Comprehensive circular RNA expression profiling and competitive endogenous RNAs regulatory networks in distal cholangiocarcinoma
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ABSTRACT:
PROVIDER: PRJNA625034 | ENA |
REPOSITORIES: ENA
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Project description:To explore the differentially expressed (DE) circular (circ)RNAs, competing endogenous RNAs networks, and potential biomarkers in distal cholangiocarcinoma (dCCA), using microarray analysis, a comprehensive circRNA expression profiling was constructed with six paired dCCA tumor and adjacent normal samples. A total of 171 DE circRNAs were identified. Three upregulated (hsa_circ_0060144, hsa_circ_0008274, and hsa_circ_0000673) and two downregulated circRNAs (hsa_circ_0139402 and hsa_circ_0001714) were validated with RT-qPCR in 40 dCCA patients. Among them, hsa_circ_0000673 had an idea prognostic efficiency (AUC=0.85, p<0.01) and high level of hsa_circ_0000673 was associated with late tumor stage (p<0.01), poor histodifferentiation (p=0.041), and residual tumor (p=0.044). Gene ontology analysis of the host genes of 171 DE circRNAs showed that “response to nutrient”, “adherens junction”, and “cell adhesion molecule binding” were mainly enriched in terms of biological process, cellular component, and molecular functions respectively. Nine target micro(mi)RNAs of the five DE circRNAs were screened out and enriched in cancer associated pathways. Thereafter, 188 DE mRNAs were predicted as target genes of the nine miRNAs. Finally, protein-protein interaction networks were constructed and 20 hubgenes were identified. This research provided a landscape of DE circRNAs in dCCA, constructed circRNA-miRNA-mRNA regulating networks, and identified hsa_circ_0000673 as a potential biomarker and target for treating dCCA.
2020-12-31 | GSE148561 | GEO
Project description:Distal cholangiocarcinoma is an aggressive malignancy with a dismal prognosis. There is a lack of diagnostic and prognostic biomarkers. An improved understanding of proteomic changes associated with malignancy and identification of potential biomarkers can help improve the survival of patients. A workflow utilizing discovery mass spectrometry and verification by parallel-reaction monitoring was used to analyze surgically resected formalin-fixed paraffin embedded samples from distal cholangiocarcinoma patients and normal bile ducts in order to identify differentially expressed proteins. 20 tumors and 6 controls were successfully analyzed in the discovery experiment and 16 tumors and 9 controls in the PRM analysis. In the discovery experiment a total of 3057 proteins were identified. 87 proteins were found to be differentially expressed between the conditions (q<0.05 and fold change ≥2 or ≤0.5). 31 proteins were upregulated in the distal cholangiocarcinoma samples as compared to controls and 56 downregulated. Bioinformatic analysis revealed an abundance of the differentially expressed proteins to be associated with the tumor reactive stroma. Parallel-reaction monitoring verified 28 proteins as upregulated and 18 as downregulated. In conclusion several proteins without prior association with cholangiocarcinoma biology were identified and verified as differentially expressed between distal cholangiocarcinoma samples and normal bile ducts. These proteins can be further evaluated to elucidate their biomarker potential and role in distal cholangiocarcinoma carcinogenesis.
2020-09-09 | PXD017906 | Pride
Project description:Characterization and identification of extrachromosomal circular DNAs in cholangiocarcinoma
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Project description:Cholangiocarcinoma (CCA) is a type of highly aggressive cancer arising from the biliary system. Through bile exosome miRNA sequencing, we screened out the differentially expressed miRNA in patients with distal cholangiocarcinoma(dCCA) and common bile duct stones(CBDS).
2025-09-28 | GSE214372 | GEO
Project description:To identify miRNAs differentially expressed in cholangiocarcinoma,3 human cholangiocarcinoma and their corresponding normal bile duct tissues were obtained from 3 patients after operation with postoperative pathological diagnosed perihilar or distal biliary cholangiocarcinoma miRNAs expression in human cholangiocarcinoma/normal bile duct samples was measured after operation.Three independent experiments were performed using different patients for each experiment.
