Journal: bioRxiv

Article Title: KDM7B-mediated demethylation of RNF113A regulates small cell lung cancer sensitivity to alkylation damage

doi: 10.64898/2026.01.03.697470

Figure Lengend Snippet: A , Immunodetection with indicated antibodies of methylated RNF113A levels after total RNF113A immunoprecipitation from HeLa cells stably expressing HA-RNF113A, either pre-treated with DMSO (Control) or treated with IOX1 inhibitor for 72 hours. KU80 was used as a loading control. B , Representative spectra after MALDI-mass spectrometry analyses of RNF113A in vitro demethylation assays using RNF113A K20me 2 peptide in the absence (left panel) or presence (right panel) of the demethylase KDM7B. C , Representative spectra after ESI-mass spectrometry analyses of KDM7B-mediated demethylation of either RNF113A K20me 2 (left panel), H3K9me 2 (middle panel) and H3K4me 3 K9me 2 (right panel) peptides. D , Quantification of the different states of methylation observed after KDM7B-mediated demethylation of RNF113A K20me 2 , H3K9me 2 and H3K4me 3 K9me 2 . Each condition represents the mean with SEM of three technical replicates.

Article Snippet: Cells were incubated with 10 μM of the pan-demethylase IOX1 (5-carboxy-8-hydroxyquinoline; Cat. No. S7234, Selleck Chemicals) for 48 hours at 37°C prior to protein extraction and immunoblotting.

Techniques: Immunodetection, Methylation, Immunoprecipitation, Stable Transfection, Expressing, Control, Mass Spectrometry, In Vitro

Journal: bioRxiv

Article Title: Deep learning predicts haematopoietic stem cell ageing from 3D chromatin images

doi: 10.64898/2025.12.11.693143

Figure Lengend Snippet: a. Schematic representation of the inference pipeline using ChromAgeNet, where the two different mechanism of actions of the epigenetic drugs are depicted: Inhibitors of Rho GTPase (CASIN and RhoA inhibitor) and modulators of H3K9 methylation (UNC0646 and IOX1). Designed with BioRender. b. Distribution plots showing soft voting-aggregated and calibrated ChromAgeNet scores at nucleus level for young and aged HSC, along with different treatments of aged HSCs. Probability values near 0 reflect more aged-like phenotypes, while values near 1 reflect more young-like phenotypes. c. Heatmap showing normalized values of top selected SHAP features (columns) distributed over images from different young, aged and drug-treated aged HSCs (rows), all acquired by the same microscopist and microscope.

Article Snippet: Where indicated, cells were treated with 100 μ M Rhosin (RhoAi) [ , ], 5 μ M CASIN [ ], 50 μ M IOX1 (8-hydroxyquinoline-5-carboxylic acid), which mimics 2-OG ( α -KG) and blocks the catalytic activity of lysine demethylases (from Tocris Biotechne), 0.25 μ M UNC0646 (Sigma), a well-described selective G9a/GLP methyltransferase inhibitor [ ] or left untreated.

Techniques: Methylation, Microscopy