Context of the study: Head and neck squamous cell carcinoma (HNSCC) is among the most common cancers worldwide, and the prognosis of patients with advanced disease remains poor. Histone lysine demethylases of the Jumonji C family (KDMs) regulate gene expression through the removal of methyl marks from histone lysines and contribute to tumour growth, cancer stemness and chemoresistance. This dataset contains the experimental data of a study that evaluated three small-molecule KDM inhibitors – GSK-J4 (KDM6), ML324 (KDM4) and JIB-04 (KDM4–6) – in HNSCC cell lines. The study asked whether these inhibitors reduce cancer cell viability in monolayer (2D) and spheroid (3D) cultures, whether they affect the expression of stemness-related genes and proteins, and whether pre-treatment with a KDM inhibitor (epigenetic priming) or simultaneous co-treatment increases the response to cisplatin. The results are published in: Dorna D., Kleszcz R., Krajka-Kuźniak V., Paluszczak J. "The Inhibition of Histone Lysine Demethylases Affects Head and Neck Cancer Cell Growth and Response to Cisplatin", Genes 2026, 17, 1047, https://doi.org/10.3390/genes17091047.
Methodology: The HPV-negative cell lines FaDu, Detroit-562 and UM-SCC-1 and the HPV-positive cell line SCC-152 were used. Monolayer cultures were grown in high-glucose DMEM with 5% fetal bovine serum; spheroids were formed in ultra-low attachment U-bottom 96-well plates in DMEM supplemented with 2% B27 and 1% N2. Cell viability was measured with the resazurin assay. Four experimental designs were used: (i) single-agent dose response to each KDM inhibitor and to cisplatin (72 h), from which IC25 and IC50 values were derived; (ii) pre-treatment with a KDM inhibitor at its IC25 followed by cisplatin; (iii) simultaneous co-treatment with a KDM inhibitor and cisplatin at half, one and two times their IC25 (spheroids); and (iv) treatment of cells that survived four consecutive doses of cisplatin with KDM inhibitors in 2D and 3D models. For every plate, the blank signal was subtracted, technical replicates were averaged and the result was normalised to the vehicle (DMSO) control of the same plate; biological replicates were then averaged. In Detroit-562 cells treated for 72 h with the inhibitors at their IC25, the transcript levels of ABCG2, ALDH1A1, NANOG, POU5F1 and SOX2 were measured by RT-qPCR (reference genes TBP and PBGD), and the levels of 15 pluripotency-associated proteins were measured with the Proteome Profiler Human Pluripotent Stem Cell Array Kit (Bio-Techne), chemiluminescence imaging on a Bio-Rad ChemiDoc system and densitometry in Image Lab Sofware. Treated groups were compared with the control using Student's t-test; single compounds and their combinations were compared by one-way ANOVA with Tukey's post hoc test (p < 0.05).
Content and structure of the dataset: The dataset consists of five parts, each corresponding to one experimental approach: 1_gene_expression_qPCR (Figure 3A), 2_antibody_array (Figures 3B–3C), 3_viability_2D_cultures (Figures 4, 5 and 9B), 4_viability_3D_spheroids (Figures 6–8 and 9C) and 5_spheroid_medium_optimisation_qPCR (Supplementary Figure S2). Within each part the data are organised in three levels: raw_data contains the unmodified instrument output (microplate-reader exports, qPCR run files, raw densitometry and antibody-array membrane images); processed_data contains the calculations for each plate or biological experiment (blank correction, averaging of technical replicates, normalisation to the control, relative expression); analysis contains the aggregation of biological replicates, statistical tests, curve fits and the values plotted in each figure panel as plain-text CSV tables. In parts 3 and 4 the files are further grouped by experiment (single-agent dose response, pre-treatment, co-treatment, cisplatin-persister cells). All spreadsheets contain a single worksheet and retain their formulas. File names state the date of measurement, cell line, biological replicate and plate where applicable. A README.txt file at the top level describes the dataset as a whole and maps every figure panel to its source-data file; a README.txt in each part gives the experimental design, plate layouts, concentrations, calculation steps and a description of every file type and table column.
