Journal: Molecular medicine reports

Article Title: Simvastatin induces growth inhibition and apoptosis in HepG2 and Huh7 hepatocellular carcinoma cells via upregulation of Notch1 expression.

doi: 10.3892/mmr.2014.2976

Figure Lengend Snippet: Figure 1. Simvastatin decreases HepG2 and Huh7 cell viability and proliferation. HepG2 and Huh7 cells were treated with various concentration of simvas tatin (0, 2, 4, 8 and 16 µM) for 24, 48 and 72 h. (A) Bar graph showing trypan blue‑positive simvastatin‑treated HepG2 cells. (B) Broken line showing MTT results of proliferation of simvastatin‑treated HepG2 cells. (C) Bar graph showing trypan blue‑positive simvastatin‑treated Huh7 cells. (D) Broken line showing MTT results of proliferation of simvastatin‑treated Huh7 cells. *P<0.05 and **P<0.01 compared with the control group.

Article Snippet: Human HCC HepG2 and Huh7 cells were obtained from the American Type Culture Collection (Manassas, VA, USA) and maintained in RPMI-1640 (Gibco-BRL, Carlsbad, CA, USA), as previously described (21), supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

Techniques: Concentration Assay, Control

Journal: Molecular medicine reports

Article Title: Simvastatin induces growth inhibition and apoptosis in HepG2 and Huh7 hepatocellular carcinoma cells via upregulation of Notch1 expression.

doi: 10.3892/mmr.2014.2976

Figure Lengend Snippet: Figure 3. Simvastatin increases mRNA levels of Notch1 and p53 in HepG2 cells. Reverse transcription quantitative polymerase chain reaction showing the mRNA expression levels of (A) Notch1 and (B) p53 in HepG2 cells treated with various concentrations of simvastatin (0, 2, 4, 8 and 16 µM) for 24, 48 and 72 h. *P<0.05 and **P<0.01 compared with control group.

Article Snippet: Human HCC HepG2 and Huh7 cells were obtained from the American Type Culture Collection (Manassas, VA, USA) and maintained in RPMI-1640 (Gibco-BRL, Carlsbad, CA, USA), as previously described (21), supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

Techniques: Reverse Transcription, Real-time Polymerase Chain Reaction, Expressing, Control

Journal: Molecular medicine reports

Article Title: Simvastatin induces growth inhibition and apoptosis in HepG2 and Huh7 hepatocellular carcinoma cells via upregulation of Notch1 expression.

doi: 10.3892/mmr.2014.2976

Figure Lengend Snippet: Figure 2. Simvastatin induces apoptosis and affects the expression of apoptosis‑related genes in HepG2 and Huh7 cells. HepG2 and Huh7 cells were treated with various concentrations of simvastatin (0, 2, 4, 8 and 16 µM) for 48 h. Flow cytometric analysis of the apoptotic rate of simvastatin‑treated (A) HepG2 and (B) Huh7 cells. (C) Reverse transcription quantitative polymerase chain reaction showing the mRNA expression level of Bcl‑2 and Bax in simvastatin‑treated (C) HepG2 and (D) Huh7 cells. *P<0.05 and **P<0.01 compared with the control group. FITC‑A, fluorescein isothiocyanate; PE, R‑phycoerythrin; Bcl‑2, B cell lymphoma 2; Bax, Bcl‑2‑associated X protein.

Article Snippet: Human HCC HepG2 and Huh7 cells were obtained from the American Type Culture Collection (Manassas, VA, USA) and maintained in RPMI-1640 (Gibco-BRL, Carlsbad, CA, USA), as previously described (21), supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

Techniques: Expressing, Reverse Transcription, Real-time Polymerase Chain Reaction, Control

Journal: Molecular medicine reports

Article Title: Simvastatin induces growth inhibition and apoptosis in HepG2 and Huh7 hepatocellular carcinoma cells via upregulation of Notch1 expression.

doi: 10.3892/mmr.2014.2976

Figure Lengend Snippet: Figure 5. Simvastatin decreases phosphorylation levels of Akt via upregulation of Notch1 expression in HepG2 cells. (A) Western blot analysis was used to determine protein expression levels of Akt and p‑Akt in HepG2 cells following Notch1 knockout. (B) Reverse transcription quantitative polymerase chain reaction demonstrated mRNA expression levels of Akt and p‑Akt in HepG2 cells following Notch1 knockout. **P<0.01 compared with the control and siMock groups. p‑Akt, phosphorylated Akt; siNotch1, cells transfected with Notch1 small interfering RNA plasmid; siMock, cells transfected with an empty vector; control, untransfected cells.

Article Snippet: Human HCC HepG2 and Huh7 cells were obtained from the American Type Culture Collection (Manassas, VA, USA) and maintained in RPMI-1640 (Gibco-BRL, Carlsbad, CA, USA), as previously described (21), supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

Techniques: Phospho-proteomics, Expressing, Western Blot, Knock-Out, Reverse Transcription, Real-time Polymerase Chain Reaction, Control, Transfection, Small Interfering RNA, Plasmid Preparation

Journal: Molecular medicine reports

Article Title: Simvastatin induces growth inhibition and apoptosis in HepG2 and Huh7 hepatocellular carcinoma cells via upregulation of Notch1 expression.

doi: 10.3892/mmr.2014.2976

Figure Lengend Snippet: Figure 4. Cell apoptosis induced by simvastatin is weakened and the expression of p53 and Bax decreased when the Notch1 gene was knocked out. (A) Western blot analysis demonstrates the successful knockout of Notch1 in HepG2 cells. (B) Reverse transcription quantitative polymerase chain reaction of Notch1 mRNA expression levels in HepG2 cells following Notch1 knockout. (C) Broken line showing MTT results of proliferation of HepG2 cells following Notch1 knockout. (D) Western blot analysis of protein expression levels of p53, Bcl‑2 and Bax in HepG2 cells. Bcl‑2, B cell lymphoma 2; Bax, Bcl‑2‑associated X protein; siNotch1, cells transfected with Notch1 small interfering RNA plasmid; siMock, cells transfected with an empty vector; control, untransfected cells.

