Similar Datasets
Project description:Cadmium is a naturally existing heavy metal and a typical environmental pollutant which is a significant threat to human health and can lead to acute and chronic damage to various organs. At present, hundreds of lncRNAs and miRNAs have been confirmed to be related to the toxicity of Cd. However, the role of circRNA in the toxicity of Cd and the involved regulatory mechanism has not been clarified. In this work, human normal liver cell (L-02) was selected as model to identify the changes in the expression level of circRNA after exposure to Cd. Total RNA of each sample was extracted by Trizol method, the original data of circRNA, miRNA and mRNA expression levels of each sample were obtained by microarray hybridization and scanning were standardized and differentially expressed. Differential circRNAs, miRNAs, and mRNAs associated with the toxic effects of Cd were identified. Construct a ceRNA network by screening the predicted circRNA, miRNA and mRNA and predict the main biological functions and metabolic pathways of the network. A total of 266 different circRNAs, 223 different miRNAs and 519 different mRNAs were identified by differential expression analysis. After screening, seven circRNAs, 10 miRNAs and 97 mRNAs were constructed into ceRNA network. After GO enrichment and KEGG pathway analysis of 97 mRNAs in circRNA-miRNA-mRNA network, indicated that circRNA in the ceRNA network may regulate cell proliferation, apoptosis, oxidative stress and inflammatory response under the toxic effect of Cd to damage L-02, and it has obvious dose-response effect and time effect.
2024-10-08 | GSE246129 | GEO
Project description:Cadmium is a naturally existing heavy metal and a typical environmental pollutant which is a significant threat to human health and can lead to acute and chronic damage to various organs. At present, hundreds of lncRNAs and miRNAs have been confirmed to be related to the toxicity of Cd. However, the role of circRNA in the toxicity of Cd and the involved regulatory mechanism has not been clarified. In this work, human normal liver cell (L-02) was selected as model to identify the changes in the expression level of circRNA after exposure to Cd. Total RNA of each sample was extracted by Trizol method, the original data of circRNA, miRNA and mRNA expression levels of each sample were obtained by microarray hybridization and scanning were standardized and differentially expressed. Differential circRNAs, miRNAs, and mRNAs associated with the toxic effects of Cd were identified. Construct a ceRNA network by screening the predicted circRNA, miRNA and mRNA and predict the main biological functions and metabolic pathways of the network. A total of 266 different circRNAs, 223 different miRNAs and 519 different mRNAs were identified by differential expression analysis. After screening, seven circRNAs, 10 miRNAs and 97 mRNAs were constructed into ceRNA network. After GO enrichment and KEGG pathway analysis of 97 mRNAs in circRNA-miRNA-mRNA network, indicated that circRNA in the ceRNA network may regulate cell proliferation, apoptosis, oxidative stress and inflammatory response under the toxic effect of Cd to damage L-02, and it has obvious dose-response effect and time effect.
2024-10-08 | GSE246130 | GEO
Project description:Cadmium is a naturally existing heavy metal and a typical environmental pollutant which is a significant threat to human health and can lead to acute and chronic damage to various organs. At present, hundreds of lncRNAs and miRNAs have been confirmed to be related to the toxicity of Cd. However, the role of circRNA in the toxicity of Cd and the involved regulatory mechanism has not been clarified. In this work, human normal liver cell (L-02) was selected as model to identify the changes in the expression level of circRNA after exposure to Cd. Total RNA of each sample was extracted by Trizol method, the original data of circRNA, miRNA and mRNA expression levels of each sample were obtained by microarray hybridization and scanning were standardized and differentially expressed. Differential circRNAs, miRNAs, and mRNAs associated with the toxic effects of Cd were identified. Construct a ceRNA network by screening the predicted circRNA, miRNA and mRNA and predict the main biological functions and metabolic pathways of the network. A total of 266 different circRNAs, 223 different miRNAs and 519 different mRNAs were identified by differential expression analysis. After screening, seven circRNAs, 10 miRNAs and 97 mRNAs were constructed into ceRNA network. After GO enrichment and KEGG pathway analysis of 97 mRNAs in circRNA-miRNA-mRNA network, indicated that circRNA in the ceRNA network may regulate cell proliferation, apoptosis, oxidative stress and inflammatory response under the toxic effect of Cd to damage L-02, and it has obvious dose-response effect and time effect.
