Identification of cholangiocarcinoma-like gene expression traits in hepatocellular carcinoma
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ABSTRACT:
ORGANISM(S): Homo sapiens
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PROVIDER: S-DIXA-D-1035 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
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
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.
2010-05-21 | GSE15765 | GEO
Project description:Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) are the major adult liver cancers. The existence of combined hepatocellular-cholangiocarcinoma (CHC), a histopathologic intermediate form between HCC and CC, suggests phenotypic overlap between these tumors. Here, we applied an integrative oncogenomic approach to address the clinical and functional implications of the overlapping phenotype between these tumors. By performing gene expression profiling of human HCC, CHC, and CC, we identified a novel HCC subtype, i.e., cholangiocarcinoma-like HCC (CLHCC), which expressed cholangiocarcinoma-like traits (CC signature). Similar to CC and CHC, CLHCC showed an aggressive phenotype with shorter recurrence-free and overall survival. In addition, we found that CLHCC coexpressed embryonic stem cell-like expression traits (ES signature) suggesting its derivation from bipotent hepatic progenitor cells. By comparing the expression of CC signature with previous ES-like, hepatoblast-like, or proliferation-related traits, we observed that the prognostic value of the CC signatures was independent of the expression of those signatures. In conclusion, we suggest that the acquisition of cholangiocarcinoma-like expression traits plays a critical role in the heterogeneous progression of HCC.
| S-EPMC3498758 | biostudies-literature
Project description:Past studies have identified hepatic tumors with mixed hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) characteristics that have a more aggressive behavior and a poorer prognosis than classic HCC. Whether this pathologic heterogeneity is due to a cell of origin of bipotent liver progenitors or the plasticity of cellular constituents comprising these tumors remains debated. In this study, we investigated the potential acquisition of CC-like traits during advanced development of HCC in mice. Primary and rare high-grade HCC developed in a genetic mouse model. A mouse model of highly efficient HCC invasion and metastasis by orthotopic transplantation of liver cancer organoids propagated from primary tumors in the genetic model was further developed. Invasive/metastatic tumors developed in both models closely recapitulated advanced human HCC and displayed a striking acquisition of CC-related pathologic and molecular features, which was absent in the primary HCC tumors. Our study directly demonstrates the pathologic evolution of HCC during advanced tumor development, providing the first evidence that tumors with mixed HCC and CC features, or at least a subset of these tumors, represent a more advanced developmental stage of HCC. Finally, liver cancer organoid-generated high-grade tumors exhibited significantly increased extracellular vesicle secretion, suggesting that identifying tumor-specific extracellular vesicle proteins in plasma may be a promising tool for liver cancer detection.
| S-EPMC5840495 | biostudies-literature
Project description:Hepatocellular carcinoma (HCC) is one of the most common malignancies, which causes serious financial burden worldwide. This study aims to investigate the potential mechanisms contributing to HCC and identify core biomarkers. The HCC gene expression profile GSE41804 was picked out to analyze the differentially expressed genes (DEGs). Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out using DAVID. We constructed a protein-protein interaction (PPI) network to visualize interactions of the DEGs. The survival analysis of these hub genes was conducted to evaluate their potential effects on HCC. In this analysis, 503 DEGs were captured (360 downregulated genes and 143 upregulated genes). Meanwhile, 15 hub genes were identified. GO analysis showed that the DEGs were mainly enriched in oxidative stress, cell cycle, and extracellular structure. KEGG analysis suggested the DEGs were enriched in the absorption, metabolism, and cell cycle pathway. PPI network disclosed that the top3 modules were mainly enriched in cell cycle, oxidative stress, and liver detoxification. In conclusion, our analysis uncovered that the alterations of oxidative stress and cell cycle are two major signatures of HCC. TOP2A, CCNB1, and KIF4A might promote the development of HCC, especially in proliferation and differentiation, which could be novel biomarkers and targets for diagnosis and treatment of HCC.
| S-EPMC5994271 | biostudies-literature
Project description: Not available
| S-DIXA-D-1101 | biostudies-other
Project description:Combined hepatocellular-cholangiocarcinoma (cHC-CC) and some hepatocellular carcinomas (HCCs) express stemness-related markers, such as epithelial adhesion molecule (EpCAM) and keratin 19 (K19), the expression of which has been reported to be associated with more aggressive behavior therein than in HCCs without. Yes-associated protein 1 (YAP1), a potential oncogene, is known to promote stem cell proliferation. In the present study, YAP1 expression and clinicopathological features were evaluated and compared among three groups comprising 36 HCCs that expressed both EpCAM and K19, 64 HCCs that did not express EpCAM and K19, and 58 cHC-CCs, which consisted of 38 cases of the classical type and 20 cases of the intermediate-cell subtype. YAP1 expression was more frequently noted in EpCAM(+)/K19(+) HCCs (55.6%) and in cHC-CCs (67.2%) than in EpCAM(-)/K19(-) HCCs (17.2%) (P<0.001 for both). In cHC-CCs, YAP1 expression was observed in 63% of classical type cHC-CCs and in 75% of the intermediate subtype; moreover, such expression was correlated with poorer histological differentiation (P?=?0.017) and was more frequently noted in transition zones than in HCC areas (P?=?0.060). Disease-free and overall survival showed a statistically significant difference among the three groups: disease-free survival was highest for EpCAM(-)/K19(-) HCCs and lowest for cHC-CCs, with EpCAM(+)/K19(+) HCCs falling in between (P<0.05). Overall survival rate was lower in HCCs and cHC-CCs with YAP1 expression compared to those without (P?=?0.05), whereas disease-free survival showed no significant difference according to YAP1 expression. Increased YAP1 expression was more frequently found in cHC-CCs and HCCs with stemness than in HCCs without, and a YAP1 pathway is suggested to be involved in the obtainment stemness characteristics in HCCs and cHC-CCs.