Article Snippet: Human HCC HepG2 and Huh7 cells were obtained from the American Type Culture Collection (Manassas, VA, USA) and maintained in RPMI-1640 (Gibco-BRL, Carlsbad, CA, USA), as previously described (21), supplemented with 10% fetal bovine serum (FBS; HyClone Laboratories, Logan, UT, USA).

Techniques: Expressing, Western Blot, Knock-Out, Reverse Transcription, Real-time Polymerase Chain Reaction, Transfection, Small Interfering RNA, Plasmid Preparation, Control

Journal: Frontiers in Cell and Developmental Biology

Article Title: CGR11 promotes hepatocellular carcinoma progression by regulating autophagy through the PI3K/AKT pathway

doi: 10.3389/fcell.2025.1692480

Figure Lengend Snippet: CGR11 inhibits proliferation, migration, invasion and inhibits apoptosis of HCC cells in vitro . (A) Clonogenic capacity of HCC cell lines with CGR11 overexpression or knockdown were assessed by colony formation assay. (B) CCK8 assay showed the proliferative curves of CGR11-knockdown MHCC-97H, CGR11-overexpressing PLC/PRF/5 and their control cells. (C) Statistical chart of MHCC-97H and PLC/PRF/5 cells in colony formation assay. (D) EdU assays showed the proliferating cells in MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and their control groups. Nuclei of proliferating cells were labelled by EdU (red), and all nuclei of HCC cells were labelled by Hoechst 33,342 (blue). The percentage of proliferating cells was compared in corresponding bar chart. Scale bars, 50 μm. (E) Wound healing assay showed the migration ability of MHCC-97H shCGR11-1 , MHCC-97H shCGR11-2 , PLC/PRF/5 CGR11 and their control cells at 0 and 48 h. Scale bars, 50 μm. (F) Transwell invasion assay showed the invasion ability of MHCC-97H shCGR11-1 , MHCC-97H shCGR11-2 , PLC/PRF/5 CGR11 and their control cells at 24 h. Scale bars, 50 μm. (G) The rate of apoptosis in HCC cells with CGR11 knockdown or overexpression and in their control cells was analyzed by flow cytometry. Data shown as mean ± SD of triplicate independent experiments. ** P < 0.01; *** P < 0.001.

Article Snippet: HCC cell lines PLC/PRF/5, Hep3B,and SNU449, as well as Human normal liver cells THLE2 were obtained from the American Type Culture Collection (ATCC, Rockville, MD).

Techniques: Migration, In Vitro, Over Expression, Knockdown, Colony Assay, CCK-8 Assay, Control, Wound Healing Assay, Transwell Invasion Assay, Flow Cytometry

Journal: Frontiers in Cell and Developmental Biology

Article Title: CGR11 promotes hepatocellular carcinoma progression by regulating autophagy through the PI3K/AKT pathway

doi: 10.3389/fcell.2025.1692480

Figure Lengend Snippet: CGR11 promotes tumor growth and invasive potential of HCC cells in vivo . (A) Subcutaneous tumor model was established using MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and the control cells (n = 5). Tumor weight and growth kinetics of subcutaneous xenografts were quantified and comparatively analyzed. (B) Subcutaneous tumors removed from nude mice of MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and the control cells (n = 5) were harvested and photographed. (C) Orthotopic tumor models in nude mice were established using MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and their control cells. Orthotopic liver tumors were longitudinally monitored via small-animal in vivo fluorescence imaging. Luciferase activity of orthotopic tumors were compared in the left panel. (D) PCNA and CGR11 expression levels in subcutaneous tumor models derived from MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and their control cells were detected by IHC, respectively. Scale bars, 200 μm ** P < 0.01; *** P < 0.001.

Article Snippet: HCC cell lines PLC/PRF/5, Hep3B,and SNU449, as well as Human normal liver cells THLE2 were obtained from the American Type Culture Collection (ATCC, Rockville, MD).

Techniques: In Vivo, Control, Fluorescence, Imaging, Luciferase, Activity Assay, Expressing, Derivative Assay

Journal: Frontiers in Cell and Developmental Biology

Article Title: CGR11 promotes hepatocellular carcinoma progression by regulating autophagy through the PI3K/AKT pathway

doi: 10.3389/fcell.2025.1692480

Figure Lengend Snippet: CGR11 influences the PI3K/AKT pathway in HCC cells. (A) RNA-seq analysis of the differential expression genes of MHCC-97H shCGR11 cells and the control cells. The volcano diagram shows that differential genes expression after knockdown of CGR11. (B) Heat-map shows these common altered differential genes expression in MHCC-97H shCGR11 cells and the control cells. (C) Representative results of PI3K-related pathways from Gene Set Enrichment Analysis (GSEA) of CGR11 in RNA-seq analysis of MHCC-97H shCGR11 cells and the control cells. (D) KEGG enrichment analysis for significantly differential expression genes from RNA-seq analysis. (E) Gene Ontology (GO) enrichment analysis of significantly differentially expressed genes (DEGs) between CGR11 knockdown and control groups in RNA-seq profiling. (F) Western blot analysis and statistical analysis of CGR11, p-PI3K, p-AKT and their total protein expression levels in MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and their control cells. (G) IHC images and statistical analysis of CGR11, p-PI3K, p-AKT, LC3 and p62 protein expression in subcutaneous tumors removed from nude mice. Scale bars, 100 μm. The data are presented as mean ± SD of three independent experiments. * P < 0.05; ** P < 0.01; *** P < 0.001.

