Journal: BMC Cancer

Article Title: High expression of forkhead box protein C2 is associated with aggressive phenotypes and poor prognosis in clinical hepatocellular carcinoma

doi: 10.1186/s12885-018-4503-6

Figure Lengend Snippet: Immunohistochemical analysis of FOXC2, E-cadherin, N-cadherin, and Ki-67 in representative HCC tissues from an identical patient. a High FOXC2 expression in an HCC tissue; b Low E-cadherin expression in an HCC tissue; c High N-cadherin expression in an HCC tissue; d High Ki-67 expression in an HCC tissue. Scale bar, 200 μm

Article Snippet: Anti-FOXC2 primary monoclonal antibody (Abnova, Taipei, Taiwan) was used at a dilution of 1:100 at 4 °C overnight, as previously described [ ].

Techniques: Immunohistochemical staining, Expressing

Journal: BMC Cancer

Article Title: High expression of forkhead box protein C2 is associated with aggressive phenotypes and poor prognosis in clinical hepatocellular carcinoma

doi: 10.1186/s12885-018-4503-6

Figure Lengend Snippet: Clinicopathological characteristics of patients with hepatocellular carcinoma (HCC) according to forkhead box protein C2 (FOXC2) expression

Article Snippet: Anti-FOXC2 primary monoclonal antibody (Abnova, Taipei, Taiwan) was used at a dilution of 1:100 at 4 °C overnight, as previously described [ ].

Techniques: Expressing, Labeling

Journal: BMC Cancer

Article Title: High expression of forkhead box protein C2 is associated with aggressive phenotypes and poor prognosis in clinical hepatocellular carcinoma

doi: 10.1186/s12885-018-4503-6

Figure Lengend Snippet: The relationship of FOXC2 expression and EMT-related markers in 84 HCC samples

Article Snippet: Anti-FOXC2 primary monoclonal antibody (Abnova, Taipei, Taiwan) was used at a dilution of 1:100 at 4 °C overnight, as previously described [ ].

Techniques: Expressing

Journal: BMC Cancer

Article Title: High expression of forkhead box protein C2 is associated with aggressive phenotypes and poor prognosis in clinical hepatocellular carcinoma

doi: 10.1186/s12885-018-4503-6

Figure Lengend Snippet: Relationship between postoperative survival and FOXC2 expression in 84 patients with HCC. Kaplan–Meier curves of the low expression of FOXC2 and high expression of FOXC2 groups are shown. a A high expression of FOXC2 indicated a poor prognosis for the disease-free survival rate ( P = 0.0022). b A high expression of FOXC2 indicated a poor prognosis for the overall survival rate ( P = 0.031)

Article Snippet: Anti-FOXC2 primary monoclonal antibody (Abnova, Taipei, Taiwan) was used at a dilution of 1:100 at 4 °C overnight, as previously described [ ].

Techniques: Expressing

Journal: BMC Cancer

Article Title: High expression of forkhead box protein C2 is associated with aggressive phenotypes and poor prognosis in clinical hepatocellular carcinoma

doi: 10.1186/s12885-018-4503-6

Figure Lengend Snippet: Results of univariate and multivariate analyses of clinicopathological factors affecting the overall survival rate following surgery

Article Snippet: Anti-FOXC2 primary monoclonal antibody (Abnova, Taipei, Taiwan) was used at a dilution of 1:100 at 4 °C overnight, as previously described [ ].

Techniques: Expressing

Journal: bioRxiv

Article Title: FOXM1 enhances DNA repair in aged cells to maintain the peripheral heterochromatin barrier to senescence enhancers

