Journal: Signal Transduction and Targeted Therapy

Article Title: The noncanonical function of liver-type phosphofructokinase potentiates the efficacy of HDAC inhibitors in cancer

doi: 10.1038/s41392-025-02443-0

Figure Lengend Snippet: PFKL deficiency triggers HDAC inhibitor tolerance in CCA cells. a Drug sensitivity scores (DSS) and areas under the drug-response curve (AUC) of drugs with a DSS score ≥ 10 in the 783C-6 and 1405R3 cell lines. b The cell viability of different CCA cell lines following 72 h of treatment with specified concentrations of romidepsin or panobinostat. c Colony-formation assay of 783C-6, SK-CHA-1, TFK1, HuCCT1, 1405R3, and RBE cells after 10 days of treatment with specified concentrations of romidepsin or panobinostat. d Schematic representation of the genome-wide CRISPR-Cas9 screening process. TFK1 and 783C-6 cells were transduced with a lentiviral genome gRNA library in three independent replicates. gRNA barcodes from the initial time point (T0, day 0) and the subsequent time point (Tu, day 7) were identified via deep sequencing. e Eight common hits were identified through CRISPR screening in TFK1 and 783C-6 cells. f Assessment of cell viability of TFK1 and 783C-6 cells following 72 h of treatment with romidepsin or panobinostat after interference with NFIA, LHCGR, PFKFB1, or PFKL. g Cell viability of TFK1 and 783C-6 cells expressing either a negative control sgRNA (sgNC) or sgRNAs targeting PFKL (sgPFKL-1 and sgPFKL-2) following treatment with specified concentrations of romidepsin or panobinostat for 72 h. h The impact of sgRNAs targeting PFKL was evaluated via a colony-formation assay following treatment with specified concentrations of romidepsin or panobinostat for 10 days. i Enrichment of sgRNAs targeting PFKL in TFK1 and 783C-6 cells. j Cell viability of HuCCT1 cells with vector or PFKL overexpression after 72 h of treatment with the indicated concentrations of romidepsin or panobinostat. k Tumor growth rates over time for TFK1-sgNC or TFK1-sgPFKL xenografts with specified treatments. Top panel: Representative tumor images at the end of the treatment. Bottom panel: Growth curves for each group of TFK1-sgNC and TFK1-sgPFKL xenografts ( n = 5 mice per group, two-way ANOVA). Scale bars, 1 cm. All the statistical data are presented as the means ± SEMs

Article Snippet: DMSO (HY-Y0320), romidepsin (HY-15149), panobinostat (HY-10224), vorinostat (HY-10221), and belinostat (HY-10225) were purchased from MedChemExpress.

Techniques: Inhibitor Tolerance, Colony Assay, Genome Wide, CRISPR, Transduction, Sequencing, Expressing, Negative Control, Plasmid Preparation, Over Expression

Journal: Signal Transduction and Targeted Therapy

Article Title: The noncanonical function of liver-type phosphofructokinase potentiates the efficacy of HDAC inhibitors in cancer

doi: 10.1038/s41392-025-02443-0

Figure Lengend Snippet: PFKL facilitates the pro-transcriptional effects of romidepsin independent of its metabolic functions. a Schematic illustrating the modulation of PFKL enzymatic activity by penfluridol, citrate, FBP and LDC7559 treatments, as well as the inhibition of the glycolytic rate by lonidamine, 2-DG, 3-BP, and shikonin treatments (2-DG, 2-deoxy-D-glucose; 3-BP, bromopyruvic acid). b The cell viability of TFK1 and 783C-6 cells after 72 h of treatment with specified concentrations of romidepsin combined with glycolysis inhibitors and the PFKL enzymatic activity modifier. c Immunoblot analyses of the expression of PFKL in PFKL-depleted TFK1 cells transfected with the GFP, PFKL-WT, PFKL-H199Y, and PFKL-F638R plasmids. d Enzymatic activity of purified wild-type PFKL (PFKL-WT), and PFKL mutants H199Y and F638R ( n = 3 biological replicates, one-way ANOVA). e Cell viability of TFK1-sgPFKL cells treated with specified concentrations of romidepsin for 72 h post-transfection with PFKL-WT, PFKL-H199Y, or PFKL-638R. f Immunoblot analyses of the expression of H3K9ac and H3K27ac in TFK1 cells expressing either a negative control sgRNA (sgNC) or sgRNA targeting PFKL (sgPFKL) following treatment with specified concentrations of romidepsin for different durations ( n = 3 biological replicates, two-way ANOVA). g CUT&Tag combined with RNA-Seq data for bioinformatics analysis via the DAVID database. h GO enrichment analysis of the pathways specifically enriched in PFKL-deficient cells response to romidepsin. i Normalized read densities for H3K9ac and H3K27ac at the Dnajb1 and Arid4a genes. j Histogram showing the GI50 values of romidepsin TFK1-sgNC and TFK1-sgPFKL cells following interference with candidate genes. All the statistical data are presented as the means ± SEMs