Article Snippet: HCC cell lines PLC/PRF/5, Hep3B,and SNU449, as well as Human normal liver cells THLE2 were obtained from the American Type Culture Collection (ATCC, Rockville, MD).

Techniques: RNA Sequencing, Quantitative Proteomics, Control, Expressing, Knockdown, Western Blot

Journal: Frontiers in Cell and Developmental Biology

Article Title: CGR11 promotes hepatocellular carcinoma progression by regulating autophagy through the PI3K/AKT pathway

doi: 10.3389/fcell.2025.1692480

Figure Lengend Snippet: CGR11 influences autophagy in HCC cells. (A) Correlation chord diagram depicting the association network between CGR11 and autophagy-related proteins based on expression profiling. (B) Correlation scatter plots between CGR11 and autophagy-associated proteins with annotated Pearson coefficients (r) and significance levels (p-values). (C) A co-expression heat-map delineates the correlation patterns between CGR11 and autophagy-associated proteins, with hierarchical clustering revealing expression synergy across biological replicates. (D) Fluorescence images and statistical analysis of MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and the corresponding control cells after transfecting with mRFP-GFP-LC3 lentivirus. Red dots represent autolysosomes while yellow dots indicate autophagosomes in the overlays. Nuclei were stained with DAPI. The average number of autophagosomes and autolysosomes per cell was quantified. A total of 50 cells from randomly selected fields in each group were counted for the analysis. Scale bars, 5 μm. (E) Western blot analysis and statistical analysis of CGR11, LC3 II and p62 levels in HCC cells with CGR11 overexpression or knockdown. Data shown as mean ± SD of triplicate independent experiments. * P < 0.05; ** P < 0.01; *** P < 0.001.

Article Snippet: HCC cell lines PLC/PRF/5, Hep3B,and SNU449, as well as Human normal liver cells THLE2 were obtained from the American Type Culture Collection (ATCC, Rockville, MD).

Techniques: Expressing, Fluorescence, Control, Staining, Western Blot, Over Expression, Knockdown

Journal: Frontiers in Cell and Developmental Biology

Article Title: CGR11 promotes hepatocellular carcinoma progression by regulating autophagy through the PI3K/AKT pathway

doi: 10.3389/fcell.2025.1692480

Figure Lengend Snippet: CGR11 regulates PI3K/AKT-mediated autophagy to promote HCC cell progression. (A) Western blot analysis of CGR11, p-AKT, and AKT expression in HCC cells with CGR11 overexpression or knockdown after further treatment with SC79 (4 μM) or MK2206 (5 μM). (B,C) Colony formation assays and EdU assays showed the proliferation ability of the indicated HCC cells after further treatment with SC79 (4 μM) or MK2206 (5 μM). (D,E) After treatment with SC79 (4 μM) or MK2206 (5 μM), the migration and invasion ability of HCC cells with knockdown or overexpression of CGR11 was determined by wound healing and Transwell assays, respectively. Scale bars, 50 μm. (F) Fluorescence images of MHCC-97H shCGR11 , PLC/PRF/5 CGR11 and the corresponding control cells, transduced with different mRFP-GFP-LC3 lentivirus, after treatment with SC79 (4 μM) or MK2206 (5 μM). Red dots represent autolysosomes while yellow dots indicate autophagosomes in the overlays. Nuclei were stained with DAPI. The average number of autophagosomes and autolysosomes per cell was quantified. A total of 50 cells from randomly selected fields in each group were counted for the analysis. Data shown as mean ± SD of triplicate independent experiments. * P < 0.05; ** P < 0.01; *** P < 0.001.

Article Snippet: HCC cell lines PLC/PRF/5, Hep3B,and SNU449, as well as Human normal liver cells THLE2 were obtained from the American Type Culture Collection (ATCC, Rockville, MD).

Techniques: Western Blot, Expressing, Over Expression, Knockdown, Migration, Fluorescence, Control, Transduction, Staining

Journal: The Journal of Biological Chemistry

Article Title: Up-regulation of the ATPase Inhibitory Factor 1 (IF1) of the Mitochondrial H + -ATP Synthase in Human Tumors Mediates the Metabolic Shift of Cancer Cells to a Warburg Phenotype *

doi: 10.1074/jbc.M110.146480

Figure Lengend Snippet: Silencing of IF1 triggers the inhibition of aerobic glycolysis and activates oxidative phosphorylation. The rates of aerobic glycolysis (A) and oxidative phosphorylation (B) were determined in HeLa cells expressing an inefficient (control: Ctr, open bars) or IF1 siRNA to promote the silencing of IF1 (closed bars). A, effect of 6 μm oligomycin treatment (OL. +) is shown in control and IF1-silenced cells. *, and #, p < 0.05 when compared with control or oligomycin-treated cells by Student's t test, respectively.

Article Snippet: Cell Cultures, Transfections, and siRNA Silencing Mouse hepatoma (Hepa 1–6), normal rat kidney (NRK), human embryonic kidney (HEK293T),human hepatocarcinoma (HepG2), breast (HS578T and T47D Tet-Off), colon (HCT116), lung (A549), and cervix (HeLa Tet-Off) carcinoma cells were cultured following the suppliers' indications (ATCC and Clontech) up to ∼70–80% confluence.