2013-06-10 | E-GEOD-47764 | biostudies-arrayexpress
Project description:To identify miRNAs differentially expressed in cholangiocarcinoma,3 human cholangiocarcinoma and their corresponding normal bile duct tissues were obtained from 3 patients after operation with postoperative pathological diagnosed perihilar or distal biliary cholangiocarcinoma
2013-06-10 | GSE47764 | GEO
Project description:Minimally- invasive diagnostic biomarkers for patients with pancreatic ductal adenocarcinoma (PDAC) and distal cholangiocarcinoma (CCA) are warranted to enhance early and accurate diagnosis. This study identified tumor tissue secreted proteins, the “secretome”, which was analysed for differential candidate diagnostic plasma proteins. Secretome of tumor and normal tissue was collected directly after resection of the primary tumor from 4 patients with PDAC and distal CCA. The tissue secretome was investigated by label-free LC-MSMS, and database searching identified a total of 5179 proteins. 696 proteins were differentially enriched in tumor secretome compared to normal tissue. Thrombospondin-2 (THBS2) emerged as most promising candidate diagnostic biomarker. Subsequent analysis of THBS2 in plasma samples of patients with PDAC and distal CCA by ELISA showed significantly higher abundance compared to healthy individuals (p<0.001) and resulted in an AUC of 0.844.
2020-05-26 | PXD012480 | Pride
Project description:Cholangiocarcinoma (CCA), consisting of three subtypes-intrahepatic (iCCA), perihilar (pCCA), and distal (dCCA), is a type of highly aggressive cancer arising from the biliary system and has an extremely poor prognosis. Through tissue miRNA sequencing, we screened out the differentially expressed miRNA in patients with 3 perihilar cholangiocarcinoma(pCCA) and 3 distal cholangiocarcinoma(dCCA) and its corresponding adjacent tissue.
2025-09-28 | GSE215146 | GEO
Project description:Distal cholangiocarcinoma (dCCA) is a biliary tract cancer with dismal prognosis and is often preceded by biliary intraepithelial neoplasia (BilIN) as a non-invasive precursor lesion. We found that miR-451a is downregulated in dCCA. Overexpression of mimic-451a in the CCA cell line SNU478 revealed multiple downregulated genes and potential miR-451a candidate targets.
2020-09-01 | GSE147969 | GEO
Project description:Introduction: Accurate diagnosis of distal cholangiocarcinoma (CCA) and pancreatic ductal adenocarcinoma (PDAC) is a challenge with clinical consequences. Both are lethal malignancies with distinct therapeutic options. This study aimed to identify a circulating microRNA (miRNA) signature to diagnose and discriminate distal CCA from PDAC. Methods: In the discovery phase, microarray profiling of 752 miRNAs was performed on plasma samples of seven patients with distal CCA and seven age- and sex-matched healthy controls. Significant candidate miRNAs were selected for validation based on predefined selection criteria. In the validation phase, these miRNAs were analyzed by RT-qPCR in an independent cohort of healthy controls (n=32), benign periampullary disease (n=20), distal CCA (n=24), and age- sex- and stage-matched PDAC (n=24). Data were normalized to a combination of two reference genes. The optimal diagnostic combination of miRNAs was determined by logistic regression. Sensitivity and specificity were evaluated by ROC curves and AUC values. Results: In the discovery phase, 19 miRNAs were significantly deregulated in patients with distal CCA compared to healthy controls. In the validation phase, 12 candidate miRNAs were selected for validation by RT-qPCR based on pre-defined selection criteria. A two-miRNA panel of downregulated miR-16 and upregulated miR-877 was able accurately distinguish distal CCA from benign disease as well as from PDAC. Conclusion: This is the first study to identify a combined panel of plasma miRNAs which shows promising diagnostic capability to serve as distal CCA signature with the potential to discriminate distal CCA from PDAC.
2019-11-26 | GSE117687 | GEO