Journal: bioRxiv

Article Title: CDK4/6 inhibition induces a DNA damage-independent senescence-associated secretory phenotype driven by delayed activation of NF-κB

doi: 10.1101/2025.08.25.672139

Figure Lengend Snippet: A. Diagram summarizing CDK4/6i (Palbo) vs. doxorubicin (Doxo) mechanisms of cell cycle arrest. B. Experimental design of drug comparison time course. C. Left: Percent nuclei counted that had cellular SABgal+ staining at different timepoints. Number of nuclei counted was > 300 per condition at 10x magnification. Each point represents a field of view, with different shapes indicating biological replicates. Error bars denote standard deviation. Statistical significance was calculated using Dunnett’s test. Right: Representative SABgal staining images at day 3 and day 14 shown at 10x magnification with scale bar = 50 µm. D. Crystal violet staining after clonogenic outgrowth for 10-12 days. 800 cells were seeded per well in a 6-well plate in drug-free media after completion of drug treatment at each timepoint. E. Number of ATRX foci (left) and macroH2A foci (indicative of SAHFs; middle) per nucleus was counted for ∼100 nuclei per timepoint. Representative images are shown at day 14 of each drug treatment at 60x magnification (right). Significance was calculated using Dunnett’s test. The scale bar is 15 µm. F. Number of γH2AX foci (indicative of DNA damage; left) & 53BP1 foci (indicative of DNA repair; middle) per nucleus was counted for ∼100 nuclei per timepoint & categorized in 0-4, 5-10 or >10 foci/nuclei. Representative images are shown at day 14 of each drug treatment at 60x magnification (right). The scale bar is 15 µm.

Article Snippet: Antibody dilutions are as follows: ATRX (Cat# A301-045A, Bethyl, Montgomery, Texas) 1:2000, macroH2A (Cat# sc-377452, Santa Cruz, Dallas, Texas) 1:500, γH2A.X (Cat# 05-636, Millipore, Burlington, Massachusetts) 1:1000, 53BP1 (Cat# ab172580, Abcam) 1:1000, NF-κB p65 (Cat #8242, Cell Signaling Technology) 1:800.

Techniques: Comparison, Staining, Standard Deviation

Journal: Oncology Letters

Article Title: A potential common role of the Jumonji C domain-containing 1A histone demethylase and chromatin remodeler ATRX in promoting colon cancer

doi: 10.3892/ol.2018.9487

Figure Lengend Snippet: Regulation of ATRX by JMJD1A. (A) Relative ATRX mRNA levels in our RNA sequencing analysis. (B) Downregulation of JMJD1A in HCT116 cells leads to reduced ATRX protein levels as determined by western blot analysis. Arrowhead marks full-length ATRX. (C) Correlation of JMJD1A and ATRX mRNA levels across normal and cancerous colorectal tissue (n=237). Data from TCGA (microarray reporters A_23_P258033 and A_24_P128044). Pearson correlation coefficient=0.17; P=0.0087. (D) Likewise, provisional TCGA RNA sequencing data from colorectal adenocarcinomas. Pearson correlation coefficient=0.33; P<0.0001. JMJD1A, Jumonji C domain-containing 1A; ATRX, α-thalassemia/mental retardation syndrome X-linked; TCGA, The Cancer Genome Atlas.

Article Snippet: The following rabbit polyclonal antibodies were utilized: Anti-Actin (A2066; Sigma-Aldrich; Merck KGaA, Darmstadt, Germany); anti-ATRX (NBP1-83077); anti-JMJD1A (NB100-77282; both Novus Biologicals, Littleton, CO, USA); and anti-H3K27me 1 (07–448; Upstate Biotechnology, Lake Placid, NY, USA).

Techniques: RNA Sequencing Assay, Western Blot, Microarray

Journal: Oncology Letters

Article Title: A potential common role of the Jumonji C domain-containing 1A histone demethylase and chromatin remodeler ATRX in promoting colon cancer

doi: 10.3892/ol.2018.9487

Figure Lengend Snippet: Role of JMJD1A at the ATRX gene promoter. (A) Human 293T or (B) HCT116 cells were transfected with an ATRX luciferase reporter construct and JMJD1A (wild-type or H1120A/D1122G catalytic mutant). Resultant relative luciferase activity is depicted. Means with standard deviations are shown (n=4). One-way ANOVA with post hoc Tukey's multiple comparisons test; **P<0.01; ****P<0.0001. (C) Chromatin immunoprecipitation assay with 293T cells transfected with indicated Flag-tagged JMJD1A expression constructs and the ATRX luciferase reporter gene. The left four panels show ethidium bromide-stained agarose gels of amplified DNA promoter fragments after immunoprecipitation with indicated antibodies or input levels of DNA. The right two panels show western blots demonstrating that comparable amounts of wild-type JMJD1A and its H1120A/D1122G mutant were expressed. JMJD1A, Jumonji C domain-containing 1A; ATRX, α-thalassemia/mental retardation syndrome X-linked; ANOVA, analysis of variance.

Article Snippet: The following rabbit polyclonal antibodies were utilized: Anti-Actin (A2066; Sigma-Aldrich; Merck KGaA, Darmstadt, Germany); anti-ATRX (NBP1-83077); anti-JMJD1A (NB100-77282; both Novus Biologicals, Littleton, CO, USA); and anti-H3K27me 1 (07–448; Upstate Biotechnology, Lake Placid, NY, USA).

Techniques: Transfection, Luciferase, Construct, Mutagenesis, Activity Assay, Chromatin Immunoprecipitation, Expressing, Staining, Amplification, Immunoprecipitation, Western Blot

Journal: Cold Spring Harbor Molecular Case Studies

Article Title: Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma

doi: 10.1101/mcs.a002246

Figure Lengend Snippet: Variant information for ATRX and TP53 germline variants, which were present in both cases

Article Snippet: Antibody incubation duration was 60 min with a rabbit polyclonal anti- ATRX antibody (dilution 1:500, HPA0001906, Atlas antibodies) and 28 min with a mouse monoclonal antibody anti-INI-1 (dilution 1:200, Clone: 25/BAF47, 612110, B&D Laboratories), both at 36°C.

Techniques: Variant Assay

Journal: Cold Spring Harbor Molecular Case Studies

Article Title: Whole-exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma

doi: 10.1101/mcs.a002246

Figure Lengend Snippet: Both the mother and the child carried a germline mutation in both TP53 and ATRX genes. ( A ) The sequencing coverage and TP53 allele fraction information in blood and tumor samples as visualized in integrative genomics viewer (IGV). The green color represents the variant allele. Copy-neutral LOH was observed in all the tumor samples. The sequencing coverage range is indicated in square brackets. The exon, transcript base, and amino acid information in the major transcript (NM_000546) are marked above the figure. ( Bottom ) TP53 mutation is located at the DNA-binding domain. ( B ) The sequencing coverage and ATRX allele fraction information in blood and tumor samples as visualized in IGV. The orange color represents the variant allele. Copy-neutral LOH was observed in both AT/RT tumor samples. The exon, transcript base, and amino acid information in the major transcript (NM_000489) are marked above the figure. ( Bottom ) ATRX mutation is located at the SNF2N domain.

Article Snippet: Antibody incubation duration was 60 min with a rabbit polyclonal anti- ATRX antibody (dilution 1:500, HPA0001906, Atlas antibodies) and 28 min with a mouse monoclonal antibody anti-INI-1 (dilution 1:200, Clone: 25/BAF47, 612110, B&D Laboratories), both at 36°C.

Techniques: Mutagenesis, Sequencing, Variant Assay, Binding Assay