Techniques: Inhibition, Expressing

Journal: Hepatology Research

Article Title: Identification of two microRNA nodes as potential cooperative modulators of liver metabolism

doi: 10.1111/hepr.13419

Figure Lengend Snippet: MicroRNAs (miRNAs) downregulated in liver‐insulin receptor knockout (LIRKO) mouse livers target the transcription factor Zinc finger E‐box‐binding homeobox 1 (ZEB1). (a) Chromosomal locations (mm10 assembly) of the genes encoding the nine miRNAs identified as potential ZEB1‐targeting molecules. (b) Sequence alignment of the nine miRNAs. Nucleotides 2–7 are underlined, representing the seed sequence through which the miRNAs are predicted or experimentally validated to bind the Zeb1 3′UTR. (c) Regulation of each of the nine Zeb1‐targeting miRNAs in the livers of LIRKO versus control mice calculated from the small RNA sequencing data. (d) Zeb1 mRNA levels normalized to levels of Ppia mRNA, as measured by quantitative reverse transcription polymerase chain reaction and (e) ZEB1 protein levels normalized to total lane protein (TLP) in the eight groups of mice calculated by quantification of western blots (Fig. ). # P < 0.05 and ### P < 0.0005 between genotypes, n = 5–11 animals per group. Note that not indicated in (D) is a significant main effect of high‐fat diet (HFD) on Zeb1 mRNA expression ( P < 0.005 between diets). (d) The 95% CIs were calculated based on the group means of transformed Zeb1 / Ppia data. (f,g) ZEB1 protein levels in Hepa‐1c1c7 cells after 48 h of miRNA mimic or negative control transfection (50 nmol/L) shown with a representative blot of one out of five independent experiments quantified as ZEB1/TLP in. * P < 0.05 and *** P < 0.0005 versus negative control. (e–g) Both bands were quantified in lanes showing a double ZEB1 band. [Color figure can be viewed at http://wileyonlinelibrary.com ]

Article Snippet: Hepa‐1c1c7 mouse hepatoma cells (ATCC CRL‐2026) were grown in MEM alpha without nucleosides (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Sigma‐Aldrich, St. Louis, MO, USA) and 1% penicillin/streptomycin (Thermo Fisher Scientific).

Techniques: Knock-Out, Binding Assay, Sequencing, Control, RNA Sequencing, Reverse Transcription, Polymerase Chain Reaction, Western Blot, Expressing, Transformation Assay, Negative Control, Transfection

Journal: Hepatology Research

Article Title: Identification of two microRNA nodes as potential cooperative modulators of liver metabolism

doi: 10.1111/hepr.13419

Figure Lengend Snippet: MicroRNAs (miRNAs) upregulated by fibroblast growth factor 21 (FGF21) potentially target polymerase I and transcript release factor (PTRF). (a) Chromosomal locations (mm10 assembly) of the genes encoding the three miRNAs identified as potential PTRF‐targeting molecules. (b) Sequence alignment of the three miRNAs. Nucleotides 2–7 are underlined, representing their seed sequence through which they are predicted to bind the Ptrf 3′UTR. (c) Regulation of each of the three PTRF‐targeting miRNAs in the livers of FGF21‐ versus saline‐treated mice calculated from the small RNA sequencing data. (d) Ptrf mRNA levels normalized to levels of Ppia mRNA as measured by quantitative reverse transcription polymerase chain reaction, and (e) PTRF protein levels normalized to total lane protein (TLP) in the eight groups of mice calculated by quantification of western blots (Fig. ). * P < 0.05 between treatments, (d) n = 5–11 and(e) 5–10 animals per group. (e) The 95% CIs were calculated based on the group means of transformed PTRF/TLP data. (f,g) PTRF protein levels in Hepa‐1c1c7 cells after 48 h of miRNA mimic or negative control transfection (50 nmol/L) shown with (f) a representative blot of one out of three independent experiments (g) quantified as PTRF/TLP. * P < 0.05 versus negative control. (f) Shown below the PTRF blot in is part of the stain‐free picture used for quantification of TLP of the specific experiment. [Color figure can be viewed at http://wileyonlinelibrary.com ]

Article Snippet: Hepa‐1c1c7 mouse hepatoma cells (ATCC CRL‐2026) were grown in MEM alpha without nucleosides (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Sigma‐Aldrich, St. Louis, MO, USA) and 1% penicillin/streptomycin (Thermo Fisher Scientific).

Techniques: Sequencing, Saline, RNA Sequencing, Reverse Transcription, Polymerase Chain Reaction, Western Blot, Transformation Assay, Negative Control, Transfection, Staining

Journal: Toxicological Sciences

Article Title: Functional genomic analysis of non-canonical DNA regulatory elements of the aryl hydrocarbon receptor

doi: 10.1093/toxsci/kfaf146

Figure Lengend Snippet: Mutations in NC-XRE DNA in Serpine1 promoter reduced TCDD-dependent expression of Serpine1 . A) Schematic of mouse Serpine1 gene showing AHR ChIP peak ∼150 bp upstream of transcription start site, which contains 5× repeated NC-XRE (nucleotides in red) and no XRE sequences. Hepa 1 to 6 cell clones containing deletions in the NC-XRE region (dashed lines) are shown below the wild-type sequence. B, C) Hepa 1 to 6 wild-type or mutant cells were exposed to 10 nM TCDD or vehicle for 2 h, followed by RNA extraction and qPCR for Serpine1 (A) or Cyp1a1 (B). Mutant cell lines with full or partial deletion of NC-XRE exhibit reduced increase in Serpine1 following TCDD exposure compared with wild-type cells. Mutant cells showed similar increase in Cyp1a1 following TCDD exposure as wild-type cells. Gene expression normalized to vehicle, 18S rRNA used as reference gene. One-way ANOVA with Tukey’s multiple comparisons test, * P < 0.05, ** P < 0.01, ns, not significant ( P > 0.05).