2024-10-08 | GSE246131 | GEO
Project description:Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [circRNA]
| PRJNA1031612 | ENA
Project description:Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [miRNA]
| PRJNA1031613 | ENA
Project description:Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [mRNA]
| PRJNA1031614 | ENA
Project description:Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model
| PRJNA1031609 | ENA
Project description:BackgroundOsteosarcoma is a common malignant primary bone tumor in adolescents and children. Numerous studies have shown that circRNAs were involved in the proliferation and invasion of various tumors. However, the role of circRNAs in osteosarcoma remains unclear. Here, we aimed to explore the regulatory network among circRNA-miRNA-mRNA in osteosarcoma.MethodsThe circRNA (GSE140256), microRNA (GSE28423), and mRNA (GSE99671) expression profiles of osteosarcoma were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed circRNAs, miRNAs and mRNAs were identified. CircRNA-miRNA interactions and miRNA-mRNA interactions were determined by Circular RNA Interactome (CircInteractome) database and microRNA Data Integration Portal (mirDIP) database, respectively. Then, we constructed a regulatory network. Function enrichment analysis of miRNA and mRNA was performed by DIANA-miRPath v3.0 and Metascape database, respectively. mRNAs with significant prognostic value were identified based on expression profiles from The Cancer Genome Atlas (TCGA) database, and we constructed a subnetwork for them. To make the most of the network, we used the CLUE database to predict potential drugs for the treatment of osteosarcoma based on mRNA expression in the network. And we used the STITCH database to analyze and validate the interactions among these drugs and mRNAs, and to further screen for potential drugs.ResultsA total of 9 circRNAs, 19 miRNAs, 67 mRNAs, 54 pairs of circRNA-miRNA interactions and 110 pairs of miRNA-mRNA interactions were identified. A circRNA-miRNA-mRNA network was constructed. Function enrichment analysis indicated that these miRNAs and mRNAs in the network were involved in the process of tumorigenesis and immune response. Among these mRNAs, STC2 and RASGRP2 with significantly prognostic value were identified, and we constructed a subnetwork for them. Based on mRNA expression in the network, three potential drugs, quinacridine, thalidomide and zonisamide, were screened for the treatment of osteosarcoma. Among them, quinacridine and thalidomide have been proved to have anti-tumor effects in previous studies, while zonisamide has not been reported. And a corresponding drug-protein interaction network was constructed.ConclusionOverall, we constructed a circRNA-miRNA-mRNA regulatory network to investigate the possible mechanism in osteosarcoma, and predicted that quinacridine, thalidomide and zonisamide could be potential drugs for the treatment of osteosarcoma.
| S-EPMC8166411 | biostudies-literature
Project description:The growing evidence suggests that circular RNAs (circRNAs) have significant associations with tumor occurrence and progression, yet the regulatory mechanism of circRNAs in lung adenocarcinoma (LUAD) remains unclear. This study clarified the potentially regulatory network and functional mechanism of circRNAs in LUAD. The expression data of circRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) were obtained from the Gene Expression Omnibus (GEO) database. Relying on GSE101586, GSE101684, and GSE112214, we identified differentially expressed circRNAs (DEcircRNAs). Depending on GSE135918 and GSE32863, we screened out differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs), respectively. Then, a novel competing endogenous RNA (ceRNA) regulatory network related to LUAD was constructed. We also revealed biological processes and signal pathways regulated by these DEcircRNAs. Based on gene expression data and survival information of LUAD patients in The Cancer Genome Atlas (TCGA) and GEO, we implemented survival analysis to select DEmRNAs related to prognosis and build a novel circRNA-miRNA-mRNA hub regulatory network. Meanwhile, quantitative real-time PCR (qRT-PCR) was utilized to validate DEcircRNAs in the ceRNA hub regulatory network. As a result, a total of 8 DEcircRNAs, 19 DEmiRNAs, and 85 DEmRNAs were identified. The novel ceRNA regulatory network included 5 circRNAs, 8 miRNAs, and 22 mRNAs. The final ceRNA hub regulatory network contained two circRNAs, two miRNAs, and two mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that the five DEcircRNAs may affect LUAD onset and progression through Wnt signaling pathway and Hippo signaling pathway. All in all, this study revealed the regulatory network and functional mechanism of circRNA-related ceRNAs in LUAD.
| S-EPMC8292838 | biostudies-literature
Project description:Circular RNA (circRNA) abnormal expression and regulation are involved in the occurrence and development of a variety of tumors. However, the role of circRNAs still remains unknown in gastrointestinal stromal tumors (GISTs). In the present study, the differential circRNA expression profile of GISTs was screened by human circRNAs chip and verified by qRT-PCR. The circRNA-miRNA-mRNA regulatory network was constructed using the cytoHubba plugin based on the Cytoscape software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore circRNA functions. Six significantly differential circRNAs were also verified in 20 pairs of GISTs and adjacent tissues by qRT-PCR. The result showed that a total of 543 differentially expressed circRNAs were identified in GISTs, of which 242 were up-regulated and 301 were down-regulated. Additionally, the circRNA-miRNA-mRNA network contained six circRNAs, 30 miRNAs, and 308 mRNAs, and the targeted mRNAs were associated with "regulation of biological process," "intracellular organelle," "protein binding," and enriched in Wnt signaling pathway. Furthermore, qRT-PCR demonstrated that hsa_circRNA_061346, hsa_circRNA_103114, and hsa_circRNA_103870 were significantly up-regulated in GISTs (n = 20), and hsa_ circRNA_405324, hsa_circRNA_406821, and hsa_circRNA_000361 were dramatically down-regulated in GISTs (n = 20). In addition, all of these circRNAs were shown to have high diagnostic values, and most of them were significantly associated with tumor size, mitotic figure, and malignant degrees in GISTs (P < 0.05). Therefore, we concluded that circRNAs were abnormally expressed in GISTs, and the circRNA-miRNA-mRNA regulatory network plays an important role in the occurrence and development of GISTs. Also, the identified six candidate circRNAs might be critical circRNAs and may present as potential diagnostic biomarkers for GISTs.
| S-EPMC7271966 | biostudies-literature