doi: 10.1101/2025.10.29.685369

Figure Lengend Snippet: a , Representative immunofluorescence images of γH2AX (green) and 53BP1 (magenta) in HDFs derived from young or aged donors. Arrowheads point to magnified nuclei in the insets. b , Percentage of nuclei positive for γH2AX or 53BP1 foci (DSBs markers) in HDFs from donors grouped by age intervals as indicated. Each dot represents a biological replicate of a distinct age (n = 400 cells per replicate). c , Representative immunofluorescence images of p53 (green) and p21 (magenta) in HDFs derived from young or aged donors. d , Percentage of cells staining positive for p53 or p21 (DDR markers) in HDFs from donors grouped by age intervals as indicated. Each dot represents a biological replicate of a distinct age (n = 400 cells per replicate). e , GSEA analysis comparing the older (>40-year-old) versus younger (1- to 40-year-old) cohorts using the “Hallmark” collection from MSigDB. Significant gene sets are ordered by normalized enrichment score (NES), and the top 25 terms ranked by p -adjust are displayed (see full list in Supplementary table 2). f, GSEA analysis comparing the older versus younger cohorts using gene sets related to DNA repair retrieved from the diverse collections available in MSigDB. Significantly enriched gene sets are ordered by normalized enrichment score (NES) (see also Supplementary table 3). g , Transcription factor enrichment analysis for downregulated DNA repair genes using ChEA3. Transcription factors are ordered by the number of gene associations. h , Representative immunofluorescence images of γH2AX (green) and 53BP1 (magenta) in young HDFs treated with either mock or FOXM1 RNAi. Arrowheads indicate nuclei shown in the insets, where dashed lines delimitate nuclear area. i , Percentage of nuclei positive for γH2AX or 53BP1 foci in mock or FOXM1 RNAi-treated HDFs. Each dot represents a biological replicate of a distinct age (n = 400 cells per replicate). j , Representative comet assay images and k , quantification of the comet olive moment in mock or FOXM1 RNAi-treated young HDFs (n ≥ 163 cells, 3 independent biological replicates of distinct age). Color scale used to interpret signal intensity is displayed on the right. l , Representative immunofluorescence images of γH2AX (green) and 53BP1 (magenta) in young or aged HDFs transduced with empty lentiviral vector or overexpressing FOXM1 (FOXM1 OE). White lines delimitate nuclear areas. n , Percentage of nuclei positive for γH2AX or 53BP1 foci in HDF samples as mentioned in l). Each dot represents an independent experiment, using two biological replicates per group (n ≥ 350 cells per experiment). m , Representative comet assay images and k , quantification of the comet olive moment in aged HDFs transduced with empty lentiviral vector or overexpressing FOXM1 (n ≥ 142 cells, 4 independent experiments using 2 biological replicates). Color scale used to interpret signal intensity is displayed on the right. Scale bars: 20 µm ( a , c , h , and i ) or 50 µm ( j and n ). Error bars indicate standard deviation. Statistics were performed comparing indicated groups using the Mann-Whitney test ( k , o ) and the two-tailed Fisher’s exact test ( b , d , i , m ).

Article Snippet: HDFs were plated in serum-free culture medium and transfected with 50 nM of a small interfering RNA (siRNA) targeting FOXM1 (SASI_Hs01_00243977 from Merck). siRNA transfections were performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM medium (Gibco) according to the manufacturer’s instructions.

Techniques: Immunofluorescence, Derivative Assay, Staining, Single Cell Gel Electrophoresis, Transduction, Plasmid Preparation, Standard Deviation, MANN-WHITNEY, Two Tailed Test

Journal: bioRxiv

Article Title: FOXM1 enhances DNA repair in aged cells to maintain the peripheral heterochromatin barrier to senescence enhancers

doi: 10.1101/2025.10.29.685369

Figure Lengend Snippet: a , GSEA comparing FOXM1 RNAi versus mock treated young HDFs, and aged HDFs overexpressing FOXM1 versus empty vector. Dots indicate significantly enriched gene sets related to DNA repair (MSigDB), divided into global and specific processes. For each condition, two biological samples were analyzed. b, c , GSEA enrichment plots showing downregulation of DNA repair (BP) genes upon FOXM1 knockdown in young HDFs ( b ), and upregulation of DNA repair (BP) genes upon FOXM1 OE in aged HDFs ( c ). d , Venn diagram displaying the intersection between robustly downregulated (Log2FC < -0.5, p -adjust < 0.05) DNA repair genes upon FOXM1 RNAi and robustly upregulated DNA repair genes (Log2FC > 0.5, p -adjust < 0.05) upon FOXM1 OE. The overlap is defined as the “FOXM1 DNA repair gene network”. e , Transcription factor enrichment analysis for the FOXM1 DNA repair gene network using ChEA3. Transcription factors were ordered by the number of gene associations. f , Heatmap showing a progressive z-scored mean expression (higher expression as red, lower expression as blue) of genes in the FOXM1 DNA repair network for human dermal fibroblasts grouped by different age intervals. FOXM1 is highlighted in red. g , Representative images of γH2AX immunostaining (green) in young HDFs (mock or FOXM1 RNAi-treated) immediately after etoposide treatment and 24 hr following recovery. Arrowheads point to nuclei magnified in the insets. h , Percentage of nuclei staining positive for γH2AX in young HDFs, mock or FOXM1 RNAi treated for 36 hr, that were then exposed to 1 µM etoposide for 1 hr and allowed to recover for the indicated hours (n = 4 independent experiments using HDFs from two distinct donors). i , Representative images of γH2AX immunostaining (green) in aged HDFs (empty vector or FOXM1 OE) immediately after etoposide treatment and 24 hr following recovery. Arrowheads point to nuclei magnified in the insets. j , Percentage of nuclei staining positive for γH2AX in aged HDFs transduced with empty vector or overexpressing FOXM1 (FOXM1 OE) for 36h, that were then treated with 1 µM etoposide for 1 h and allowed to recover for the indicated hours (n = 4 independent experiments using HDFs from two distinct donors). Scale bars: 20 µm. Error bars represent the standard deviation. Statistics were performed comparing indicated groups using two-way analysis of variance (ANOVA) with Sidak’s multiple-comparison correction.

