normal tissues.

2023-09-10 | GSE157807 | GEO

Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed

Project description:Circular RNAs (circRNAs) are an endogenous class of animal RNAs. Despite their abundance, their function and expression in the nervous system are unknown. Therefore, we sequenced RNA from different brain regions, primary neurons, isolated synapses, as well as during neuronal differentiation. Using these and other available data, we discovered and analyzed thousands of neuronal human and mouse circRNAs. circRNAs were extraordinarily enriched in the mammalian brain, well conserved in sequence, often expressed as circRNAs in both human and mouse, and sometimes even detected in Drosophila brains. circRNAs were overall upregulated during neuronal differentiation, highly enriched in synapses, and often differentially expressed compared to their mRNA isoforms. circRNA expression correlated negatively with expression of the RNA-editing enzyme ADAR1. Knockdown of ADAR1 induced elevated circRNA expression. Together, we provide a circRNA brain expression atlas and evidence for important circRNA functions and values as biomarkers. To assess circRNA expression in mammalian brain, we sequenced and analyzed mouse brain regions (hippocampus, cerebellum, prefrontal cortex and olfactory bulb), various neuronal differentiation (mouse P19 and human SH-SY5Y cells) and maturation (mouse cortical neurons) stages, and subcellular compartments in mouse (synaptoneurosomal fraction, cytoplasmic fraction, whole brain lysate).

2015-04-24 | E-GEOD-65926 | biostudies-arrayexpress

Integrative analysis of differential circular RNA and long noncoding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma

Project description:We constructed a competing endogenous RNA (ceRNA) network of ESCC based on the bovementioned pathways. Our findings provide important insight into the role of lncRNAs and circRNAs in ESCC; the differentially expressed lncRNAs and circRNAs may represent potential targets for ESCC diagnosis and therapy.

2023-09-02 | GSE157373 | GEO

Profiling circular RNA in esophageal squamous cell carcinoma (ESCC) with lymph node metastasis

Project description:Circular RNAs (circRNAs) have been identified as a novel class of non-conding RNAs, which are stable and have covalently single-stranded loop configuration.With the improvement of RNA-sequencing and bioimofrmatics, numerous dysregulated expression of circRNAs has been identified in kinds of physiological and pathological processes, especially in tumorigenesis. To date, however, the discovery of cirtical circRNA abnormalities, as well as their functions and underlying mechanisms, in the progress of esophageal squamous cell carcinoma (ESCC), is still unknown.

2021-08-31 | GSE150476 | GEO

Identification of circRNA-miRNA-mRNA network and primary blast lung injury-related circRNAs in mouse

Project description:Background. Primary blast lung injury (PBLI) was the main cause of death for blast injury patients, however, there is no diagnosis and effective treatment for PBLI in clinical practice. Circular RNAs (circRNAs) is becoming new regulators of various diseases, and the performance of circRNAs in PBLI remain largely unknown. This study aimed to investigate the PBLI-related circRNA, to provide a new idea for the PBLI diagnosis and treatment. Methods. The differentially expressed (DE) circRNAs and mRNAs profile were screened by transcriptome high throughput sequencing. The differentially expressed circRNA linear transcripts and mRNAs were used to performed GO and KEGG pathway enrichment to investigate the potential function. The circRNA-miRNA-mRNA network was based on DE circRNA-miRNA pairs and PBLI-related mRNAs-miRNA pairs. Results. A total of 117 circRNAs and 681 mRNAs were aberrantly expressed in PBLI, including 64 up-regulated and 53 down-regulated circRNAs, and 315 up-regulated and 366 down-regulated mRNAs. GO and KEGG analysis revealed that the up-regulated circRNAs might involve MAPK signaling pathways, and down-regulated circRNAs might involve in the TGF-β signaling pathway. And the differentially expressed mRNAs might involve TNF signaling pathway and fanconi anemia pathway. A total of 89 PBLI-related circRNAs and 156 circRNAs-miRNA-mRNA interactions were predicted, these circRNAs might involve in the inflammation, oxidative stress or DNA damage repair in PBLI. Conclusion. This study reveals the circRNA-miRNA-mRNA network based on altered expression of circRNAs and mRNA in PBLI. Our results may provide information about the occurrence of PBLI and new ideas for diagnosing and treating PBLI.

