Similar Datasets
Project description:MicroRNA expression profiles were sucessfully contructed in 63 patients with ICC and 9 normal intrahepatic bile ducts using a custom microarray containing probes for 1094 miRNAs and an outcome prediction of miRNA signature was successfully identified for predicting prognosis in ICC.
2015-03-06 | GSE53870 | GEO
Project description:Intrahepatic cholangiocarcinoma (ICC) is the second most common type of primary cancer in the liver. ICC is an aggressive cancer with poor prognosis and limited therapeutic strategies. The identification of new drug targets and prognostic biomarkers is an important clinical challenge for ICC. The presence of an abundant stroma is a histological hallmark of ICC. Given the well established role of the stromal compartment in the progression of cancer diseases, we hypothesized that relevant biomarkers could be identified by analyzing the stroma of ICC. By combining laser capture microdissection and gene expression profiling we demonstrated that ICC stromal cells exhibit dramatic genomic changes. We identified a signature of 1,073 non-redundant genes that significantly discriminate the tumor stroma from non tumor fibrous tissue. Functional analysis of differentially expressed genes demonstrated that up-regulated genes in the stroma of ICC were related to cell cycle, extracellular matrix and Transforming Growth Factor beta (TGFM-NM-2) pathways. Tissue microarray analysis using an independent cohort of 40 ICC patients validated at a protein level the increase expression of Collagen 4, Laminin, Osteopontin/SPP1, KIAA0101 and TGFM-NM-22 genes in the stroma of ICC. Statistical analysis of clinical and pathological features demonstrated that the expression of Osteopontin, TGFM-NM-22 and Laminin in the stroma of ICC was significantly correlated with patient overall survival. More importantly, multivariate analysis demonstrated that the stromal expression of Osteopontin was an independent prognostic marker for overall and disease-free survival. Conclusion: The study identifies clinically relevant genomic alterations in the stroma of ICC, including candidates biomarkers for prognosis, supporting the idea that tumor stroma is an important factor for ICC onset and progression. 20 RNA samples were analyzed, from 10 patients with ICC. For each patient, RNA were isolated from laser capture microdissected (LCM) stroma from tumor and non tumor areas.
2013-06-21 | E-GEOD-45001 | biostudies-arrayexpress
Project description:CircRNA microarray was used to screen significantly up-regulated circRNAs in paired ICC and non-tumor tissues 7 paired ICC and non-tumor tissues was used to screen significantly CircRNAs
2021-08-09 | GSE181523 | GEO
Project description:We compared transcriptomic profiles of 23 ICC tumor specimens to hepatocellular carcinoma (HCC) specimens using Affymetrix mRNA array and the miRNA array platforms to search for unique gene signatures linked to patient prognosis. ICC and HCC share common stem-like molecular characteristics and stem-like tumor features associated with poor prognosis. Gene expression profiling of 16 intrahepatic cholangiocarcinoma (ICC), 7 mixed type of combined HCC and ICC (CHC), 2 Hepatic Adenoma, 5 Focal Nodular Hyperplasia, and 7 Non-Tumor Tissues were performed.
2012-09-28 | E-GEOD-32879 | biostudies-arrayexpress
Project description:In this study,we performed integrated glycoproteomic and global proteomic analysis of tumor tissues of ICC and HCC to investigate the differences in site-specific glycosylation and proteins between ICC and HCC tumors. The paired paracancer tissue were also included as controls to determine the site-specific glycosylation changes in ICC and HCC tumors. The alteration extents in glycopeptide, global proteome, and normalized glycosylation in different sample groups were systematically compared.
2022-08-11 | PXD020277 | Pride
Project description:We found that the isolated and expanded MCAM positive vCAF subpopulations significantly accelerated ICC growth. To further investigate the effect of vCAF on ICC cells (GFP-FRH or GFP-RBE), we co-cultured the vCAF with GFP ICC cells or ICC cells alone for seven days, then we sorted the GFP-FRH or GFP-RBE cells via FACS and conducted transcriptome microarray analysis of GFP ICC cells alone or vCAF co-cultured GFP-ICC cells.