Article Snippet: DMSO (HY-Y0320), romidepsin (HY-15149), panobinostat (HY-10224), vorinostat (HY-10221), and belinostat (HY-10225) were purchased from MedChemExpress.

Techniques: Activity Assay, Inhibition, Western Blot, Expressing, Transfection, Purification, Negative Control, RNA Sequencing

Journal: Signal Transduction and Targeted Therapy

Article Title: The noncanonical function of liver-type phosphofructokinase potentiates the efficacy of HDAC inhibitors in cancer

doi: 10.1038/s41392-025-02443-0

Figure Lengend Snippet: The PFKL-552-572-R8 peptide increases the efficacy of romidepsin in vitro and in vivo. a Histogram showing the energy contribution of crucial residues in binary (HDAC1 and reduced-romidepsin) and ternary (HDAC1, reduced-romidepsin, and PFKL) complexes. b Molecular dynamics clustering analysis of binding modes in binary and ternary complexes. HDAC1 is represented by a cyan surface, PFKL is depicted with a green surface, and key residues are displayed as cyan and green sticks, respectively. The HDAC inhibitor romidepsin is shown as wheat-colored sticks, and zinc is represented as a gray sphere. The purple dashed lines denote coordination bonds, and the gray dashed lines indicate hydrophobic interactions. c Line chart showing the distances between the zinc and sulfur atoms of romidepsin in binary and ternary complexes. Binary complexes are represented in red, whereas ternary complexes are depicted in blue. d Cell viability of TFK1-sgPFKL cells treated with specified concentrations of romidepsin for 72 h post-transfection with PFKL-WT, PFKL-∆562, or PFKL-T562A. e Co-IP showing the interactions between Flag-tagged HDAC1 and Myc-tagged full-length or Thr562 mutant PFKL in HEK293T cells. f Schematics of the amino acid sequences of the peptides. g Cell viability of TFK1-sgPFKL and HuCCT1 cells treated with specified concentrations of romidepsin for 72 h combined with normal saline (NS), 552-572-R8, or ∆562-R8. h Molecular dynamics clustering analysis of binding modes in HDAC1-reduced romidepsin-peptide complexes. HDAC1 is shown as a blue-green (cyan) cartoon (cartoon), 552572-R8 and ∆562-R8 are shown as orange (orange) and dark blue-gray (slate) cartoons, respectively. Romidepsin is shown as a wheat (wheat) stick, and zinc ions are shown as a gray (gray) sphere (sphere); the key residues are presented as sticks (stick). The gray dashed line indicates hydrophobic interactions, and the magenta (magenta) dashed line indicates coordination. i Line chart showing the distances between the zinc and sulfur atoms of romidepsin in the two complexes. Complex A is represented in blue, whereas complex B is depicted in red. j Representative tumor images of each group of HuCCT1 xenografts at the end of treatment ( n = 6 mice per group). k Growth curves of each group of HuCCT1 xenografts ( n = 6 mice per group, two-way ANOVA). All the statistical data are presented as the means ± SEMs

Article Snippet: DMSO (HY-Y0320), romidepsin (HY-15149), panobinostat (HY-10224), vorinostat (HY-10221), and belinostat (HY-10225) were purchased from MedChemExpress.

