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: PLoS ONE

Article Title: Expression and Functions of Immediate Early Response Gene X-1 (IEX-1) in Rheumatoid Arthritis Synovial Fibroblasts

doi: 10.1371/journal.pone.0164350

Figure Lengend Snippet: RA-SFs were stimulated with the HDAC inhibitors TSA (HDACs1-10), CI994 (HDAC1), romidepsin (HDAC1, 2), RGFP966 (HDAC3), tubastatin (HDAC6), or PCI-34051 (HDAC8) for 24 h at the indicated doses, and the IEX-1 expression was measured by quantitative RT-PCR. The means ± SD are shown from 4 experiments from different patients. ANOVA was applied and followed by Tukey Method; *P<0.05, **P<0.01.

Article Snippet: TSA was purchased from Sigma-Aldrich (St Louis, MO, USA), CI994 from Biovision (Milpitas, CA, USA), romidepsin (FK228) and RGFP966 from BPS Bioscience (San Diego, CA, USA), tubastatin from Focus Biomolecules (Plymouth Meeting, PA, USA), and PCI-34051 from Santa Cruz Biotechnology, Inc. (Dallas, Texas, USA).

Techniques: Expressing, Quantitative RT-PCR