kat2a primary cell based screening assays cell culture ht1080 human fibrosarcoma cell line ht1080  (ATCC)

Journal: Biochemistry and Biophysics Reports

Article Title: Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells

doi: 10.1016/j.bbrep.2026.102528

Figure Lengend Snippet: Landscape of differentially methylated (DM) m 6 A sites after X-ray exposure. HT1080 cells were irradiated with 10 Gy X-rays and sampled at 1 min, 2 min, 10 min, 1 h, and 24 h (n = 3 per timepoint). A – E) Volcano plots of per-site differential methylation. Each dot is a candidate m 6 A site; DM sites (FDR <0.1, Benjamini–Hochberg) are red. 10 Gy: change in m 6 A stoichiometry (treated − control). y-axis: −log10( p value). Statistics from moderated beta-binomial regression on modified vs unmodified read counts derived from m6Anet. F) Number of DM sites detected at each timepoint. G – I) Aggregated counts of DM sites across all timepoints, showing (G) the distribution of DM sites across transcript regions (5′UTR, CDS, 3′UTR), (H) a histogram of the number of transcript isoforms on which each DM site occurs, and (I) a histogram of the number of DM sites per transcript. J – K) Over-representation of DM sites by (J) transcript biotype and (K) local 5-mer sequence context. Enrichment is relative to all tested sites as background, using a hypergeometric test with FDR correction; bars show log2 fold-enrichment and significance (∗∗∗∗p < 1e−4, ∗∗∗p < 1e−3, ∗∗p < 1e−2, ∗p < 0.05). L – M) Temporal clustering of DM sites showing distinct methylation dynamics. Stoichiometry per site was z-scored across timepoints and hierarchically clustered; the two largest clusters are shown (Groups A and B). Points show site-level z-scores; boxes indicate median and interquartile range; cyan and green splines trace the cluster means. N) Gene Ontology summary for genes whose transcripts contain ≥1 DM site. Cell numbers are the number of genes with methylated transcripts per term at each timepoint; colour encodes the row-scaled z-score of those counts. Ontology categories: BP (Biological Process), CC (Cellular Component), MF (Molecular Function). Enrichment tested against all expressed genes.

Article Snippet: HT1080 human cell line was obtained from ATCC (ATCC CCL-121) and maintained in Minimum Essential Medium (MEM) containing 10% FBS (fetal bovine serum) and 1% penicillin/streptomycin, at 37 °C and 5% CO2.

Techniques: Methylation, Irradiation, Control, Modification, Derivative Assay, Sequencing

Journal: Biochemistry and Biophysics Reports

Article Title: Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells

doi: 10.1016/j.bbrep.2026.102528

Figure Lengend Snippet: Overview of m 6 A response to IR in the HT1080 KO cell lines exposed to 10 Gy and sampled at 1 h and 24 h (n = 3 per group). WT shown for comparison purposes. A) to D) Volcano plots at 1 h for WT, and the 3 KOs FTO, METTL3, and YTHDF2 respectively. Each dot is a candidate site; red = DM (FDR <0.1). x-axis: change in stoichiometry (irradiated − matched non-irradiated control within genotype). y-axis: −log10( p value). Statistics from moderated beta-binomial regression on modified vs unmodified read counts derived from m6Anet. E – H) The same sampled at 24 h. I) Heatmap showing the degree of hypermethylation in each of the different genotypes at 1 h and 24 h post-exposure. Colour intensity is the scaled (row-wise z-score) change in stoichiometry with respect to the genotype-matched control condition. Only sites found to have a significantly different methylation response to IR between each of the KOs and the WT shown (significant genotype × treatment interaction, FDR <0.1). J) Boxplots showing the per-replicate change in m 6 A stoichiometry of the site found on transcript UQCR10-201, shown for each genotype and for each timepoint. Control conditions at baseline (dashed horizontal line) added for comparison purposes.

Article Snippet: HT1080 human cell line was obtained from ATCC (ATCC CCL-121) and maintained in Minimum Essential Medium (MEM) containing 10% FBS (fetal bovine serum) and 1% penicillin/streptomycin, at 37 °C and 5% CO2.