Techniques: In Vitro, In Vivo, Binding Assay, Transfection, Co-Immunoprecipitation Assay, Mutagenesis, Saline

Journal: Signal Transduction and Targeted Therapy

Article Title: The noncanonical function of liver-type phosphofructokinase potentiates the efficacy of HDAC inhibitors in cancer

doi: 10.1038/s41392-025-02443-0

Figure Lengend Snippet: The PFKL-552-572-R8 peptide broadens the application of romidepsin in various solid tumors. a Cell viability of different solid tumor cell lines following treatment with specified concentrations of romidepsin for 72 h. b Colony-formation assay of MCF7, BT-549, NCI-H596, A549, TOV21G, and RMG-1 cells following treatment with specified concentrations of romidepsin for 10 days. c Cell viability of romidepsin-resistant cells following treatment with specified concentrations of romidepsin combined with NS, 552-572-R8, or ∆562-R8 for 72 h. d Colony-formation assay of romidepsin-resistant cells following treatment with specified concentrations of romidepsin combined with normal saline (NS), 552-572-R8, or ∆562-R8 for 10 days. e Representative tumor images of each group of A549 xenografts at the end of treatment ( n = 6 mice per group). f Growth curves of each group of A549 xenografts ( n = 6 mice per group, two-way ANOVA). g Schematic representation of PFKL regulation of epigenetic states and the efficacy of HDAC inhibitors in cancer. All the statistical data are presented as the means ± SEMs. Image created with BioRender.com

Article Snippet: DMSO (HY-Y0320), romidepsin (HY-15149), panobinostat (HY-10224), vorinostat (HY-10221), and belinostat (HY-10225) were purchased from MedChemExpress.

Techniques: Colony Assay, Saline

Journal: Frontiers in Oncology

Article Title: Combination Therapy With Histone Deacetylase Inhibitors (HDACi) for the Treatment of Cancer: Achieving the Full Therapeutic Potential of HDACi

doi: 10.3389/fonc.2018.00092

Figure Lengend Snippet: Classification of histone deacetylases (HDACs) and the histone deacetylase inhibitors (HDACi) that target them.

Article Snippet: FK228 (Romidepsin, IstodaxTM, Celgene Corp., USA), a cyclic peptide was later approved in 2009 for treating CTCL in patients who had received at least one prior systemic therapy ( ).

Techniques: Histone Deacetylase Assay, Cell Function Assay, Control

Journal: Science Advances

Article Title: Temporal regulation of gene expression through integration of p53 dynamics and modifications

doi: 10.1126/sciadv.adp2229

Figure Lengend Snippet: ( A ) Phosphorylations or acetylations at the indicated residues of p53 were monitored by Western blots of total cell lysates (left) or of p53 immunoprecipitates (IP) (right) in the first and second pulses. Loading was normalized for total p53. Modifications indicated in red showed differences in levels between the two pulses. ( B ) Quantification of the Western blot from A, normalized to total p53 levels ( n = 3 biological replicates, error bars indicate SD). ( C ) Western blot of acetylation at lysine-373 (K373-Ac) or lysine-382 (K382-Ac) of p53 at the indicated time points after 10-Gy x-ray irradiation. Actin is shown as a loading control. ( D ) Quantification of time-course Western blot signal from (B), normalized to the maximum level attained for each species over the time course ( n = 3 biological replicates, error bars indicate SD). ( E ) Schematic of experiment showing addition of inhibitor(s) at the trough between p53 peaks (4.5 hours post irradiation). ( F ) Western blot of p53 acetylated at K373, K381, or K382 in the presence or absence of HDACi or SIRTi added at the time point shown in A. Total p53 is shown as a loading control. ( G ) Left: BTG2 mRNA levels following 48-hour knockdown with control or BTG2 short interfering (si)RNA. Right: Western blot of p53 acetylated at K373 or K382 following siRNA silencing of BTG2 (see Materials and Methods) and after the indicated number of hours after irradiation.