Article Snippet: The mouse hepatoma cell line Hepa 1 to 6 was obtained from ATCC (Manassas, VA) ( ).

Techniques: Expressing, Clone Assay, Sequencing, Mutagenesis, RNA Extraction, Gene Expression

Journal: Frontiers in oncology

Article Title: GBM tumors are heterogeneous in their fatty acid metabolism and modulating fatty acid metabolism sensitizes cancer cells derived from recurring GBM tumors to temozolomide.

doi: 10.3389/fonc.2022.988872

Figure Lengend Snippet: FIGURE 2 Fatty acid metabolism in GBM cancer cells is linked to cell fate. (A) Desaturation activity of SCD (palmitate-to-palmitoleate ratio) and FADS2 (sapienate-to-palmitate ratio) in fresh frozen GBM tissue from eight patients (patient details in Supplementary Table S2). (B) Desaturation activity of SCD (palmitate-to-palmitoleate ratio) and FADS2 (sapienate-to-palmitate ratio) in human cell lines: hepatocellular carcinoma (HUH7), lung adenocarcinoma (A549), immortalized GBM cells (U87, U251, U118, LN18) and patient-derived GBM cell lines (LBT 001, LBT 002, CME 005, CME 037, CME 038, LBT 070, LBT 086, LBT 096, LBT 123, CME 014, CME 016, CME 035, CME 036) (patient details corresponding to cell lines in Supplementary Table S1). Color scale represents mean desaturation activity (n=3). HUH7, U87, U251, LN18, U118 were cultured in 1% FBS medium, A549 cells were cultured in 0.5% FBS medium. Patient-derived GBM cells were cultured in NSA medium without FBS. (C) Brief overview of the fatty acid mono-desaturation pathway. (D) Average gene expression levels of FASN, SCD1 and FADS2 in cancer cell sub-clusters of interest (SC: 6, 7, 8, 11, 17) among those in Figure 1B. The color scale indicates Z-scores, based on the overall mean expression level (and associated standard deviation) for each gene across all sub-cluster. (E) GSVA scores for gene sets representing different GBM cell fates in cancer cell sub-clusters of interest (SC: 6, 7, 8, 11, 17) among those in Figure 1B. The color scale indicates Z-scores, based on the overall mean GSVA score (and associated standard deviation) for each gene set across all sub-clusters. MES, mesenchymal; AC, astrocytic cells; OPC, oligodendrocytic precursor cell; NPC, neuronal progenitor cell.

Article Snippet: Frontiers in Oncology 04 Human adenocarcinoma A549 and human hepatocellular carcinoma HUH7 cells were obtained from ATCC and cultured in DMEM (Life Technologies) supplemented with 10% heat-inactivated fetal bovine serum (Life Technologies), A B D C FIGURE 1 Glioblastoma cancer cells have a highly heterogeneous lipid metabolism. (A) Uniform manifold approximation and projection (UMAP) plots of single-cell RNA sequencing data of fresh GBM tissue derived from six patients newly diagnosed with GBM. (B) UMAP plots of sub-clustering analysis performed on single-cell RNA sequencing data from fresh GBM tissue derived from six patients newly diagnosed with GBM. (C) Results of GSEA-based metabolic pathway-heterogeneity analysis for GBM cancer cells.

Techniques: Activity Assay, Derivative Assay, Cell Culture, Gene Expression, Expressing, Standard Deviation

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Deep Learning based multi-omics integration robustly predicts survival in liver cancer

doi: 10.1158/1078-0432.CCR-17-0853

Figure Lengend Snippet: (A) Autoencoder architecture used to integrate 3 omics of HCC data. (B) Workflow combining deep learning and machine learning techniques to predict HCC survival subgroups. The workflow includes two steps. Step 1: inferring survival subgroups and Step 2: predicting risk labels for new samples. In step 1: mRNA, DNA methylation and miRNA features from TCGA HCC cohort are stacked up as input features for autoencoder, a deep learning method; then each of the new, transformed features in the bottle neck layer of autoencoder is then subject to single variate Cox-PH models, to select the features associated with survival; then K-mean clustering is applied to samples represented by these features, to identify survival-risk groups. In step 2, mRNA, methylation and miRNA input features are ranked by ANOVA test F-values, those features that are in common with the predicting dataset are selected, then top features are used to build SVM model(s) to predict the survival risk labels of new datasets.

Article Snippet: 166 pairs of HCC/matched noncancerous normal tissue samples were downloaded, with CapitalBio custom Human miRNA array data ( {"type":"entrez-geo","attrs":{"text":"GSE31384","term_id":"31384"}} GSE31384 ) ( 33 ).

Techniques: DNA Methylation Assay, Transformation Assay, Methylation

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Deep Learning based multi-omics integration robustly predicts survival in liver cancer

doi: 10.1158/1078-0432.CCR-17-0853

Figure Lengend Snippet: Performance of classifier for the five external confirmation cohorts.

Article Snippet: 166 pairs of HCC/matched noncancerous normal tissue samples were downloaded, with CapitalBio custom Human miRNA array data ( {"type":"entrez-geo","attrs":{"text":"GSE31384","term_id":"31384"}} GSE31384 ) ( 33 ).