2023-11-21 | GSE195726 | GEO

Circular RNA cFUT8 acts as an epithelialâmesenchymal transition trigger in liver cancer.

Project description:Using the highly sensitive cricRNA array, we screened 13617 circRNAs abundant in the human liver cancer and Adjacent normal liver tissues, and the function of differentially expressed circRANs were analyzed by bioinformatics. The results revealed that cFUT8 controls epithelialâmesenchymal transition in liver cancer by cFUT8/miR-548c-3p/FUT8 axis. In this study, three cases of liver cancer samples were used to acquire the circRNA expression profiling, and qRT-PCR was employed to confirm the results of circRNA microarrays. The functions of the differentially expressed circRNA were analyzed by bioinformatics methods. Finally, through in vivo and ex vivo experimentsï¼the âcFUT8/miR-548c-3p/FUT8 axisâ was found to control epithelialâmesenchymal transition in liver cancer

2016-02-26 | E-GEOD-78520 | biostudies-arrayexpress

rat bladder LC-MS/MS proteomics

Project description:Objective: Bladder outlet obstruction (BOO) is a common urologic disease associated with poorly understood molecular mechanisms. This study aimed to investigate the possible involvements of circRNAs (circular RNAs) and circRNA-encoded proteins in BOO development. Methods: The rat BOO model was established by the partial bladder outlet obstruction surgery. Differential expression of circRNA and protein profiles were characterized by deep RNA sequencing and iTRAQ quantitative proteomics respectively. Novel proteins encoded by circRNAs were predicted through ORF (open reading frame) selection using the GETORF software and verified by the mass spectrometry in proteomics, combined with the validation of their expressional alterations by quantitative RT-PCR. Results: Totally 3051 circRNAs were differentially expressed in bladder tissues of rat BOO model with widespread genomic distributions, including 1414 up-regulated and 1637 down-regulated circRNAs. Our following quantitative proteomics revealed significant changes of 85 proteins in rat BOO model, which were enriched in multiple biological processes and signaling pathways such as the PPAR and Wnt pathways. Among them, 21 differentially expressed proteins were predicted to be encoded by circRNAs and showed consistent circRNA and protein levels in rat BOO model. The expression of five protein-encoding circRNA were further validated by quantitative RT-PCR and mass spectrometry. Conclusion: The circRNA and protein profiles were substantially altered in rat BOO model, with great expressional changes of circRNA-encoded novel proteins.

2022-02-22 | PXD029337 | Pride

Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals

Project description:Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human Alu repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified new circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched compared to linear controls. By scoring the presence of reverse complementary sequences in human introns we predicted and experimentally validated novel circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyper-editing events. Knockdown of the double-strand RNA editing ADAR1 enzyme significantly and specifically up-regulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA:RNA interactions of introns form larger structures which promote circularization of embedded exons, while ADAR1 antagonizes circRNA expression by melting stems within these interactions. Thus, we assign a new function to ADAR1. Examination of 12 samples in different stages of C.elegans development.

2015-01-06 | E-GEOD-63823 | biostudies-arrayexpress

Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing

Project description:Background: Ischemic stroke is a disease with high rate of death and disability worldwide. This study investigated key circRNAs related to ischemic stroke. Methods: Three ischemic stroke patients and three healthy individuals were included in the current study to obtain the circRNA expression profiles by RNA sequencing. Through bioinformatic analysis, differentially expressed circRNAs (DEcircRNAs) were identified, and GO and pathway analyses for the host genes of DEcircRNAs were conducted. To further explore the functions of key circRNAs, a DEcircRNA-miRNA interaction network was constructed. Finally, the expression levels of selected circRNAs were validated with qRT-PCR. Results: A total of 736 DEcircRNAs were detected in ischemic stroke. Functional annotation of host genes of DEcircRNAs revealed several significantly enriched pathways, including Fc epsilon RI signaling pathway, B cell receptor signaling pathway, and T cell receptor signaling pathway. A circRNA-miRNA network, including 1544 circRNA-miRNA pairs, 456 circRNAs and 4 miRNAs, was obtained. The qRT-PCR results were largely in keeping with our RNA-seq data. Conclusion: The results of our study may help to elucidate the specific mechanism underlying ischemic stroke.

2021-06-24 | GSE178764 | GEO

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