Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Annexin V–FITC/propidium iodide (PI) apoptosis assay of SK-Mel-103 cells treated with CX-4945 (40 µM, 24 h) or DMSO. Scatterplots depict four different quadrant: viable cells (Annexin V⁻/PI⁻, Q4), early apoptotic (Annexin V⁺/PI⁻, Q3), late apoptotic/necrotic (Annexin V⁺/PI⁺, Q2), and necrotic (Annexin V⁻/PI⁺, Q1). b, Apoptosis DNA fragmentation analysis in SK-Mel-103 following CX-4945 treatment. c, Immunoblot analysis of caspase-3 cleavage in SK-Mel-103 cells treated with CX-4945 (5–40 µM) or DMSO; actin serves as loading control. d, Subcellular fractionation of SK-Mel-103 cells into cytosolic, nucleosolic and salt-extracted chromatin fractions (100, 250 and 450 mM NaCl), followed by immunoblotting for DEK. e, Immunoprecipitation of endogenous DEK from SK-Mel-103 cells treated with CX-4945 (40 µM, 24 h) or DMSO, followed by immunoblotting with a pan-phosphoserine antibody. f, Re-probing of the immunoprecipitated DEK membrane with a polyclonal anti-DEK antibody (K877). Clean-Blot IP Detection Reagent was used to minimize interference from immunoglobulin heavy and light chains. g, Representative LC–MS/MS spectra of DEK-derived phosphopeptides from SK-Mel-103 cells treated with DMSO or CX-4945. h, Summary of DEK phosphorylation sites identified by LC-MS/MS and schematic of DEK domains (top); site alignment is shown for endogenous DEK from SK-Mel-103 and HeLa S3 cells, and GFP–DEK expressed in HeLa S3 cells (bottom). i, Immunofluorescence of SK-Mel-103 cells after CK2 inhibition (CX-4945, 40 µM, 24 h) stained for DEK (scale bars:10µm).

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Apoptosis Assay, Western Blot, Control, Fractionation, Immunoprecipitation, Membrane, Liquid Chromatography with Mass Spectroscopy, Derivative Assay, Phospho-proteomics, Immunofluorescence, Inhibition, Staining

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Gels of immunoprecipitated DEK or GFP-DEK from HeLa S3 and SK-Mel-103 cells prepared for mass spectrometry analysis. Endogenous DEK or GFP-tagged DEK (GFP-DEK) was immunoprecipitated from HeLa S3 or SK-Mel-103 cells using DEK-specific antibodies or GFP-Trap beads, respectively. ( Left ) IP of endogenous DEK from HeLa S3 cells. ( Middle ) IP of DEK from SK-Mel-103 cells treated with DMSO or the CK2 inhibitor CX-4945. ( Right ) GFP-DEK immunoprecipitated from HeLa S3 cells expressing GFP-tagged DEK using GFP-Trap. All samples were resolved by SDS-PAGE and stained with Coomassie Brilliant Blue. The major DEK or GFP-DEK bands (highlight with red box) were excised for downstream mass spectrometry (MS) analysis to investigate phosphorylation sites. b , Mascot search results of DEK immunoprecipitates. Representative MASCOT search results from LC-MS/MS analysis of DEK protein treated with DMSO and CX-4945 from SK-Mel103, DEK and GFP-DEK from HeLa S3 cells, as well as GFP-DEK 12A mutant from 1E7. c , Phosphorylated DEK peptides detected in the indicated immunoprecipitates are shown, with modified residues and their positions in the DEK sequence annotated (S/T).

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Immunoprecipitation, Mass Spectrometry, Expressing, SDS Page, Staining, Phospho-proteomics, Liquid Chromatography with Mass Spectroscopy, Mutagenesis, Modification, Sequencing