Techniques: Microarray, DNA Methylation Assay

Journal: Cell Reports Medicine

Article Title: CV1-secreting sCAR-T cells potentiate the abscopal effect of microwave ablation in heterogeneous tumors

doi: 10.1016/j.xcrm.2025.101965

Figure Lengend Snippet: sCAR-T cells contribute to an enhanced abscopal effect of MWA and enable the control of distant antigenically heterogeneous tumors (A–D) Mouse Hepa1-6-chGPC3 cells were engrafted into both flanks of C57BL/6J immunocompetent mice. Mice underwent lymphodepletion (LD) on the day before treatment, and only the right-side tumors in MWA monotherapy group or other MWA-combined treatment groups were treated with MWA (A). Tumor growth in the local (B) and distant (C) sites following rCV1, mCART, and msCART, with or without MWA treatment, was monitored ( n = 5, one experiment). Immunohistochemistry to detect the GPC3 expression post-treatment in different groups (200×). Scale bar represents 100 μm (D). (E) Individual distant tumor growth of C57BL/6J mice bearing heterogeneous Hepa1-6-chGPC3 + Hepa1-6 tumors upon MWA ± mCAR-T/msCAR-T treatment ( n = 5, one experiment). Hepa1-6-chGPC3 + Hepa1-6 cells were pre-mixed at the indicated ratios. Tumor-bearing C57BL/6J mice received lymphodepletion (LD) on the day before treatment. (F and G) Tumor growth (G) of humanized mice bearing Hep3B cells in the right flank and SK-HEP-1 cells in the left flank (F) following MWA ± CAR-T or sCAR-T ( n = 5, one experiment). (H and I) Tumor growth (I) of humanized mice bearing HCC PDX in both flanks (H) following MWA ± CAR-T or sCAR-T ( n = 5, one experiment). Error bars are means ± SD. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001 by two-way ANOVA with Tukey’s multiple comparisons test for (B), (C), (G), and (I). See also Figures S2 and .

Article Snippet: Hep3B cells , ATCC , HB-8064.

Techniques: Control, Immunohistochemistry, Expressing

Journal: Cell Reports Medicine

Article Title: CV1-secreting sCAR-T cells potentiate the abscopal effect of microwave ablation in heterogeneous tumors

doi: 10.1016/j.xcrm.2025.101965

Figure Lengend Snippet:

Article Snippet: Hep3B cells , ATCC , HB-8064.

Techniques: Recombinant, Protease Inhibitor, Selection, Cell Isolation, Enzyme-linked Immunosorbent Assay, RNA Extraction, Software

Journal: Oncology Letters

Article Title: MicroRNA-9 enhances sensitivity to cetuximab in epithelial phenotype hepatocellular carcinoma cells through regulation of the eukaryotic translation initiation factor 5A-2

doi: 10.3892/ol.2017.7399

Figure Lengend Snippet: Overexpression of miR-9 enhances sensitivity of epithelial HCC cells to cetuximab. (A-D) Viability of HCC cells treated with cetuximab in the presence of a miR-9 mimic or inhibitor. (E-H) Photomicrographs and bar charts depicting EdU staining and relative EdU-positive ratios, respectively, of HCC cells following treatment with cetuximab, with cetuximab plus a miR-9 mimic or with cetuximab plus miR-9 inhibitor for 48 h. *P<0.05, **P<0.01 vs. control, Hep3B: P miR-9 mimic+Cet =0.0025, P miR-9 inhibitor+Cet =0.0295, Huh7: P miR-9 mimic+Cet =0.0356, P miR-9 inhibitor+Cet =0.0480. All experiments were performed ≥3 times. miR-9, microRNA-9; HCC, hepatocellular carcinoma; EdU, 5-ethynyl-2′-deoxyuridine; Cet, cetuximab.

Article Snippet: Human HCC cell lines (Hep3B, Huh7, SNU387 and SNU449) were obtained from American Type Culture Collection (ATCC; Manassas, VA, USA).

Techniques: Over Expression, Staining, Control

Journal: Oncology Letters

Article Title: MicroRNA-9 enhances sensitivity to cetuximab in epithelial phenotype hepatocellular carcinoma cells through regulation of the eukaryotic translation initiation factor 5A-2

doi: 10.3892/ol.2017.7399

Figure Lengend Snippet: miR-9 modulates expression of eIF-5A-2 in HCC cell lines. (A) miR-9 target site in eIF-5A-2 predicted by TargetScan. (B) Expression of miR-9 and eIF-5A-2 mRNA in HCC cells as determined by RT-qPCR. *P<0.05, **P<0.01, ***P<0.001 vs. Huh7; # P<0.05, ## P<0.01 vs. Hep3B. (C) eIF-5A-2 expression in HCC cells following treatment with a miR-9 mimic or inhibitor as determined by RT-qPCR. **P<0.01, ***P<0.001 vs. the control. (D) Expression levels of miR-9 following treatment with a miR-9 mimic or inhibitor as determined by RT-qPCR. *P<0.05, **P<0.01, ***P<0.001 vs. the control (E) Western blot analysis was used to detect eIF-5A-2 expression in the various HCC cell lines in the presence of the miR-9 mimic, inhibitor and control. *P<0.05 vs. negative siRNA. miR-9, microRNA-9; eIF-5A-2; eukaryotic translation initiation factor 5A-2; HCC, hepatocellular carcinoma; RT-qPCR, reverse transcription-quantitative polymerase chain reaction; miRNA, microRNA; UTR, untranslated region.

Article Snippet: Human HCC cell lines (Hep3B, Huh7, SNU387 and SNU449) were obtained from American Type Culture Collection (ATCC; Manassas, VA, USA).