Article Snippet: HDFs were plated in serum-free culture medium and transfected with 50 nM of a small interfering RNA (siRNA) targeting FOXM1 (SASI_Hs01_00243977 from Merck). siRNA transfections were performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM medium (Gibco) according to the manufacturer’s instructions.

Techniques: Plasmid Preparation, Knockdown, Expressing, Immunostaining, Staining, Transduction, Standard Deviation, Comparison

Journal: bioRxiv

Article Title: FOXM1 enhances DNA repair in aged cells to maintain the peripheral heterochromatin barrier to senescence enhancers

doi: 10.1101/2025.10.29.685369

Figure Lengend Snippet: a, Representative immunofluorescence images of G9a (green) and H3K9me2 (magenta) in young HDFs treated with either vehicle control (DMSO), etoposide (ETO 3 µM) or ETO in the presence of MG132 (5 µM; see methods for details). b, Quantification of G9a and H3K9me2 nuclear levels in young HDFs treated as mentioned in (a). Each condition is represented by n = 450 cells obtained from 3 independent biological replicates. c, Representative images of G9a (green) and H3K9me2 (magenta) immunostainings in young versus aged HDFs. d, Quantification of G9a and H3K9me2 nuclear levels in n = 900 cells obtained from 3 independent biological replicates per age condition. e, Single-cell correlation analysis between the fluorescence nuclear intensity levels of G9a and H3K9me2 in young and aged HDFs (see panels c, d). ρ = Spearman’s rank correlation coefficient. f, Representative confocal microscopy images of H3K9me2 (green-fire-blue gradient) and Lamin A/C (magenta) immunostainings in HDFs from donors grouped by age intervals as indicated (DNA in blue). g, h, Quantification of the H3K9me2 peripheral/internal signal brightness (P/I) ratio ( g ) and percentage of H3K9me2 signal at the nuclear periphery ( h ) in HDFs from donors grouped by age intervals as indicated (n ≥ 122 cells obtained from 3 independent biological replicates in each age group). i, Representative immunofluorescence images of G9a (green) and H3K9me2 (magenta) in young HDFs treated with mock vs. FOXM1 RNAi. j, Quantification of G9a and H3K9me2 nuclear levels in young HDFs treated with mock vs. FOXM1 RNAi. Each condition is represented by n = 1200 cells obtained from 4 independent biological replicates. k, Representative immunofluorescence images of G9a (green) and H3K9me2 (magenta) in young or aged HDFs transduced with empty lentiviral vector or overexpressing FOXM1 (FOXM1 OE). l, Quantification of G9a and H3K9me2 nuclear levels in HDFs as mentioned in (k). Each group is represented by n = 1600 cells obtained from 4 independent experiments using 2 biological samples of different ages. m, Representative confocal microscopy images of H3K9me2 (green-fire-blue gradient) and Lamin A/C (magenta) immunostainings in aged HDFs overexpressing FOXM1 vs. empty vector, in the presence of either DMSO or G9a inhibitor (BIX-01294). n, Quantification of H3K9me2 nuclear levels in aged HDFs as mentioned in (m). Each group is represented by n = 600 cells obtained from 3 independent replicates from 2 biological samples of different ages. o, p, Quantification of the H3K9me2 P/I ratio (o) and percentage of H3K9me2 signal at the nuclear periphery ( p ) in HDFs as mentioned in (m). Each group is represented by n ≥ 45 cells obtained from 3 independent biological replicates. Scale bars: 20 µm ( a, c, i and k ) or 5 µm ( f, m ). Statistics were performed comparing indicated groups using the Kruskal-Wallis test with Dunn’s multiple-comparison correction ( b, g, n, l ), the one-way ANOVA test with Sidak’s multiple-comparison correction ( h, o, p ), the Mann-Whitney test ( d, j ) and Spearman’s rank correlation ( e ).

