The diagnostic and prognostic value of hsa_circ_0084927 in colon adenocarcinoma and its ceRNA network construction (miRNA-Seq)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE189908 | GEO | 2021/12/06
REPOSITORIES: GEO
Similar Datasets
Project description:The diagnostic and prognostic value of hsa_circ_0084927 in colon adenocarcinoma and its ceRNA network construction (miRNA-Seq)
| PRJNA784982 | ENA
Project description:Previous studies have demonstrated that members of the brain-expressed X-linked (BEX) family participate in a wide range of biological functions in normal and tumor tissues. However, their role and clinical significance in lung adenocarcinoma (LUAD) remains unclear. The present study investigated The Cancer Genome Atlas data and revealed that the BEX family was downregulated in LUAD tissues compared with adjacent non-cancerous tissues. Additionally, analysis of LUAD cohorts from the Oncomine database revealed similar results. Furthermore, the expression of BEX members was significantly decreased in several LUAD cell lines compared with normal lung epithelial cells . The aforementioned data mining and results suggested that the BEX family may be involved in the development of LUAD. Furthermore, receiver operating characteristic curve analysis revealed that BEX members exhibited high sensitivity and specificity for the diagnosis of patients with LUAD. The low expression levels of BEX1, BEX4 and BEX5 were associated with certain pathologic features, particularly in advanced LUAD. Survival analysis demonstrated that BEX members, particularly BEX4, were involved in the prognosis of patients with LUAD at early and late clinical stages. The results obtained in the current study suggested that BEX members may serve as potential tumor biomarkers for the diagnosis and prognosis of patients with LUAD.
| S-EPMC6781490 | biostudies-other
Project description:BackgroundMore and more studies have proven that circular RNAs (circRNAs) play vital roles in cancer development via sponging miRNAs. However, the expression pattern of competing endogenous RNA (ceRNA) in lung adenocarcinoma (LUAD) remains largely unclear. The current study explored functional roles and the regulatory mechanisms of circRNA as ceRNAs in LUAD and their potential impact on LUAD patient prognosis.MethodsIn this study, we systematically screened differential expression circRNAs (DEcircRNAs), miRNAs (DEmiRNAs) and mRNAs (DEGs) associated with LUAD. Then, DEcircRNAs, DEmiRNAs and DEGs were selected to construct a circRNA-miRNA-mRNA prognosis-related regulatory network based on interaction information from the ENCORI database. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the genes in the network to predict the potential underlying mechanisms and functions of circRNAs in LUAD. In addition, Kaplan-Meier survival analysis was performed to evaluate clinical outcomes of LUAD patients, and drug sensitivity analysis was used to screen potential biomarkers for drug treatment of patients with LUAD.ResultsAs a result, 10 circRNAs were aberrantly expressed in LUAD tissues. The ceRNA network was built, which included 3 DEcircRNAs, 6 DEmiRNAs and 157 DEGs. The DEGs in the ceRNA network of hsa_circ_0049271 enriched in biological processes of cell proliferation and the Jak-STAT signaling pathway. We also detected 7 mRNAs in the ceRNA network of hsa_circ_0049271 that were significantly associated with the overall survival of LUAD patients (P < 0.05). Importantly, four genes (PDGFB, CCND2, CTF1, IL7R) identified were strongly associated with STAT3 activation and drugs sensitivity in GDSC.ConclusionsIn summary, a ceRNA network of hsa_circ_0049271 was successfully constructed, which including one circRNA, two miRNAs, and seven mRNAs. Seven mRNAs (PDGFB, TNFRSF19, CCND2, CTF1, IL11RA, IL7R and MAOA) were remarkably associated with the prognosis of LUAD patients. Among seven mRNA species, four genes (PDGFB, CCND2, CTF1, and IL7R) could be considered as drug targets in LUAD. Our research will provide new insights into the prognosis-related ceRNA network in LUAD.