Techniques: Expressing, Quantitative RT-PCR, Control, Western Blot, Reverse Transcription, Real-time Polymerase Chain Reaction

Journal: Oncology Letters

Article Title: MicroRNA-9 enhances sensitivity to cetuximab in epithelial phenotype hepatocellular carcinoma cells through regulation of the eukaryotic translation initiation factor 5A-2

doi: 10.3892/ol.2017.7399

Figure Lengend Snippet: Sensitivity of HCC cell lines to cetuximab. (A) Western blot analysis of eIF-5A-2 expression in eIF-5A-2 siRNA-transfected cells. GAPDH served as a loading control. Knockdown of eIF-5A-2 enhanced the sensitivity of the epithelial phenotype HCC cells, (B) Hep3B and (C) Huh7, to cetuximab, but had no significant effect on the mesenchymal phenotype HCC cells, (D) SNU387 and (E) SNU449. *P<0.05 vs. negative siRNA. HCC, hepatocellular carcinoma; eIF-5A-2; eukaryotic translation initiation factor 5A-2; siRNA, small interfering RNA.

Article Snippet: Human HCC cell lines (Hep3B, Huh7, SNU387 and SNU449) were obtained from American Type Culture Collection (ATCC; Manassas, VA, USA).

Techniques: Western Blot, Expressing, Transfection, Control, Knockdown, Small Interfering RNA

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: Characteristics of circFOXP1 in HCC. ( A ) Flowchart for screening differentially expressed circular RNAs (DECs) between HCC and adjacent normal tissues. ( B ) Ratio of DECs to p-values in the assessment of seven GEO datasets. ( C ) Heatmap identifying top 20 common DECs between HCC and adjacent samples across seven datasets. ( D ) hsa_circ_0008234 can be amplified by different cDNA primers but not from genomic DNA of Huh7 cells. ( E ) hsa_circ_0008234 is derived from the host gene FOXP1 and verified by Sanger sequencing. ( F and G ) RT-qPCR analysis of hsa_circ_0008234 expression levels in HCC cell lines ( F ) and tissues ( G ). H ) RT-qPCR analysis of RNA levels of circFOXP1 and FOXP1 in Huh7 cells after RNase R treatment. ( I ) FISH assay showing cytoplasmic localization of circFOXP1 in Huh7 cells (green). Scale bar: 10 μm. ( J ) RT-qPCR analysis of circFOXP1 expression in Huh7 and MHCC97-H cells transfected with circFOXP1 expression vector, Vector control, sh-circFOXP1, or sh-NC. ( K ) Representative images, growth curves, and final weights of xenografts formed by subcutaneous transplantation of Huh7 cells stably transfected with Vector or circFOXP1 into the dorsal side of nude mice (n = 4 per group). ( L ) Representative images and quantitation of immunohistochemical staining for Ki-67 expression in xenografts formed by subcutaneous injection of Huh7 cells stably transfected with Vector or circFOXP1. Scale bars represent 50 µm. ***P<0.001, ns, not significant.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Amplification, Derivative Assay, Sequencing, Quantitative RT-PCR, Expressing, Transfection, Plasmid Preparation, Control, Transplantation Assay, Stable Transfection, Quantitation Assay, Immunohistochemical staining, Staining, Injection

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: circFOXP1 encodes a novel protein p196 with 196 amino acids (aa). ( A ) Schematic diagram shows that circFOXP1 has an internal ribosome entry site (IRES) and a predicted open reading frame, which may encode a 196 amino acid (aa) polypeptide. ( B ) Dual luciferase assay shows that the Luc/Rluc activity of the wild-type IRES is higher than that of its mutant and deletion mutant. ( C ) Sequence diagram of p196 and FOXP1 recognizable by antibodies. ( D ) Western blot (WB) analysis shows that p196 is highly expressed in HCC cells. ( E ) HCC cells were transfected with empty vector, circFOXP1 vector, circFOXP1 IRES mutant vector, and linearized FOXP1-196aa vector, respectively. The levels of FOXP1 and p196 were detected by WB. (F ) HCC cells were transfected with junction-specific shRNA targeting circFOXP1. The levels of FOXP1 and p196 were detected by WB. ( G ) Silver staining shows that p196 is within the predicted molecular weight range. ***P<0.001.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Luciferase, Activity Assay, Mutagenesis, Sequencing, Western Blot, Transfection, Plasmid Preparation, shRNA, Silver Staining, Molecular Weight

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: P196 promotes proliferation and invasiveness of HCC cells. ( A–D ) P196-overexpressing Huh7 and MHCC97-H cell lines were established by transfection with linearized FOXP1-196aa plasmid and circFOXP1 plasmid. P196 stably knockdown Huh7 and MHCC97-H cell lines were established by connecting specific shRNA. The expression level of P196 in stably knockdown HCC cells was restored using linearized FOXP1-196aa plasmid. The proliferation of HCC cells was detected using the Edu assay (scale: 100 μm) ( A and B ) and colony formation assay ( C and D ). ( E and F ) The invasion ability of HCC cells was detected using the matrix invasion assay. Scale: 100 μm. ( G and H) . The effect of P196 on the cell cycle of HCC cells was detected by flow cytometry. ( I and J) WB analysis of the expression levels of cell cycle regulatory proteins and EMT-related proteins. **P<0.01, and ***P<0.001.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Transfection, Plasmid Preparation, Stable Transfection, Knockdown, shRNA, Expressing, EdU Assay, Colony Assay, Invasion Assay, Flow Cytometry