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, DEK ChIP-seq profiling in SK-Mel-103 cells treated with DMSO or CX-4945. Heatmap and principal component analysis (PCA) summarize DEK occupancy across samples (PC1 = 61%, PC2 = 30%). b, Differential DEK binding analysis between CX-4945 and DMSO conditions shown as a volcano plot (log2 fold change versus −log10 FDR); significantly differential regions are highlighted. c, Genomic annotation of CX-4945-specific DEK-bound regions. d, ChIP-qPCR validation of CX-4945–specific DEK occupancy at indicated loci (UFD1, RADIL, FBXL16, CSF3R and CALHM1) using DEK ChIP and IgG control; data are shown as percent input (mean ± s.d., n = 3). e, Association of DEK occupancy with active (H3K27ac) and repressive (H3K9me3) chromatin features. DEK ChIP-seq tags from DMSO- and CX-4945-reated cells were counted within ± 5kb windows centered on H3K27ac or H3K9me3 peak coordinates. f, Representative CX-4945-associated DEK peaks in ChIP-seq tracks (left). RT-qPCR of the corresponding genes showing reduced mRNA levels upon CX-4945 treatment (right; mean ± s.d., n = 3; two-tailed Student’s t-test, P < 0.05, ** P < 0.005).

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: ChIP-sequencing, Binding Assay, ChIP-qPCR, Biomarker Discovery, Control, Quantitative RT-PCR, Two Tailed Test

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Replicate experiment relating to . Subcellular fractionation of SK-Mel-103 cells into cytosolic, nucleosolic and salt-extracted chromatin fractions (100, 250 and 450 mM NaCl), followed by immunoblotting for DEK. b , ChIP-qPCR validation was performed for CX-4945-specific DEK-accessible genes (UFD1, RADIL, FBXL16, CSF3R, and CALHM1) identified in SK-Mel-103 cells. ChIP was conducted in UACC-62 cells using antibodies against DEK and IgG as a negative control. This validation experiment was performed once to assess DEK enrichment at the corresponding loci . c. Representative genome browser tracks showing DEK ChIP – seq signal in HeLa S3 and FM232 cells at the TOP1 locus. d . Bar plot shows the number of DEK ChIP–seq peaks in human mammary epithelial cells (HMEC) and dermal fibroblasts.

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Fractionation, Western Blot, ChIP-qPCR, Biomarker Discovery, Negative Control, ChIP-sequencing

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Confocal imaging of nuclear chromatin morphology (DAPI) in SK-Mel-103 cells and DEK-depleted 1E7 cells following CX-4945 treatment; quantification of DAPI-positive nuclear area is shown (each dot represents one nucleus; n = 43, 50, 59, 60 as indicated; two-tailed Student’s t-test, P < 0.05, ** P < 0.005). Contrast-adjusted grayscale renderings of the DAPI channel are shown to aid visualization of chromatin compaction. Scale bar, 10 μm. b, RT-qPCR analysis of selected transcripts in DEK-depleted 1E7 cells versus controls following CX-4945 treatment (mean ± s.d., n = 3; two-tailed Student’s t-test, P < 0.05, ** P < 0.005). c, MNase digestion time course of nuclei isolated from DMSO-or CX-4945-treated SK-Mel-103 cells; purified DNA was resolved by agarose gel electrophoresis. d, Immunofluorescence staining for DEK in SK-Mel-103 cells following siRNA-mediated DEK knockdown and CX-4945 treatment, with DAPI counterstaining. Scale bar, 10 μm. e, ATAC-seq Metaprofiles centered on DMSO-specific (left) and CX-4945-specific (right) DEK binding sites (±5 kb) with DEK siRNA-mediated knockdown and control f, MNase accessibility assay following CX-4945 treatment in control and DEK knockdown SK-Mel-103 cells; DNA recovered from supernatant and pellet fractions was resolved by agarose gel electrophoresis.

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Imaging, Two Tailed Test, Quantitative RT-PCR, Isolation, Purification, Agarose Gel Electrophoresis, Immunofluorescence, Staining, Knockdown, Binding Assay, Control

Journal: bioRxiv

Article Title: Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

doi: 10.64898/2026.01.19.700267

Figure Lengend Snippet: a, Additional representative confocal images of nuclear chromatin morphology in SK-Mel-103 cells and DEK-depleted 1E7 cells following treatment with DMSO or the CK2 inhibitor CX-4945 (40 μM), corresponding to . Shown are the DAPI channel, a contrast-adjusted grayscale rendering of the DAPI channel (for visualization of chromatin compaction), and DIC images. Scale bar, 10 μm. b, Additional representative immunofluorescence images of DEK staining in SK-Mel-103 cells following siRNA-mediated DEK knockdown and treatment with DMSO or CX-4945 (40 μM), corresponding to . DAPI marks nuclei and DIC images are shown. Scale bar, 10 μm.