Techniques: Comparison, Irradiation, Control, Modification, Derivative Assay, Methylation

Journal: Biochemistry and Biophysics Reports

Article Title: Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells

doi: 10.1016/j.bbrep.2026.102528

Figure Lengend Snippet: Integration of transcriptomic and epitranscriptomic responses to 10 Gy X-ray exposure in HT1080 WT and KO cell lines. A) Bar plot showing the number of differentially up- (red) and down-regulated (blue) genes (DEGs) at each timepoint (1 min – 24 h) for the WT HT1080 cell line, (FDR <0.1). B) Similar to A but for the KO cell line timepoints (1 h and 24 h), WT timepoints also shown for comparison purposes. C) Relationship between Gene Ontology terms enriched in differentially methylated transcripts (p < 1e-3; columns) at any timepoint post-exposure, and differentially expressed transcripts (p < 1e-3; rows) at the 24 h timepoint. Heatmap colour shows the Jaccard index between gene sets of the corresponding Gene Ontology terms. Only terms with at least one Jaccard index greater than 0.25 are shown. D – E) Genes with a significantly different transcriptional response to IR between WT and KO cell lines at 1 h and 24 h respectively. Heatmap colour intensities (and numbers for the 1 h) correspond to the expression log2 fold-change. Genes are hierarchically clustered in 3 and 6 main groups, for 1 h and 24 h respectively. The black lines on the left of each gene indicates which KO cell line has a significantly different response in expression with respect to the WT. The red lines on the left of each gene indicate whether the gene was hypermethylated in the WT at any timepoint after the treatment. Gene Ontology analysis of each of the clusters shown in .

Article Snippet: HT1080 human cell line was obtained from ATCC (ATCC CCL-121) and maintained in Minimum Essential Medium (MEM) containing 10% FBS (fetal bovine serum) and 1% penicillin/streptomycin, at 37 °C and 5% CO2.

Techniques: Comparison, Methylation, Expressing

Journal: Biochemistry and Biophysics Reports

Article Title: Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells

doi: 10.1016/j.bbrep.2026.102528

Figure Lengend Snippet: Effect of 2 Gy X-ray exposure on m 6 A levels in human skin biopsies after 24 h post-exposure (n = 5, each paired with a non-exposed matching-donor sample). A) Volcano plot showing the site-level methylation response at 24 h post-exposure. x-axis is the change in m 6 A methylation (logit scale), y-axis is the significance ( p value, -log10 scale). Statistics obtained using a paired moderated beta-binomial regression model on modified vs unmodified read counts derived from m6Anet. Colour indicates the m 6 A site ranking (lighter = higher rank) which was used for the site-level GSEA analysis. B) Site-level Gene Set Enrichment plot, showing that the m 6 A sites in human skin with increased methylation at 24 h post-exposure are significantly enriched for sites found to be DM in HT1080 following 10 Gy exposure (NES = 1.62, p value = 0.008). x-axis shows the rank of each site in the human skin, y-axis is the running sum statistic, dashed red line denotes the GSEA score; blue ticks mark the positions of the HT1080 DM m 6 A sites in the skin biopsy ranking; the green area denotes the leading-edge (LE) subset (DM m 6 A sites contributing most to the enrichment). C) Heatmap showing the scaled m 6 A stoichiometry (row-wise z-score) before and after X-ray exposure across the 5 donors, for the genes with m 6 A sites found in the LE subset of the site-level GSEA. D) Boxplots showing the m 6 A stoichiometry of the site found on the UQCR10-202 transcript in the 5 donor paired skin biopsies, before and after X-ray exposure.

Article Snippet: HT1080 human cell line was obtained from ATCC (ATCC CCL-121) and maintained in Minimum Essential Medium (MEM) containing 10% FBS (fetal bovine serum) and 1% penicillin/streptomycin, at 37 °C and 5% CO2.

Techniques: Methylation, Modification, Derivative Assay