Article Snippet: Romidepsin/Depsipeptide (HDACi) (Adooq Bioscience, FK228) and Sirtinol (SIRTi) (Sigma-Aldrich, 566320) were added at 10 nM, and 50 μM, respectively.

Techniques: Western Blot, Irradiation, Control, Knockdown

Journal: Science Advances

Article Title: Temporal regulation of gene expression through integration of p53 dynamics and modifications

doi: 10.1126/sciadv.adp2229

Figure Lengend Snippet: ( A ) qPCR analysis of the mRNA levels of the indicated genes at 8 hours after irradiation treated with or without HDACi, normalized to mRNA levels in unirradiated cells. Error bars represent SD from three biological replicates. * P < 0.05, ** P < 0.01 by t test. ( B ) Schematic of p53 constructs harboring single or double K➔R mutations. ( C ) qPCR analysis of mRNA levels of CDKN1A , PAI1 , PML , and PUMA after the second p53 pulse in cells expressing the indicated p53 variants and treated with or without HDACi. Error bars represent SD from three biological replicates. * P < 0.05, ** P < 0.01 by t test (all conditions compared to WT + HDACi).

Article Snippet: Romidepsin/Depsipeptide (HDACi) (Adooq Bioscience, FK228) and Sirtinol (SIRTi) (Sigma-Aldrich, 566320) were added at 10 nM, and 50 μM, respectively.

Techniques: Irradiation, Construct, Expressing

Journal: Biomolecules & Therapeutics

Article Title: Combinatorial Antitumor Activity of Oxaliplatin with Epigenetic Modifying Agents, 5-Aza-CdR and FK228, in Human Gastric Cancer Cells

doi: 10.4062/biomolther.2018.061

Figure Lengend Snippet: Antiproliferative activity of 5-Aza-CdR, FK228 and oxaliplatin in SNU-638 and SNU-719 human gastric cancer cells

Article Snippet: FK228 (Romidepsin, depsipeptide) and oxaliplatin (Eloxatin TM , LOHP) was kindly provided by Sanofi-Aventis (Malvern, PA, USA).

Techniques: Activity Assay

Journal: Biomolecules & Therapeutics

Article Title: Combinatorial Antitumor Activity of Oxaliplatin with Epigenetic Modifying Agents, 5-Aza-CdR and FK228, in Human Gastric Cancer Cells

doi: 10.4062/biomolther.2018.061

Figure Lengend Snippet: Effects of combined treatment with 5-Aza-CdR and FK228. SNU-638 (A) and SNU-719 cells (B) were treated with single agent of 5-Aza-CdR (0.1 μM) and FK228 (3 nM), or with doublet combination of 5-Aza-CdR/FK228 for 24 h. After removal of drug-containing media, cells were further incubated in drug-free media for an additional 72 h and were then subjected to MTS assay. Data are presented as the survival rate relative to the control, which was assigned a value of “100%”. Data are presented as the mean ± SD from three independent experiments. ** indicates synergistic effects.

Article Snippet: FK228 (Romidepsin, depsipeptide) and oxaliplatin (Eloxatin TM , LOHP) was kindly provided by Sanofi-Aventis (Malvern, PA, USA).

Techniques: Incubation, MTS Assay, Control

Journal: Biomolecules & Therapeutics

Article Title: Combinatorial Antitumor Activity of Oxaliplatin with Epigenetic Modifying Agents, 5-Aza-CdR and FK228, in Human Gastric Cancer Cells

doi: 10.4062/biomolther.2018.061

Figure Lengend Snippet: Zta induction after treatment with 5-Aza-CdR and/or FK228 in SNU-719 cells. Immunofluorescence was used to measure Zta. Representative fluorescence images are shown using anti-Zta primary antibody (1:40) after 24 h and 48 h of drug treatment. Bars, 100 μm. The data are expressed as relative fold change to control, 5-Aza-CdR single treatment. Data are presented as the mean ± SD from three independent experiments. ** indicates synergistic effects.