Article Snippet: When cells reached approximately 80% confluency, 40 μM CX-4945 (Silmitasertib; MCE) dissolved in DMSO, or an equivalent volume of DMSO as vehicle control, was added to parallel cultures.

Techniques: Immunofluorescence, Staining, Knockdown

Journal: bioRxiv

Article Title: CK2 inhibitor, CX-4945, enhances BH3 priming and promotes apoptosis of venetoclax-resistant AML by targeting antiapoptotic proteins

doi: 10.64898/2025.12.24.696284

Figure Lengend Snippet: A) Overall survival analysis of AML patients with low and high expression of CSNK2A1 (probe ID: 212072_s_at) from TCGA data (AML vs normal; accessed from BloodSplot database at https://www.fobinf.com/ ). B) The plot depicts the median difference (95% confidence interval) of CK2α ( CSNK2A1 ) expression in the presence or absence of mutations in the indicated gene calculated using Mann-Whitney tests. The gene mutations that significantly (p<0.05) associated with increased CSNK2A1 expression were shown along with the sample number for mutated (denoted by M) and wildtype normal (denoted by N) in the BeatAML cohort. C) Volcano plot shows the association of gene mutation with venetoclax activity (accessed from BeatAML database at https://www.vizome.org/aml2/inhibitor/ ). Increased sensitivity is indicated by red, increased resistance indicated by blue as determined by the effect size (X-axis). D) Correlation between CSNK2A1 (CK2α) and BCL2L1 (BCL-XL) gene expression levels from Beat AML patient samples as determined by both Spearman and Pearson correlation coefficients. E) Heatmap summarizing the average log 2 fold change of sgRNA abundance in kinase domain-focused CRISPR screening in AML cell lines (data adapted from ). F) Enrichment of individual sgRNAs for genes encoding CK2 catalytic subunit ( CSNK2A1 ) and regulatory subunit ( CSNK2B ), BCL-XL ( BCL2L1 ), MCL1, and TP53 plotted as log-fold change over control cells following 14 days of treatment with 0.5-1µM VEN in a CRISPR drop-out screening (data adopted from [ , ]). Genes encoding BCL-XL, MCL1, and TP53 were used as known controls that alter VEN activity. Data are presented as Mean ± SEM (n=4-5 sgRNAs targeting each gene). G ) Parental and VR-AML cell lines were treated with different concentrations of venetoclax for 48 h and assessed for cell viability using WST. H) The basal level expression of indicated genes was assessed in different AML cell lines by qRT-PCR. The data are presented as mean ± SEM (n=3 replicates from a representative run). *p<0.05 and **p<0.01 by unpaired t-test (Welch’s correction) denotes statistical significance. I ) Schematic presentation of AML cells profiling with BH3 peptides (activators: BIM, BID; and sensitizer: PUMA) for the assessment of cytochrome c (Cyt C) release. Created with BioRender.com . J) Molm-13 and Molm-13/VR cells were tested for Cyt C release by priming with BH3 peptides and calculated the delta priming. The data are presented as mean ± SD (n=3) and analyzed by two-way ANOVA (Sidak’s multiple comparisons test). *p<0.05, **p<0.01, ***p<0.001, and ****p<0.0001 are considered statistically significant. K) The surface expression of chemoresistance markers (CD47 and CD123) on Molm-13, Molm-13VR, U937, and PDX 2016-7 cells was analyzed using flow cytometry. L ) The basal level expression of CK2α, CK2 substrate phosphorylation, and other BCL2 family members in parental and VR-AML cell lines was analyzed by western blotting.

Article Snippet: CX-4945 (#HY-50855B) and venetoclax (#HY-15531) were purchased from MedChemExpress (Monmouth Junction, NJ, USA).

Techniques: Expressing, MANN-WHITNEY, Mutagenesis, Activity Assay, Gene Expression, CRISPR, Control, Quantitative RT-PCR, Flow Cytometry, Phospho-proteomics, Western Blot