scholarly journals The circular RNA expression profile in ovarian serous cystadenocarcinoma reveals a complex circRNA–miRNA regulatory network

2021 ◽  
Vol 14 (S2) ◽  
Author(s):  
Minhui Zhuang ◽  
Jian Zhao ◽  
Jing Wu ◽  
Shilong Fu ◽  
Ping Han ◽  
...  
Keyword(s):  
Potential Function ◽  
Expression Profile ◽  
Regulatory Network ◽  
Noncoding Rna ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Mirna Sponge ◽  
Normal Tissues ◽  
Serous Cystadenocarcinoma

Abstract Background Ovarian serous cystadenocarcinoma is one of the most serious gynecological malignancies. Circular RNA (circRNA) is a type of noncoding RNA with a covalently closed continuous loop structure. Abnormal circRNA expression might be associated with tumorigenesis because of its complex biological mechanisms by, for example, functioning as a microRNA (miRNA) sponge. However, the circRNA expression profile in ovarian serous cystadenocarcinoma and their associations with other RNAs have not yet been characterized. The main purpose of this study was to reveal the circRNA expression profile in ovarian serous cystadenocarcinoma. Methods We collected six specimens from three patients with ovarian serous cystadenocarcinoma and adjacent normal tissues. After RNA sequencing, we analyzed the expression of circRNAs with relevant mRNAs and miRNAs to characterize potential function. Results 15,092 unique circRNAs were identified in six specimens. Approximately 46% of these circRNAs were not recorded in public databases. We then reported 353 differentially expressed circRNAs with oncogenes and tumor-suppressor genes. Furthermore, a conjoint analysis with relevant mRNAs revealed consistent changes between circRNAs and their homologous mRNAs. Overall, construction of a circRNA–miRNA network suggested that 4 special circRNAs could be used as potential biomarkers. Conclusions Our study revealed the circRNA expression profile in the tissues of patients with ovarian serous cystadenocarcinoma. The differential expression of circRNAs was thought to be associated with ovarian serous cystadenocarcinoma in the enrichment analysis, and co-expression analysis with relevant mRNAs and miRNAs illustrated the latent regulatory network. We also constructed a complex circRNA–miRNA interaction network and then demonstrated the potential function of certain circRNAs to aid future diagnosis and treatment.

scholarly journals Circular RNA Expression Profile of Pancreatic Ductal Adenocarcinoma Revealed by Microarray

2016 ◽  
Vol 40 (6) ◽  
pp. 1334-1344 ◽  
Author(s):  
Haimin Li ◽  
Xiaokun Hao ◽  
Huimin Wang ◽  
Zhengcai Liu ◽  
Yong He ◽  
...  
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Expression Profile ◽  
Mammalian Cells ◽  
Noncoding Rna ◽  
Circular Rna ◽  
Pathological Process ◽  
Ductal Adenocarcinoma ◽  
Circular Rnas ◽  
Normal Tissues ◽  
Polymerase Chain

Background/Aims: Circular RNAs (circRNAs) are a special novel type of a stable, diverse and conserved noncoding RNA in mammalian cells. Particularly in cancer, circRNAs have been reported to be widely involved in the physiological/pathological process of life. However, it is unclear whether circRNAs are specifically involved in pancreatic ductal adenocarcinoma (PDAC). Methods: We investigated the expression profile of circRNAs in six PDAC cancer samples and paired adjacent normal tissues using microarray. A high-throughput circRNA microarray was used to identify dysregulated circular RNAs in six PDAC patients. Bioinformatic analyses were applied to study these differentially expressed circRNAs. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm these results. Results: We revealed and confirmed that a number of circRNAs were dysregulated, which suggests a potential role in pancreatic cancer. Conclusions: this study demonstrates that clusters of circRNAs are aberrantly expressed in PDAC compared with normal samples and provides new potential targets for the future treatment of PDAC and novel insights into PDAC biology.

scholarly journals Comprehensive Analysis of a Long Noncoding RNA-Associated Competing Endogenous RNA Network in Wilms Tumor

2020 ◽  
Vol 27 (2) ◽  
pp. 107327482093699
Author(s):  
Feng Zhang ◽  
Liping Zeng ◽  
Qinming Cai ◽  
Zihao Xu ◽  
Ruida Liu ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Wilms Tumor ◽  
Interaction Network ◽  
Tumor Stage ◽  
Messenger Rnas ◽  
Competing Endogenous Rna ◽  
Ontology Term ◽  
Normal Tissues ◽  
Pathway Analyses