| S-EPMC8299662 | biostudies-literature
Project description:BackgroundLong noncoding RNAs (lncRNAs) could function as competitive endogenous RNAs (ceRNAs) to competitively adsorb microRNAs (miRNAs), thereby regulating the expression of their target protein-coding mRNAs. In this study, we aim to identify more effective diagnostic and prognostic markers for lung adenocarcinoma (LUAD).MethodsWe obtained differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) for LUAD by using The Cancer Genomes Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) was performed to unveil core gene modules associated with LUAD. The Cox proportional hazards model was performed to determine the prognostic significance of DElncRNAs. The diagnostic and prognostic significance of DElncRNAs was further verified based on the receiver operating characteristic curve (ROC). Cytoscape was used to construct the ceRNA networks comprising the lncRNAs-miRNAs-mRNAs axis based on the correlation obtained from the miRcode, miRDB, and TargetScan.ResultsCompared with normal lung tissues, 2355 DElncRNAs, 820 DEmiRNAs, and 17289 DEmRNAs were identified in LUAD tissues. We generated 8 WGCNA core modules in the lncRNAs coexpression network, 5 modules in the miRNAs, and 12 modules in the mRNAs coexpression network, respectively. One lncRNA module (blue) consisting of 441 lncRNAs, two miRNA modules (blue and turquoise) containing 563 miRNAs, and one mRNA module (turquoise), which consisted of 15162 mRNAs, were mostly significantly related to LUAD status. Furthermore, 67 DEmRNAs were found to be tumor-associated as well as the target genes of the DElncRNAs-DEmiRNAs axis. Survival analyses showed that 6 lncRNAs (LINC01447, WWC2-AS2, OGFRP1, LINC00942, LINC01168, and AC005863.1) were significantly correlated with the prognosis of LUAD patients. Ultimately, the potential ceRNA networks including 6 DElncRNAs, 4 DEmiRNAs, and 22 DEmRNAs were constructed.ConclusionOur study indicated that 6 DElncRNAs had the possibilities as diagnostic and prognostic biomarkers for LUAD. The lncRNA-mediated ceRNA networks might provide novel insights into the molecular mechanisms of LUAD progression.
| S-EPMC8723861 | biostudies-literature
Project description:Colorectal cancer (CRC) includes colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ). Competitive endogenous RNA (ceRNA) is crucial for cancer pathogenesis. Abnormal expression of MYC is generally associated with a poor colon adenocarcinoma prognosis. The present study aimed to identify a novel MYC-associated ceRNA regulatory network and identify potential prognostic markers associated with COAD. We obtained the transcriptome sequencing profiles of 462 COAD cases from the TCGA database and analyzed differentially expressed genes (DEGs) in MYC high expression (MYChigh) and MYC low expression (Myclow) tumors. We identified an important lncRNA, LINC00114, which effectively predicts overall survival and plays a protective role in COAD. Moreover, the LINC00114/miR-216a-5p axis was identified as a clinical prognostic model. The predicted target genes of the LINC00114/miR-216a-5p axis include uromodulin Like 1 (UMODL1) and oncoprotein induced transcript 3 (OIT3), which are closely related to the survival and prognosis of COAD patients. In summary, we constructed a novel ceRNA regulatory network and identified potential biomarkers for the targeted therapy and prognosis of COAD.
| S-EPMC9277212 | biostudies-literature
Project description:Colorectal cancer (CRC) ranks as the second leading cause of cancer-related mortality globally and is the third most prevalent cancer. The effective treatment of CRC is challenged by tumor drug resistance, underscoring the urgent need for novel therapeutic strategies. It is well recognized that epigenetic modifications, particularly DNA methylation, significantly contribute to the initiation and advancement of CRC. Tumors frequently exhibit hypermethylation of specific gene promoters alongside a general hypomethylation of genomic DNA. In normal tissues, gene promoters, particularly those of tumor suppressor genes, are typically unmethylated, whereas they are often hypermethylated in cancerous tissues. Previous studies have identified the methylation status of the CpG island within the SLC30A10 gene as a reliable biomarker for CRC. Notably, a hypermethylated phenotype is inversely correlated with SLC30A10 expression. However, the precise functional implications of SLC30A10 suppression in the context of CRC progression remain to be elucidated.). The investigation of molecular pathways involved in metal metabolism in CRC has not been conducted previously at the transcriptomic level. Furthermore, the relationship between the mutational characteristics of tumors—such as individual mutations, mutational burden, and microsatellite instability—and the activity of genes related to metal metabolic pathways has not been explored. This project aims to be the first to examine the antitumor potential of modulating the transport systems for manganese and zinc ions in CRC. The molecular function of SLC30A10 is to export zinc (Zn) and manganese (Mn) ions from the cell. Additionally, SLC30A10 plays a crucial role in mitigating Mn-induced cytotoxicity and facilitates Zn transport to early endosomes while promoting endosomal recirculation to avert Zn toxicity. Our findings indicate that overexpression of SLC30A10 is correlated with the knockout of its functional antagonist, SLC39A14 in the HuTu80 and HCT-15 cell lines.