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: P196 regulates the proliferation and invasion of liver cancer mediated by autophagy through ULK1. ( A ) RNA immunoprecipitation (RIP) assay validates the interaction between circFOXP1 and Ago2. ( B ). qRT-PCR analysis of ULK1 mRNA in HCC stably transfected with Vector, circFOXP1, and sh-circFOXP1. ( C) WB analysis of p196 and ULK1 expression in HCC cells with p196 knockdown and overexpression. (D ) Western blot analysis of ULK1 expression in HCC transfected with sh-ULK1-1, sh-ULK1-2, and sh-NC lentiviruses. ( E ) WB experiments showed that sh-ULK1-2 could reverse the positive effect of p196 on LC3II/I in HCC cells. ( F and G ). Huh7 and MHCC97-H cell lines were transfected with circFOXP1 plasmid and/or sh-ULK1-2, and the proliferation of HCC cells was detected using the Edu method (scale: 100 μm) ( E ) and colony formation method ( F ). ( H) . The invasion ability of HCC cells was detected using the matrix invasion method. Scale: 100 μm. ( I) . Flow cytometry was used to detect the effect of P196 on the cell cycle of HCC cells. **P<0.01, ***P<0.001.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: RNA Immunoprecipitation, Quantitative RT-PCR, Stable Transfection, Transfection, Plasmid Preparation, Expressing, Knockdown, Over Expression, Western Blot, Flow Cytometry

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: The interaction between p196 and KHDRBS3 stabilizes ULK1 mRNA. ( A and B ) HCC cells with p196 knockdown and overexpression were treated with 2 μg/mL actinomycin at specified time points, followed by qRT-PCR to detect the relative expression of ULK1 mRNA. ( C) RNA immunoprecipitation experiments indicated that p196 could bind to ULK1 mRNA. ( D ) Silver Staining assay showed that proteins co-precipitated by p196 from Huh7 cell lysates identified a specific band at 55 kDa. ( E ). Mass spectrometry analysis detected a peptide of KHDRBS3 (n = 1 for both IgG and p196 groups), indicating an interaction between p196 and KHDRBS3. ( F ). Co-immunoprecipitation experiments demonstrated the interaction between p196 and KHDRBS3. ( G ) IF detection showed the co-localization of p196 (red) and KHDRBS3 (green) in liver cancer cells. Scale: 10 μm. ( H ). Schematic diagram of KHDRBS3 truncated domains. ( I ). In vitro binding experiments revealed the specific region of p196 that binds to KHDRBS3. ( J ) WB experiments indicated that sh-KHDRBS3 could reverse the positive effect of p196 on LC3II/I and ULK1 in liver cancer cells. ( K ) KHDRBS3 was knocked down in HCC cells with p196 overexpression, followed by treatment with 2 μg/mL actinomycin at specified time points, and then qRT-PCR was used to detect the relative expression of ULK1. *P<0.05, **P<0.01, ***P<0.001.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Knockdown, Over Expression, Quantitative RT-PCR, Expressing, RNA Immunoprecipitation, Silver Staining, Mass Spectrometry, Immunoprecipitation, In Vitro, Binding Assay

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: P196 acts as a scaffold to promote KHDRBS3 binding to ULK1, enhancing autophagy and liver cancer progression. ( A ) Western blot (WB) experiments showed that knockdown of p196 could reverse the positive effect of KHDRBS3 on ULK1 and LC3II/I in HCC cells. ( B ) Observation of autophagosomes by electron microscopy. ( C) Immunofluorescence staining of autophagosomes and autolysosomes. ( D and E ) Detection of proliferation of HCC cells using the EdU method (scale: 100 μm) ( D ) and colony formation assay ( E ). ( F ) Detection of invasion ability of HCC cells using the matrix invasion assay. Scale: 100 μm. ( G ). Flow cytometry analysis of the cell cycle of HCC cells. *P<0.05, **P<0.01, ***P<0.001.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Binding Assay, Western Blot, Knockdown, Electron Microscopy, Immunofluorescence, Staining, Colony Assay, Invasion Assay, Flow Cytometry

Journal: International Journal of Nanomedicine

Article Title: Exosome-Delivered circFOXP1 Upregulates Autophagy and Promotes Hepatocellular Carcinoma Progression Through Its Encoded p196 Protein Targeting the KHDRBS3/ULK1 Axis

doi: 10.2147/IJN.S505157

Figure Lengend Snippet: Exosomes are the primary carriers of extracellular circFOXP1. ( A ) qRT-PCR analysis of circFOXP1 expression in the HCC cell culture medium treated with PBS, RNase A alone, or RNase A in combination with Triton X-100. ( B ) Transmission electron microscopy images showing the morphology of exosomes isolated from the supernatants of MIHA, Huh7, and MHCC97-H cultures. ( C ) NTA analysis displays the quantity and size distribution of exosomes isolated from the supernatants of MIHA, Huh7, and MHCC97-H cultures. ( D ) Western blot analysis demonstrating the expression of exosomal markers in the exosomes isolated from the supernatants of Huh7 and MHCC97-H cultures. ( E ) qRT-PCR analysis shows the relative expression of circFOXP1 in exosomes and cell culture medium. ( F ) qRT-PCR analysis displaying the relative expression of circFOXP1 in exosomes from different cell lines. ( G ) qRT-PCR analysis indicates the expression of circFOXP1 after co-culturing exosomes isolated from Huh7 and MHCC97-H cells stably transfected with sh-NC (negative control short hairpin RNA) or sh-circFOXP1 (short hairpin RNA targeting circFOXP1). ( H ) Schematic illustration of the uptake of exosomes secreted by MHCC97-H cells by Huh7. ( I ) Immunofluorescence analysis showing changes in fluorescence after Huh7 uptake of exosomes secreted by MHCC97-H cells. Scale: 20X. * p < 0.05, *** p < 0.001, ns, not significant.

Article Snippet: The human normal liver cell line (MIHA) and HCC cell lines (SNU449, Hep3B, Huh7, MHCC97-H) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Quantitative RT-PCR, Expressing, Cell Culture, Transmission Assay, Electron Microscopy, Isolation, Western Blot, Stable Transfection, Transfection, Negative Control, shRNA, Immunofluorescence, Fluorescence