Article Snippet: HDFs were plated in serum-free culture medium and transfected with 50 nM of a small interfering RNA (siRNA) targeting FOXM1 (SASI_Hs01_00243977 from Merck). siRNA transfections were performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM medium (Gibco) according to the manufacturer’s instructions.

Techniques: Immunofluorescence, Control, Fluorescence, Confocal Microscopy, Transduction, Plasmid Preparation, Comparison, MANN-WHITNEY

Journal: bioRxiv

Article Title: FOXM1 enhances DNA repair in aged cells to maintain the peripheral heterochromatin barrier to senescence enhancers

doi: 10.1101/2025.10.29.685369

Figure Lengend Snippet: a , Heatmap of the top thousand regions differentially bound by H3K9me2 (DBRs) upon FOXM1 knockdown in young HDFs (mock vs. FOXM1 RNAi) or FOXM1 overexpression in aged HDFs (empty vector vs. FOXM1 OE). Two biological replicates were used per condition. b , Volcano plots of H3K9me2 DBRs upon FOXM1 knockdown in young HDFs and ectopic FOXM1 expression in aged HDFs. c , Human genome annotation of H3K9me2 DBRs upon FOXM1 knockdown in young HDFs and ectopic FOXM1 expression in aged HDFs using ChIPSeeker . d , Heatmap showing the percentage of H3K9me2 DBRs in FOXM1 RNAi and FOXM1 OE overlapping with four main cCREs categories from ENCODE. e , Dot plot showing “Hallmark” gene sets inversely correlated between H3K9me2 GREAT analysis and RNA-seq GSEA analysis. Dots indicate gene sets enriched in regions losing H3K9me2 upon FOXM1 RNAi or gaining H3K9me2 upon FOXM1 OE in CUT&RUN data using GREAT, which are negatively correlated with RNA-seq data (i.e., upregulated upon FOXM1 RNAi and downregulated upon FOXM1 OE using GSEA). Color gradient indicates NES (for RNA-seq data) or the fold enrichment score FES (for CUT&RUN) (see Methods). Dot size indicates -log 10 of adjusted p -value. f , Dot plot showing significantly enriched motifs ( q -value < 0.05) for individual transcription factors in regions losing H3K9me2 upon FOXM1 RNAi or gaining H3K9me2 upon FOXM1 OE using HOMER. Triangles are ordered by nominal p -value and colored triangles indicate motifs targeted by known subunits of the AP-1 complex. g , Heatmap displaying the level of similarity between the top 100 motifs ( q -value < 0.05, ranked by nominal p -value) enriched in enhancers losing or gaining H3K9me2 signal. Bar plots on the right indicate the enrichment p- value after log 10 transformation. A cluster containing motifs targeted by several subunits of the AP-1 complex is highlighted using dashed lines. Transcription factors associated with each motif in HOMER are indicated on the right. h , Dot plot showing GSEA analysis in the CUT&RUN and RNA-seq datasets for “Hallmark” and “Biological Processes” related to inflammation and immunity, senescence and SASP gene sets curated and validated elsewhere, and the senescence gene signature associated with AP-1 activity . Color gradient indicates NES (for RNA-seq data) or FES (for CUT&RUN). Dot size indicates -log 10 of adjusted p -value. i , Representative images of Lamin B1 (green) and p16 (magenta) immunostainings in young HDFs treated either with G9a inhibitor (G9ai) or vehicle control (DMSO). j , k , Quantification of Lamin B1 nuclear levels ( j ) and p16-positive nuclei ( k ) in young HDFs treated as mentioned in (i). Each group is represented by n = 900 cells obtained from 3 independent biological replicates. l , Representative images of p53 (green) and p21 (magenta) immunostainings in young HDFs treated either with DMSO or G9ai. m , n , Quantification of p53-positive ( m ) and p21-positive ( n ) nuclei in young HDFs treated as mentioned in (l). Each group is represented by n = 900 cells obtained from 3 independent biological replicates. Scale bars: 20 µm ( i and l ). Statistics comparing indicated groups were performed using the Mann-Whitney test ( k , n ) and two-tailed Fisher’s exact ( b , j , m ), and standard methods for sequencing data (see Methods).

Article Snippet: HDFs were plated in serum-free culture medium and transfected with 50 nM of a small interfering RNA (siRNA) targeting FOXM1 (SASI_Hs01_00243977 from Merck). siRNA transfections were performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) in Opti-MEM medium (Gibco) according to the manufacturer’s instructions.

Techniques: Knockdown, Over Expression, Plasmid Preparation, Expressing, RNA Sequencing, Transformation Assay, Activity Assay, Control, MANN-WHITNEY, Two Tailed Test, Sequencing