| S-EPMC3782432 | biostudies-literature
Project description:BACKGROUND:Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Frequent cytogenetic abnormalities that occur in HCC suggest that tumor-modifying genes (oncogenes or tumor suppressors) may be driving selection for amplification or deletion of these particular genetic regions. In many cases, however, the gene(s) that drive the selection are unknown. Although techniques such as comparative genomic hybridization (CGH) have traditionally been used to identify cytogenetic aberrations, it might also be possible to identify them indirectly from gene-expression studies. A technique we have called comparative genomic microarray analysis (CGMA) predicts regions of cytogenetic change by searching for regional gene-expression biases. CGMA was applied to HCC gene-expression profiles to identify regions of frequent cytogenetic change and to identify genes whose expression is misregulated within these regions. RESULTS:Using CGMA, 104 HCC gene-expression microarray profiles were analyzed. CGMA identified 13 regions of frequent cytogenetic change in the HCC samples. Ten of these regions have been detected in previous CGH studies (+lq, -4q, +6p, -8p, +8q, -13q, -16q, -17p, +17q, +20q). CGMA identified three additional regions that have not been previously identified by CGH (+5q, +12q, +19p). Genes located in regions of frequent cytogenetic change were examined for changed expression in the HCC samples. CONCLUSIONS:Our results suggest that CGMA predictions using gene-expression microarray datasets are a practical alternative to CGH profiling. In addition, CGMA might be useful for identifying candidate genes within cytogenetically abnormal regions.
| S-EPMC151177 | biostudies-literature
Project description:Hepatocellular carcinoma (HCC) is sexually disparate in humans, with a significantly increased prevalence in males. The molecular mechanisms by which the inhibition or development of liver cancer are facilitated require further investigation with regard to sex factors affecting disease progression. In the present study, functional signatures of differentially expressed genes (DEGs) were screened in female and male tumors via bioinformatics analysis. The following gene chip expression profiles were downloaded from the Gene Expression Omnibus: GSE19665, GSE23342 and GSE9843. They comprised cancerous and non‑cancerous tissue from patients with HCC and included critical sex features. Further evaluation of selected DEGs in the two sexual groups was performed via hierarchical clustering analysis. Venn diagram and functional protein‑protein interaction (PPI) network analyses were performed. Survival analysis of patients with differences in gene expression levels was subsequently performed using the Kaplan‑Meier Plotter database. Certain identified DEGs were common in female and male tumor samples, whereas others exhibited a sexually‑biased expression profile. Gene Ontology revealed that the cell cycle module 'biological process' was enriched in tumors derived from both sexes, whereas the metabolic pathways and drug metabolism modules were only significantly enriched in cancer tissues from male subjects. A number of hub DEGs in the cell cycle and p53 signaling pathways were involved in significant protein‑protein interaction (PPI) modules, including CDK1 and CCNB1. These DEGs were upregulated in tumors derived from female subjects compared with those derived from male subjects, and could be used as markers of poor prognosis in male patients. Other genes, such as CYP3A4 and SERPINA4, were identified in metabolic pathways, and were downregulated in male compared with female subjects. These genes were associated with a decreased survival rate. The data demonstrated that sex differences in physiology may regulate the levels of gene expression and/or activity, including gene function associated with oncogenesis and the outcomes of liver cancer. Additional surveys are required to explore in detail the molecular mechanisms underlying the differences in gene expression between the two sexes during the development of liver cancer.
| S-EPMC6667920 | biostudies-literature
Project description:Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. The landscape of HCC's molecular alteration signature has been explored over the last few decades. Even so, more comprehensive research is still needed to improve understanding of tumorigenesis and progression of HCC, as well as to identify potential biomarkers for the malignancy. In this research, a comprehensive bioinformatics analysis was conducted based on the publicly available databases from both the Cancer Genome Atlas (TCGA) program and the gene expression omnibus (GEO) database. R/Bioconductor was used to analyze differentially expressed genes (DEGs) between HCC tumor and normal control (NC) samples, and then a protein-protein interaction (PPI) network of DEGs was established through the STRING platform. Finally, the application of specific candidate genes as diagnostic or prognostic biomarkers of HCC was explored and evaluated by ROC and survival analysis. A total of 310 DEGs were detected in the HCC tumor samples. Thirty-six hub DEGs in the PPI network and 10 candidates of the 36 genes showed significant alterations in tumor expression, including CDKN3, TOP2A, UBE2C, CDC20, PBK, ASPM, KIF20A, NCAPG, CCNB2, CYP3A4. The 10-gene signature had relatively significant effects when distinguishing tumors from normal samples (sensitivity >70%, specificity >70%, AUC >0.8, p < 0.001). Eight candidate genes were negatively correlated with the overall survival rate of the patients (p < 0.05) and were all up-regulated in HCC tumor samples. The age and gender factors had no significant impact on the overall survival rate of HCC patients (p > 0.05), and the TNM stage status factor had a significant negative prognosis correlation (p < 0.05). This research provides evidence for a better understanding of tumorigenesis and progression of HCC and helps to explore candidate targets for disease diagnosis and treatment.
| S-EPMC10450782 | biostudies-literature