2024-09-15 | GSE276849 | GEO
Project description:Accumulating evidence suggested that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to interact with other RNA transcripts and ceRNAs perturbation play important roles in cancer initiation and progression including pancreatic adenocarcinoma (PAAD). In this study, we constructed a PAAD-specific hallmark gene-related ceRNA network (HceNet) using paired genome-wide expression profiles of mRNA, lncRNA and miRNA and regulatory relationships between them. Based on "ceRNA hypothesis", we analyzed the characteristics of HceNet and identified a ceRNA module comprising of 29 genes (12 lncRNAs, two miRNAs and 15 mRNAs) as potential prognostic biomarkers related to overall survival of patients with PAAD. The prognostic value of ceRNA module biomarkers was further validated in the train (Hazard Ratio (HR) =1.661, 95% CI: 1.275-2.165, p<1.00e-4), test (HR=1.546, 95% CI: 1.238-1.930, p<1.00e-4), and entire (HR=1.559, 95% CI: 1.321-1.839, p<1.00e-4) datasets. Our study provides candidate prognostic biomarkers for PAAD and increases our understanding of ceRNA-related regulatory mechanism in PAAD pathogenesis.
| S-EPMC5706890 | biostudies-other
Project description:BackgroundCircular RNAs (circRNAs), a new class of regulatory noncoding RNAs, are involved in gene regulation and may play a role in cancer development. The aim of this study was to identify circRNAs involved in lung adenocarcinoma (LUAD) using bioinformatics analysis.MethodsCircRNA (GSE101684, GSE101586), miRNA (GSE135918), and mRNA (GSE130779) microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed circRNAs (DECs), miRNAs (DEMs), and mRNAs (DEGs) in LUAD. Circinteractome and StarBase were used to predict miRNAs and mRNAs, respectively. A circRNA-miRNA-mRNA-ceRNA network was constructed. Patient survival was analyzed using UALCAN, and a sub-network was established. Real-time quantitative PCR (qRT-PCR) was used to verify the expressed of DECs between LUAD tissues and paired adjacent normal tissues.ResultsHsa_circ_0072088 was identified as a differentially expressed (upregulated) circRNA in the two datasets. Intersection analysis identified hsa-miR-532-3p and hsa-miR-942 as the two miRNAs with the highest potential for binding to hsa_circ_0072088. Differential expression analysis and target gene prediction were performed to build a ceRNA network of hsa_circ_0072088 using Circinteractome/StarBase 3.0. Intersection analysis showed that TMEM52, IL24, POF1B, KIF1A, NHS, LBH, HIST2H2BE, ABCC3, PYCR1, CD79A, IGF2BP3, ANKRD17, GTSE1, MKI67, CLSPN, PLAU, LUC7L, MAGIX, GPATCH4, and ABAT were potential downstream mRNAs. The association between the expression level of 20 DEGs and LUAD patient survival was analyzed using UALCAN and GEPIA, which showed that IGF2BP3, MKI67, CD79A, and ABAT were related to patient survival. Hsa_circ_0072088 was verified upregulated by qRT-PCR.ConclusionThe circRNA hsa_circ_0072088, the DEMs (hsa-miR-532-3p and hsa-miR-942-5p), and the DEGs (IGF2BP3, MKI67, CD79A, and ABAT) may serve as prognostic markers in LUAD.
| S-EPMC8197624 | biostudies-literature
Project description:Purpose:Accumulating evidence has indicated that circRNAs are closely involved in tumorigenesis and progression of human cancers. However, the molecular mechanism underlying function of circRNAs in breast cancer has not been thoroughly elucidated. Currently, we aimed to characterize the circRNA-related competing endogenous RNA (ceRNA) regulatory network in breast cancer and to construct prognostic model. Materials and Methods:First, we constructed circRNA expression profiles for paired breast cancer in a Chinese population using a human circRNA microarray. Expression profiles of circRNAs, miRNAs, and mRNAs were retrieved from our circRNA dataset, the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. We applied the limma and edgeR packages to identify differentially expressed RNAs. Weighted gene correlation network analysis (WGCNA) was used to identify critical modules of mRNAs. Next, a ceRNA network was established based on circRNA-miRNA and miRNA-mRNA intersections. Both Cox regression analysis and ROC curve analysis were performed to generate prognostic model. Additionally, we performed Gene Set Enrichment Analysis (GSEA) on prognostic signatures. Results:Total of 59 circRNAs, 98 miRNAs and 3966 mRNAs were identified as differentially expressed RNAs. We first identified 38 miRNA-mRNA pairs and 38 circRNA-miRNA pairs to construct the circRNA-miRNA-mRNA regulatory network and then generated a prognostic model based on 7 signatures (MMD, SLC29A4, CREB5, FOS, ANKRD29, MYOCD, and PIGR), and patients with high-risk scores presented poor prognosis. Several cancer-related pathways were enriched, including the TGF-? pathway, the focal adhesion pathway, and the JAK-STAT signaling pathway, and 20 prognostic ceRNA regulatory networks were subsequently identified. Conclusion:In all, we screened a series of dysregulated circRNAs, miRNAs, and mRNAs, and constructed circRNA-related ceRNA network in breast cancer. Our findings may help to deepen the understanding of circRNA-related regulatory mechanisms. Moreover, we generated a prognostic model that provided new insight into postoperative management for breast cancer.
| S-EPMC7455596 | biostudies-literature
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