Project description:Using single-cell RNA sequencing, spatial transcriptomic and bulk multi-omics, we elaborated a molecular architecture of 3 PLC types, namely hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC) from a high-resolution perspective.
Project description:Compared to classical drug screening, single-cell screening not only significantly enhances throughput but also provides richer transcriptional response information. In this study, we employed the high-throughput single-cell sequencing technology, snHH-seq, to screen clinical drug combinations with anti-hepatocellular carcinoma activity. Single-cell transcriptomics revealed that the combination of HHT and YM155 (HY) exhibited the most potent inhibitory effect on cellular proliferation, which was also validated through in vitro and in vivo functional assays. Mechanistically, transcription factor regulatory network analysis identified cell type-specific regulators in each subpopulation with HY treatment, and revealed that the anticancer effects primarily target apoptosis-related subpopulations. These findings provide critical insights for precision diagnosis and treatment of hepatocellular carcinoma.
Project description:The incidence of TP53 loss-of-function in hepatocellular carcinoma is very high. In order to clarify the gene expression differences induced by the changes of TP53 gene, we used two human hepatocellular carcinoma cell lines, SK-HEP-1 and Hep 3B with TP53 knockdown or overexpression for RNA sequencing . SK-HEP-1 is a TP53 wild-type hepatocellular carcinoma cell line. Thus, we knockdown TP53 in SK-HEP-1. Hep 3B is a TP53 loss-of-function hepatocellular carcinoma cell line. Thus, we overexpress TP53 in Hep 3B. Results of RNA-seq analysis showed the differences after knocking-down or overexpressing TP53.
2023-12-06 | GSE240197 | GEO
Project description:Hepatocellular Carcinoma cell line RNA-sequencing
Project description:The purpose of the study is to detect somatic mutations in hepatocellular carcinoma using circulating free-DNA. We used deep-sequencing data of a panel of 60 commonly mutated genes in hepatocellular carcinoma.
Project description:The aim of this study is to estimate gene expression variations involved in glucose meatbolism in HepG2 cell line after cell cycle(G1 to S phase) inhibition by using drug(PD-0332991) or CDK4-6-knock down. We hypothesized that transition of glycolytic gene expression might indicates the effect of PD-0332991 drug treatment in Hepatocellular carcinoma cells.
Project description:Hepatocellular carcinoma is one of the most prevalent malignancies worldwide, and the role of stress in hepatocellular carcinoma progression remains incompletely understood. In this study, we integrated clinical and preclinical models to investigate how stress-associated gut microbiota remodeling contributes to hepatocellular carcinoma progression. Stress profoundly altered the gut microbiota, with Phocaeicola vulgatus significantly reduced. Restoration of Phocaeicola vulgatus or administration of its tryptophan-derived metabolite indole-3-propionic acid attenuated hepatocellular carcinoma progression in vivo. Single-cell RNA sequencing was performed to characterize changes in the hepatocellular carcinoma tumor microenvironment. Indole-3-propionic acid treatment reduced endothelial JAM2 expression and was associated with reduced JAM2-F11R-mediated endothelial-macrophage crosstalk. These findings support a role for the stress-gut microbiota-metabolite-tumor microenvironment axis in hepatocellular carcinoma progression and suggest potential translational targets for microbiome-based therapeutic strategies.
Project description:To explore the miRNA expression profiles between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma To performe microarray analysis to detect the miRNA expression profiles between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma
Project description:The purpose of this experiment of high-coverage DNA sequencing of 58 frequently mutated genes in hepatocellular carcinoma (HCC) is to confirm clonal distribution of the known HCC drivers in samples corresponding to multiple regions of a tumor.
Project description:We conducted a quantitative assessment of drug-inducible cis-regulatory elements (CREs) based on transcription initiation profiling of mRNAs and noncoding RNAs, including enhancer RNAs, by using CAGE (Cap Analysis of Gene Expression). Candidate CREs were identified in a hepatocellular carcinoma HepG2 cell line with stable expression of drug-responsive transcription factor pregnane X receptor (PXR) .