Long noncoding RNA (lncRNA) plays crucial roles in various biological processes of different cancers, especially acting as a competing endogenous RNA (ceRNA). However, the role of lncRNA-mediated ceRNA in Wilms tumor (WT), which is the most common malignant kidney cancer in children, remains unknown. In present study, RNA sequence profiles and clinical data of 125 patients with WT consisting of 119 tumor and 6 normal tissues from Therapeutically Applicable Research To Generate Effective Treatments database were analyzed. A total of 1833 lncRNAs, 156 microRNAs (miRNAs), and 3443 messenger RNAs (mRNAs) were identified as differentially expressed (DE) using “DESeq2” package. The lncRNA-miRNA-mRNA ceRNA regulatory network involving 748 DElncRNAs, 33 DEmiRNAs, and 189 DEmRNAs was constructed based on miRcode, Targetscan, miRTarBase, and miRDB database. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that DEmRNAs were mainly enriched in cell proliferation-related processes and tumor-related pathways, respectively, and 13 hub genes were identified by a protein–protein interaction network. Survival analysis detected 48 lncRNAs, 7 miRNAs, and 16 mRNAs to have significant impact on the overall survival of patients with WT. Additionally, we found that 6 DElncRNAs with potential prognostic value were correlated with tumor stage ( DENND5B-AS1) and histologic classification ( TMPO-AS1, RP3-523K23.2, RP11-598F7.3, LAMP5-AS1, and AC013275.2) of patients with WT. Our research provides a great insight into understanding the molecular mechanism underlying occurrence and progression of WT, as well as the potential to develop targeted therapies and prognostic biomarkers.

scholarly journals Circular RNA Expression Profiles and Features in NAFLD Mice: A Study Using RNA-Seq Data

2020 ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously.Methods: A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).Results: The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development.Conclusions: Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

scholarly journals High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Junzhuo Si ◽  
Xia Tang ◽  
Lei Xu ◽  
Huichao Fu ◽  
Huayi Li ◽  
...  
Keyword(s):  
Regulatory Network ◽  
High Throughput Sequencing ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Infected Group ◽  
Biological Functions ◽  
Rd Cells ◽  
Enterovirus D68 ◽  
Whole Transcriptome ◽  
First Time

Abstract Background With the advancement of sequencing technologies, a plethora of noncoding RNA (ncRNA) species have been widely discovered, including microRNAs (miRNAs), circular RNAs (circRNAs), and long ncRNAs (lncRNAs). However, the mechanism of these non-coding RNAs in diseases caused by enterovirus d68 (EV-D68) remains unclear. The goal of this research was to identify significantly altered circRNAs, lncRNAs, miRNAs, and mRNAs pathways in RD cells infected with EV-D68, analyze their target relationships, demonstrate the competing endogenous RNA (ceRNA) regulatory network, and evaluate their biological functions. Methods The total RNAs were sequenced by high-throughput sequencing technology, and differentially expressed genes between control and infection groups were screened using bioinformatics method. We discovered the targeting relationship between three ncRNAs and mRNA using bioinformatics methods, and then built a ceRNA regulatory network centered on miRNA. The biological functions of differentially expressed mRNAs (DEmRNAs) were discovered through GO and KEGG enrichment analysis. Create a protein interaction network (PPI) to seek for hub mRNAs and learn more about protein–protein interactions. The relative expression was verified using RT-qPCR. The effects of Fos and ARRDC3 on virus replication were confirmed using RT-qPCR, virus titer (TCID50/ml), Western blotting. Results 375 lncRNAs (154 upregulated and 221 downregulated), 33 circRNAs (32 upregulated and 1 downregulated), 96 miRNAs (49 upregulated and 47 downregulated), and 239 mRNAs (135 upregulated and 104 downregulated) were identified as differently in infected group compare to no-infected group. A single lncRNA or circRNA can be connected with numerous miRNAs, which subsequently coregulate additional mRNAs, according to the ceRNA regulatory network. The majority of DEmRNAs were shown to be connected to DNA binding, transcription regulation by RNA polymerase II, transcription factor, MAPK signaling pathways, Hippo signal pathway, and apoptosis pathway, according to GO and KEGG pathway enrichment analysis. The hub mRNAs with EGR1, Fos and Jun as the core were screened through PPI interaction network. We preliminarily demonstrated that the Fos and ARRDC3 genes can suppress EV-D68 viral replication in order to further verify the results of full transcriptome sequencing. Conclusion The results of whole transcriptome analysis after EV-D68 infection of RD cells were first reported in this study, and for the first time, a ceRNA regulation network containing miRNA at its center was established for the first time. The Fos and ARRDC3 genes were found to hinder viral in RD cells. This study establishes a novel insight host response during EV-D68 infection and further investigated potential drug targets.