2020-06-06 | GSE148773 | GEO
Project description:Intrahepatic cholangiocarcinoma (ICC) is the second most common type of primary cancer in the liver. ICC is an aggressive cancer with poor prognosis and limited therapeutic strategies. The identification of new drug targets and prognostic biomarkers is an important clinical challenge for ICC. The presence of an abundant stroma is a histological hallmark of ICC. Given the well established role of the stromal compartment in the progression of cancer diseases, we hypothesized that relevant biomarkers could be identified by analyzing the stroma of ICC. By combining laser capture microdissection and gene expression profiling we demonstrated that ICC stromal cells exhibit dramatic genomic changes. We identified a signature of 1,073 non-redundant genes that significantly discriminate the tumor stroma from non tumor fibrous tissue. Functional analysis of differentially expressed genes demonstrated that up-regulated genes in the stroma of ICC were related to cell cycle, extracellular matrix and Transforming Growth Factor beta (TGFβ) pathways. Tissue microarray analysis using an independent cohort of 40 ICC patients validated at a protein level the increase expression of Collagen 4, Laminin, Osteopontin/SPP1, KIAA0101 and TGFβ2 genes in the stroma of ICC. Statistical analysis of clinical and pathological features demonstrated that the expression of Osteopontin, TGFβ2 and Laminin in the stroma of ICC was significantly correlated with patient overall survival. More importantly, multivariate analysis demonstrated that the stromal expression of Osteopontin was an independent prognostic marker for overall and disease-free survival. Conclusion: The study identifies clinically relevant genomic alterations in the stroma of ICC, including candidates biomarkers for prognosis, supporting the idea that tumor stroma is an important factor for ICC onset and progression.
2013-06-21 | GSE45001 | GEO
Project description:The experiment was designed to display differential gene expression profiling in three human intrahepatic cholangiocarcinoma (ICC) cells upon knockdow of LKB1 tumor suppressor, by using RNAseq technology. LKB1 was first attenuated in three ICC cells: HuH-28, RBE, and SSP-25 by siRNA-mediated knockdown. Total RNA was extracted from duplicated cancers cells transfected with control siRNA and LKB1 specific siRNA at 48h posttransfection for RNAseq analysis. Differentially expressed genes in LKB1-attenuated ICC cells were identified in comparison to that in ICC cells transfected with control siRNA.
2014-07-29 | E-GEOD-59855 | biostudies-arrayexpress
Project description:Background & Aims: Intrahepatic cholangiocarcinoma (ICC) is known to heterogeneous with diverse etiology, morphology, and clinical outcomes. Recently, cholangiolar differentiation of ICC has been suggested to associate with prognostic outcomes, however, its molecular patho-biological features and clinical significances were not evaluated extensively. Methods:Integrative analysis was performed using transcriptomic profiles (n=27) and tissue microarrays (n=142) from ICC specimens. Results:ICCs were classified into ICC with cholangiolar differentiation (ICC-CD, n=20) and ICC with bile duct differentiation (ICC-BD, n=122). ICC-CD showed favorable overall survival (OS) compared to ICC-BD (Hazard Ratio=0.38, P=0.020, log-rank test). Transcriptomic profiling of ICC-CD and ICC-BD revealed a cholangiolar differentiation signature (CD signature, n=794), which could predict prognostic outcomes of ICC in an independent data. Interestingly, the expression of CD signature demonstrated that the ICC-BD but not ICC-CD harbored pancreatic ductal adenocarcinoma (PDAC) like expression trait, implying its cellular origin from multipotent biliary tree stem cells or the cells committed to differentiate into pancreatic lineage cells. The CD signature might be a key determinant for ICC heterogeneity indicating spectral continuum of cellular differentiation of ICC-CD → ICC-BD → PDAC. In addition, we identified four genes (i.e., CRP, CDH2, TFF1, and S100P) from integrated analysis of tissue microarrays and transcriptome profiles as prognostic as well as differential histologic markers for ICC-CD and ICC-BD. Strikingly, combined expression status of the four genes were more beneficial in predicting prognostic outcomes of ICC. Conclusions:Our integrative genomic-pathologic analysis could reveal new molecular and clinical significance of cholangiolar differentiation in association with PDAC-like expression traits, which might play pivotal roles in heterogeneous progression of ICC.
2017-07-01 | GSE66255 | GEO
Project description:Intrahepatic cholangiocarcinoma (ICC) is the second most common malignancy within the liver, with a high degree of tumor heterogeneity and a very poor prognosis. In this study, single-cell transcriptome sequencing analysis was performed on 3 samples (1 plasma, 1 tumor and 1 paracancerous tissue) from an ICC patient with the aim of studying cell type variations in different tissue types.
2022-12-31 | GSE181878 | GEO