Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [SMART-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE103866 | GEO | 2018/06/11
REPOSITORIES: GEO
Similar Datasets
Project description:Combined transcriptomic and functional analyses of HCC cells at single-cell level were performed to assess CSC heterogeneity.
2018-06-11 | GSE103867 | GEO
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:Clinical heterogeneity of hepatocellular carcinoma (HCC) reflected in unequal outcome of treatment is poorly defined in molecular level, and molecular subtypes and their associated biomarkers have not been established to improve prognostification and treatment of HCC. Using microarray technologies, we analyzed gene expression profiling data from HCC patients, uncovered mesenchymal subtype, and identified gene expression signature associated with mesenchymal phenotype of HCC.
2020-07-01 | GSE134568 | GEO
Project description:To explore the target genes of long noncoding RNA lncTCF7, we established lncTCF7-silenced HCC primary CSC cells and conducted transcriptome microarray analysis. We used microarrays to identify distinct gene expression underlying shCtrl and shlncTCF7 of hepatocellular carcinoma sample stem cells. We cultured shlncTCF7 and shCtrl cells from hepatocellular carcinoma (HCC) clinical sample, then hybridized on Affymetrix microarrays. We sought to identify distinct target genes of lncTCF7 in liver cancer stem cells (CSCs).
2015-03-05 | E-GEOD-66515 | biostudies-arrayexpress
Project description:We interrogated single-cell transcriptomes, proteomes and epigenetic information revealing metastasis potential heterogeneity in 5 HCC cell lines across metastasis capacity.
2022-05-31 | GSE188289 | GEO
Project description:Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death worldwide. Like in many cancers, tumor heterogeneity in HCC hampers the development of personalized therapies. Integrative genomics contributed to characterize HCC subtypes by identifying specific genetic alterations and molecular signatures, leading to targeted drug candidates. However, no consensus was achieved for genes and pathways recurrently altered in HCC. Here, a meta-analysis of 15 independent HCC datasets identifies a comprehensive signature consisting of 935 genes commonly deregulated in HCC as compared to the surrounding non-tumor tissue (P<0.01). The 935-gene HCC signature covers well-established cancer hallmarks (e.g. proliferation, metabolic reprogramming, microenvironment remodeling) together with specific hallmarks associated with protein turnover and epigenetics. Accordingly, the 935-gene HCC signature highlights relevant drugs for systemic therapies, including including two histone deacetylase (HDAC) inhibitors (trichostatin A and vorinostat), PI3K inhibitor LY294002, mTOR inhibitor sirolimus (also known as rapamycin), alpha-estradiol and resveratrol. The impact of these drugs as compared to sorafenib that is currently used for the treatment of advanced HCC was evaluated on the viability of 6 HCC-derived cell lines. We concluded that combined therapies targeting common and subtype-specific cancer networks may represent a relevant strategy to efficiently treat liver cancer.
2016-11-15 | GSE79246 | GEO
Project description:Cancer stem cells (CSCs), a small population of cancer cells, have been considered to be the origin of cancer initiation, recurrence, and metastasis. Tumor microenvironment provides crucial signals for CSCs to maintain stem cell properties and promote tumorigenesis. Therefore, establishment of an appropriate cell culture system to mimic the microenvironment for CSC studies is an important issue. In this study, we grew colon and hepatocellular carcinoma (HCC) cells on chitosan membranes and evaluated the tumor progression by transwell migration, drug resistance, microarray, and RT-PCR analysis. We also evaluated the CSC properties by flow cytometry, sphere forming assay, luciferase reporter assay, western blot, and gene knockdown. Experimental results showed that culturing cancer cells on chitosan increased cell motility, drug resistance, quiescent population, self-renewal capacity, and the expression levels of stemness and CSC marker genes, such as OCT4, NANOG, CD133, CD44, and EpCAM. Furthermore, we demonstrated that chitosan might activate canonical Wnt/β-catenin-CD44 axis signaling in CD44positive colon cancer cells and noncanonical Wnt-STAT3 signaling in CD44negative HCC cells. In conclusion, chitosan as culture substrates activated the essential signaling of CSCs and promoted CSC properties. The chitosan culture system provides a convenient platform for the research of CSC biology and screening of anticancer drugs.
2017-01-18 | GSE93704 | GEO
Project description:Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Understanding of the intratumoral heterogeneity of HCC is instructive for developing personalized therapy and molecular biomarkers. We applied whole exome sequencing to a total of 63 samples from 11 patients to resolve the genetic architecture and subclonal diversification. Notably, spatial genomic diversity was found in all 11 HCC cases, with 33% of the driver mutations being heterogeneous. Temporal dissection of mutational signatures suggested that exogenous and endogenous factors have different contributions in shaping the mutational spectrum during the development of HCC. Moreover, we observed extensive intratumoral epigenetic heterogeneity in HCC, and showed that integrative analysis of both genetic and epigenetic phylogenies could generate more robust resolution of clonal architecture than single profiling approach. Our results also demonstrated prominent epigenetic subclonal diversification even in a stable HCC genome. Together, these findings highlight the widespread intratumoral heterogeneity at both genomic and epigenomic levels in HCC, and provide important molecular foundation for better understanding of the biology and pathogenesis of this malignancy.
2017-03-03 | GSE83691 | GEO
Project description:To explore the target genes of long noncoding RNA lncTCF7, we established lncTCF7-silenced HCC primary CSC cells and conducted transcriptome microarray analysis. We used microarrays to identify distinct gene expression underlying shCtrl and shlncTCF7 of hepatocellular carcinoma sample stem cells.
2015-03-05 | GSE66515 | GEO
Project description:BACKGROUND & AIMS: In approximately 70% of patients with hepatocellular carcinoma (HCC) treated by resection or ablation, disease recurs within 5 years. Although gene expression signatures have been associated with outcome, there is no method to predict recurrence based on combined clinical, pathology, and genomic data (from tumor and cirrhotic tissue). We evaluated gene expression signatures associated with outcome in a large cohort of patients with early stage (Barcelona-Clinic Liver Cancer 0/A), single-nodule HCC and heterogeneity of signatures within tumor tissues. METHODS: We assessed 287 HCC patients undergoing resection and tested genome-wide expression platforms using tumor (n = 287) and adjacent nontumor, cirrhotic tissue (n = 226). We evaluated gene expression signatures with reported prognostic ability generated from tumor or cirrhotic tissue in 18 and 4 reports, respectively. In 15 additional patients, we profiled samples from the center and periphery of the tumor, to determine stability of signatures. Data analysis included Cox modeling and random survival forests to identify independent predictors of tumor recurrence. RESULTS: Gene expression signatures that were associated with aggressive HCC were clustered, as well as those associated with tumors of progenitor cell origin and those from nontumor, adjacent, cirrhotic tissues. On multivariate analysis, the tumor-associated signature G3-proliferation (hazard ratio [HR], 1.75; P = .003) and an adjacent poor-survival signature (HR, 1.74; P = .004) were independent predictors of HCC recurrence, along with satellites (HR, 1.66; P = .04). Samples from different sites in the same tumor nodule were reproducibly classified. CONCLUSIONS: We developed a composite prognostic model for HCC recurrence, based on gene expression patterns in tumor and adjacent tissues. These signatures predict early and overall recurrence in patients with HCC, and complement findings from clinical and pathology analyses. Center and peripheral portions of hepatocellular carcinoma tumors as well as surrounding non-tumor cirrhotic liver tissues were obtained from fresh frozen surgically resected tissues, and isolated total RNA samples were analyzed for genome-wide expression profiles.
2014-03-25 | E-GEOD-56140 | biostudies-arrayexpress