scholarly journals A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

2018 ◽  
Author(s):  
Benjamin Kleaveland ◽  
Charlie Y. Shi ◽  
Joanna Stefano ◽  
David P. Bartel
Keyword(s):  
Long Noncoding Rna ◽  
Regulatory Network ◽  
Noncoding Rna ◽  
Gene Editing ◽  
Noncoding Rnas ◽  
Circular Rna ◽  
Mammalian Brain ◽  
Viral Rnas ◽  
Gene Regulatory ◽  
Regulatory Rnas

SUMMARYNoncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncRNAs—a long ncRNA, a circular RNA, and two microRNAs—using gene editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncRNA Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microRNA. Cyrano-directed miR-7 degradation is much more efficient than previously described examples of target-directed microRNA degradation, which come from studies of artificial and viral RNAs. By reducing miR-7 levels, Cyrano prevents repression of miR-7–targeted mRNAs and enables the accumulation of Cdr1as, a circular RNA known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as, in part through enhanced slicing of Cdr1as by a second miRNA, miR-671. Thus, several types of ncRNAs can collaborate to establish a sophisticated regulatory network.HIGHLIGHTSA long noncoding RNA, a circular RNA, and two microRNAs form a regulatory networkThe Cyrano long noncoding RNA directs potent, multiple-turnover destruction of miR-7Unchecked miR-7 prevents accumulation of Cdr1as circular RNA in cytoplasm of neurons miR-7 prevents this accumulation by enhancing the miR-671-directed slicing of Cdr1as

scholarly journals Circular RNA expression profiles and features in NAFLD mice: a study using RNA-seq data

2020 ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously. Methods: A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results: The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development. Conclusions: Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

scholarly journals Circular RNA expression profile and potential function of hsa_circ_0045272 in systemic lupus erythematosus

Immunology ◽  
2018 ◽  
Vol 155 (1) ◽  
pp. 137-149 ◽  
Author(s):  
Lian-Ju Li ◽  
Zhi-Wei Zhu ◽  
Wei Zhao ◽  
Sha-Sha Tao ◽  
Bao-Zhu Li ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Potential Function ◽  
Expression Profile ◽  
Lupus Erythematosus ◽  
Circular Rna ◽  
Rna Expression ◽  
Systemic Lupus

Prediction and Analysis of Hub Genes in Ovarian Cancer Based on Network Analysis

2020 ◽  
Author(s):  
Yan Li ◽  
Juan Wang ◽  
Yan Zhu ◽  
Youguo Chen
Keyword(s):  
Gene Expression ◽  
Regulatory Network ◽  
Prognostic Value ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Hub Genes ◽  
R Language ◽  
Serous Cystadenocarcinoma ◽  
Tcga Dataset ◽  
Blue Module

Abstract Objective The aim of the present study was to identify the interactions among transcription factors (TFs), microRNAs (miRNAs) and mRNAs in ovarian serous cystadenocarcinoma (OV) to investigate the mechanisms. Method: Gene expression data were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened between tumor and nontumor samples using the online tool GEO2R based on the limma package of R language. The coexpression between genes was identified using the weighted gene corepression analysis (WGCNA) package of R language to construct a coding-noncoding network. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted for the genes in the coexpression network. The expression and prognostic value of the hub genes in coexpression were further validated in The Cancer Genome Atlas (TCGA) dataset. The interactions among miRNAs, mRNAs and TFs were predicted using miRGen and mirWalk to construct the TF-miRNA-mRNA regulatory network. Result The blue module was identified as significantly associated with OV, and a coexpression network were constructed through WGCNA analysis. The expression and prognostic value of the hub genes in the blue module were validated in the TCGA dataset. A total of 164 common differentially expressed miRNAs (DEMs) were screened from 2 miRNA datasets. A TF-miRNA-mRNA regulatory network composed of 2 TFs, 6 miRNAs and 199 mRNAs was constructed. QRT-PCR was also conducted to identify the expression of the 6 key miRNAs (hsa-mir-193b, hsa-mir-296, hsa-mir-29b-2, hsa-mir-29c, hsa-mir-34a and hsa-mir-421) in ovarian serous cystadenocarcinoma. Conclusion We constructed a validated TF-miRNA-mRNA network in OV, and TFs might regulate mRNAs by regulating miRNAs to act on the progression of OV.

scholarly journals Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 90 ◽  
Author(s):  
Xiaoyue Li ◽  
Cunyuan Li ◽  
Junchang Wei ◽  
Wei Ni ◽  
Yueren Xu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Endocrine Organ ◽  
Reverse Transcription Quantitative Pcr ◽  
Significant Difference ◽  
Profiling Analysis

The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9,231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.

Sign in / Sign up

Export Citation Format

Share Document