Article Snippet: FK228 (Romidepsin, depsipeptide) and oxaliplatin (Eloxatin TM , LOHP) was kindly provided by Sanofi-Aventis (Malvern, PA, USA).

Techniques: Immunofluorescence, Fluorescence, Control

Journal: Biomolecules & Therapeutics

Article Title: Combinatorial Antitumor Activity of Oxaliplatin with Epigenetic Modifying Agents, 5-Aza-CdR and FK228, in Human Gastric Cancer Cells

doi: 10.4062/biomolther.2018.061

Figure Lengend Snippet: Pre-treatment with 5-Aza-CdR/FK228 antagonized the anti-proliferative effect of oxaliplatin. Cells were pre-treated with 5-Aza-CdR (0.1 μM)/FK228 (1 nM or 3 nM) for 24 h, washed and then exposed to 1 μM of oxaliplatin for subsequent 72 h (A). Relative rate of proliferation was determined in SNU-638 (B) and SNU-719 (C) cells using the MTS assay. Data are presented as the mean ± SD from three independent experiments. All triplet combinations showed antagonism in both cell lines.

Article Snippet: FK228 (Romidepsin, depsipeptide) and oxaliplatin (Eloxatin TM , LOHP) was kindly provided by Sanofi-Aventis (Malvern, PA, USA).

Techniques: Relative Rate, MTS Assay

Journal: Biomolecules & Therapeutics

Article Title: Combinatorial Antitumor Activity of Oxaliplatin with Epigenetic Modifying Agents, 5-Aza-CdR and FK228, in Human Gastric Cancer Cells

doi: 10.4062/biomolther.2018.061

Figure Lengend Snippet: Combination indexes (CI x ) versus affected fraction (fa) determined for combination of FK228 and oxaliplatin. Cells were treated with FK228/oxaliplatin for 72 h at fixed equitoxic ratios. CI x ≤0.8, CI x ≥1.2, and 0.8

Article Snippet: FK228 (Romidepsin, depsipeptide) and oxaliplatin (Eloxatin TM , LOHP) was kindly provided by Sanofi-Aventis (Malvern, PA, USA).

Techniques:

Journal: Biomolecules & Therapeutics

Article Title: Combinatorial Antitumor Activity of Oxaliplatin with Epigenetic Modifying Agents, 5-Aza-CdR and FK228, in Human Gastric Cancer Cells

doi: 10.4062/biomolther.2018.061

Figure Lengend Snippet: Combination effects of 5-Aza-CdR pre-treatment combined with FK228/oxaliplatin treatment. Cells were treated with 0.25 μM of 5-Aza-CdR for 24 h, and then incubated for 72 h with FK228/oxaliplatin (A). SNU-638 (B) and SNU-719 (C) cells were exposed to drugs at the concentrations indicated. Relative rate of proliferation was determined using the MTS assay. Data are presented as the mean ± SD based on at least three replicate experiments. * indicates additive effects.

Article Snippet: FK228 (Romidepsin, depsipeptide) and oxaliplatin (Eloxatin TM , LOHP) was kindly provided by Sanofi-Aventis (Malvern, PA, USA).

Techniques: Incubation, Relative Rate, MTS Assay

Journal: Experimental & Molecular Medicine

Article Title: Molecular targeted therapy for anticancer treatment

doi: 10.1038/s12276-022-00864-3

Figure Lengend Snippet: Additional targeted therapies that have been clinically used for cancer treatment.

Article Snippet: HDAC , Romidepsin (FK228, FR901228) , Istodax (Celgene Corp./Bristol-Myers Squibb) , CTCL (2009) , PTCL 5 (2011) , P-glycoprotein-mediated drug efflux HDAC alterations Epigenetic alterations Protection of oxidative stress Alterations in apoptosis/autophagy , Thrombocytopenia, anemia, neutropenia, fatigue, nausea, vomiting, anorexia, tumor lysis syndrome , , .

Techniques: Homologous Recombination, Cell Counting, Biomarker Discovery, Over Expression, Lysis, Mutagenesis, Activation Assay