Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-Wide Molecular Signature of Cholangiocarcinoma and Its Trandifferentation-Related Genes

ABSTRACT: Cholangiocarcinoma (CC) is an aggressive tumor that shows a poor survival rate even after resection. The present study aimed at identification of the genome-wide expressed genes related to CC oncogenesis and its sarcomatous transdifferentiation using DNA microarray technology. The differentially expressed genes in 9 cholangiocarcinoma cell lines (Choi.CK, Cho.CK, J.CK, S.CK, CK.L1, CK.L2, CK.P1, CK.P2 and CK.Y1) were analyzed in comparison with 4 kinds of cultured biliary epithelial cells (ND.1, ND.2, ND.3 and ND.4) using the Illumina Human-6 v2 BeadChip (48 K). Unsupervised hierachical clustering analysis perfectively classified the 13 cell samples into two groups, normal biliary epithelial (N) and immortalized biliary epithelial cells and CC (T) cells. We identified 120 commonly upregulated ( > 2.5 fold) genes and 340 commonly downregulated ( < 0.4-fold) genes in the two groups. Hierachical clustering analysis of sarcomatoid CC cells (S.CK) revealed 316 differentially upregulated genes (> 4-fold) and 335 downregulated genes (< 0.25-fold).) compared with 3 CC cell lines (Choi.CK, Cho.CK, and J.CK). In conclusion, these data will contribute to better understand the molecular mechanisms of oncogenesis and transdifferentiation in CC and provide the molecular targets for CC diagnosis and therapy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22633 | GEO | 2014/02/07

SECONDARY ACCESSION(S): PRJNA128189

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-Wide Molecular Signature of Cholangiocarcinoma and Its Trandifferentation-Related Genes

Project description:Cholangiocarcinoma (CC) is an aggressive tumor that shows a poor survival rate even after resection. The present study aimed at identification of the genome-wide expressed genes related to CC oncogenesis and its sarcomatous transdifferentiation using DNA microarray technology. The differentially expressed genes in 9 cholangiocarcinoma cell lines (Choi.CK, Cho.CK, J.CK, S.CK, CK.L1, CK.L2, CK.P1, CK.P2 and CK.Y1) were analyzed in comparison with 4 kinds of cultured biliary epithelial cells (ND.1, ND.2, ND.3 and ND.4) using the Illumina Human-6 v2 BeadChip (48 K). Unsupervised hierachical clustering analysis perfectively classified the 13 cell samples into two groups, normal biliary epithelial (N) and immortalized biliary epithelial cells and CC (T) cells. We identified 120 commonly upregulated ( > 2.5 fold) genes and 340 commonly downregulated ( < 0.4-fold) genes in the two groups. Hierachical clustering analysis of sarcomatoid CC cells (S.CK) revealed 316 differentially upregulated genes (> 4-fold) and 335 downregulated genes (< 0.25-fold).) compared with 3 CC cell lines (Choi.CK, Cho.CK, and J.CK). In conclusion, these data will contribute to better understand the molecular mechanisms of oncogenesis and transdifferentiation in CC and provide the molecular targets for CC diagnosis and therapy. Total RNA was extracted from each sample. Five-hundred nanograms of total RNA were used for labeling and hybridization, according to the manufacturerM-bM-^@M-^Ys protocols (Illumina). After the bead chips were scanned with an Illumina BeadArray Reader (Illumina), the microarray data were normalized using the quantile normalization method in the Linear Models for Microarray Data package in the R language environment. The expression level of each gene was transformed into a log 2 base before further analysis.

2014-02-07 | E-GEOD-22633 | biostudies-arrayexpress

An exosomal circRNA signature in the diagnosis and prognostification of cholangiocarcinoma: circRNA microarray analysis for 10 human bile samples

Project description:We have completed the Arraystar Human circRNA Array V2 analysis of 10 bile exosome samples (5 cholangiocarcinoma-induced biliary obstruction vs. 5 benign biliary obstruction). Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

2024-04-20 | GSE228477 | GEO

Identification of cholangiocarcinoma-like gene expression traits in hepatocellular carcinoma

Project description:We performed gene expression profiling of hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and mixed type of combined HCC and CC (CHC). In comparison of the profiles, a novel class of HCC expressing CC-like traits was identified. Gene expression profiling of 70 hepatocellular carcinoma (HCC), 13 cholangiocarcinoma (CC), and 7 mixed type of combined HCC and CC (CHC) were performed.

2010-06-09 | E-GEOD-15765 | biostudies-arrayexpress

miRNA profiling of biliary intraepithelial neoplasia reveals step-wise tumorigenesis in cholangiocarcinoma

Project description:Biliary intraepithelial neoplasia (BilIN) is a common precursor lesion of distal cholangiocarcinoma (dCCA). However, the sequence leading from a single epithelial layer in normal biliary epithelia to intraepithelial precursor lesions and finally to the invasive tumor is poorly understood. Here, we aimed to elucidate key miRNAs involved in this stepwise process and to identify their possible mRNA target genes in distal cholangiocarcinogenesis. As basis of our study, we conducted Laser Capture Microdissection of FFPE tissue sections of 12 patients with distal cholangiocarcinoma. For each patient, we isolated three matched sample sets, including non-neoplastic biliary epithelia, high grade BilIN (grade 3), and invasive dCCA, thereby representing different stages of distal cholangiocarcinogenesis. This resulted in a total of 36 samples. Total RNA was extracted and the expression of ~800 miRNAs was assessed using the Nanostring® technology. Significantly deregulated miRNAs were validated by quantitative RT-PCR. Target genes were identified using miRWalk2.0 and validated by qRT-PCR and Western blot.

2020-08-07 | GSE140001 | GEO

Cholangiocarcinoma tissues VS. corresponding normal bile duct tissues

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

Cholangiocarcinoma tissues VS. corresponding normal bile duct tissues

2013-06-10 | GSE47764 | GEO

RNA-sequencing of whole lungs from mice with activating Kras mutations and epithelial Stat3 deletion

Project description:We have previously shown that Kras mutant-induced lung tumors in CCSPCre/LSL-K-rasG12D mice (CC-LR) exhibited Stat3 activation. Here we sought to study the role of epithelial Stat3 in Kras-mutant lung tumor oncogenesis through derivation of a lung epithelial specific CC-LR/Stat3 conditional knockout (LR/Stat3D/D or LRDD) model. Analysis of tumor burdens revealed marked gender disparity following epithelial Stat3 deletion, LRDD males exhibited increased tumor burdens compared to male CC-LR animals whereas female LRDD mice displayed attenuated tumor development when compared to female CC-LR littermates. We then performed RNA-sequencing of whole lungs from the mice in order to understand global expression programs that may underlie this gender-specific effect of epithelial Stat3 deletion.

2018-12-26 | GSE109000 | GEO

Identification of cholangiocarcinoma-like gene expression traits in hepatocellular carcinoma

2010-05-21 | GSE15765 | GEO

miRNA profiling of biliary intraepithelial neoplasia reveals step-wise tumorigenesis in distal cholangiocarcinoma via the miR-451a/ATF2 axis

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

Serum exosome miRNA expression profile in patients with cholangiocarcinoma(CCA) and common bile duct stones(CBDS)

Project description:Cholangiocarcinoma (CCA) is a type of highly aggressive cancer arising from the biliary system. Through serum exosome miRNA sequencing, we screened out the differentially expressed miRNA in patients with cholangiocarcinoma(CCA) and common bile duct stones(CBDS).

2022-10-20 | GSE215448 | GEO