ddb2  (Proteintech)

Journal: Frontiers in Cell and Developmental Biology

Article Title: New insights into keloid pathogenesis: biomarker potential for CDK7 and DDB2

doi: 10.3389/fcell.2025.1718189

Figure Lengend Snippet: Identification and GSEA of hub genes. (A) Venn diagram with two colors representing distinct data sources. (B) PPI network of hub genes, with crimson nodes indicating hub genes. (C) Bubble plot of GO pathway enrichment analysis for the 41 DEGs. (D) Chord diagram of KEGG pathway enrichment analysis for the 41 DEGs. (E) Box plot of CDK7 expression levels. (F) Box plot of DDB2 expression levels. (G) GSEA for hub gene CDK7. (H) GSEA for hub gene DDB2.

Article Snippet: Antibodies were sourced as follows: CDK7 (67889-1-Ig, 1:1000, Proteintech Group), DDB2 (10431-1-AP, 1:1000, Proteintech Group), and β-Actin (TDYO51, 1:5000, TDY BIOTECH).

Techniques: Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: New insights into keloid pathogenesis: biomarker potential for CDK7 and DDB2

doi: 10.3389/fcell.2025.1718189

Figure Lengend Snippet: Interactive network analysis. (A) DDB2–miRNA and CDK7–miRNA networks. (B) DDB2–transcription factor and CDK7–transcription factor networks. (C) CDK7–drug interaction network.

Article Snippet: Antibodies were sourced as follows: CDK7 (67889-1-Ig, 1:1000, Proteintech Group), DDB2 (10431-1-AP, 1:1000, Proteintech Group), and β-Actin (TDYO51, 1:5000, TDY BIOTECH).

Techniques:

Journal: Frontiers in Cell and Developmental Biology

Article Title: New insights into keloid pathogenesis: biomarker potential for CDK7 and DDB2

doi: 10.3389/fcell.2025.1718189

Figure Lengend Snippet: The result of the basic experiment of CDK7 and DDB2. (A,B) The plots showed the results of qRT-PCR. (C–E) The result of the expression levels of CDK7 and DDB2 proteins in normal skin and keloid. (F,G) The result of the total expression levels of CDK7 and DDB2 proteins in normal skin and keloid. (H,I) Observation of intracellular localization and expression patterns of CDK7 and DDB2 proteins in normal skin and keloid.The results are presented as mean ± SD. **, ***, **** respectively represent P values of t-test < 0.01, < 0.001, < 0.0001.

Article Snippet: Antibodies were sourced as follows: CDK7 (67889-1-Ig, 1:1000, Proteintech Group), DDB2 (10431-1-AP, 1:1000, Proteintech Group), and β-Actin (TDYO51, 1:5000, TDY BIOTECH).

Techniques: Quantitative RT-PCR, Expressing

Journal: bioRxiv

Article Title: The NAT10 acetyltransferase modulates DNA damage-related factors and global 3D-genome architecture

doi: 10.1101/2025.03.05.641614

Figure Lengend Snippet: Data from AlphaFold 3, predicting (A) NAT10 dimerization and the degree of interaction between (B) NAT10-DDB2, (C) NAT10-p53, and (D) DDB2-p53, were imported to ChimeraX 1.9 software showing individual proteins. NAT10 is highlighted by orange, DDB2 is green, p53 is blue colour. The source data are shown at https://www.ibp.cz/en/research/departments/cellular-biology-and-epigenetics/open-data . This raw data from AlphaFold 3 can be uploaded to ChimeraX 1.9 for more detailed analysis.

Article Snippet: Following this, the membranes were blocked with 5% non-fat dry milk for 2 hours and were incubated overnight at 4 °C with specific primary antibodies: anti-NAT10 (#sc-271770, Santa Cruz Biotechnology Inc., USA), anti-p53 (#sc-126), anti-XPC (#sc-30156); anti-XPA (#sc-28353), anti-DDB2 (#sc-25368), and anti-GAPDH (#60004-1, Proteintech, Germany).

Techniques: Software

Journal: bioRxiv

Article Title: The NAT10 acetyltransferase modulates DNA damage-related factors and global 3D-genome architecture

doi: 10.1101/2025.03.05.641614

Figure Lengend Snippet: (A) The following proteins were studied in non-irradiated and UVC-irradiated NAT10 wt and dn cells: NAT10, p53, XPA, XPC, and DDB2. In detail, panel (A) shows western blot analysis of proteins NAT10, p53, XPA, XPC, and DDB2 in non-irradiated and UVC-irradiated cells without and with a depletion of the NAT10 acetyltransferase. Data revealed lower p53, XPA, XPC, and DDB2 protein levels in NAT10 dn cells, with further reductions of XPA, XPC, and DDB2 protein levels upon UVC exposure. UVC irradiation also decreased the pool of p53, XPA, and XPC in NAT10 wt cells. Panels (B-D) show the quantification of western blot data from panel (A) using ImageJ software (NIH freeware, USA). Non-irradiated cells and cells irradiated by UVC light were analyzed. (E) TP53 deficiency led to a decrease in the pool of NAT10 and DDB2 proteins. Panel (F) shows the quantification of western blot data from panel (E) using ImageJ software (NIH freeware, USA). The protein levels were normalized to GAPDH (reference and loading control). The asterisks in panels B-D and F represent statistically significant differences with either a p-value ≤ 0.05 (*) or a p-value ≤ 0.001 (***). AlphaFold 3 models of ( G) NAT10 interaction with p53 (pTM = 0.53), ( H ) NAT10 and DDB2 (pTM = 0.5), and ( I ) DDB2 and p53 protein (pTM = 0.47). Structures are colored with AlphaFold 3 pLDDT confidence score.

Article Snippet: Following this, the membranes were blocked with 5% non-fat dry milk for 2 hours and were incubated overnight at 4 °C with specific primary antibodies: anti-NAT10 (#sc-271770, Santa Cruz Biotechnology Inc., USA), anti-p53 (#sc-126), anti-XPC (#sc-30156); anti-XPA (#sc-28353), anti-DDB2 (#sc-25368), and anti-GAPDH (#60004-1, Proteintech, Germany).

Techniques: Irradiation, Western Blot, Software, Control

Journal: bioRxiv

Article Title: The NAT10 acetyltransferase modulates DNA damage-related factors and global 3D-genome architecture

doi: 10.1101/2025.03.05.641614

Figure Lengend Snippet: Panels (A, B) show AlphaFold 3 multimer prediction of human NAT10 interaction with (A) NAT10 and p53 and DDB2 proteins (pTM = 0.48) or (B) NAT10 and p53 and DDB1-DDB2 protein complex complex (pTM = 0.53).

Article Snippet: Following this, the membranes were blocked with 5% non-fat dry milk for 2 hours and were incubated overnight at 4 °C with specific primary antibodies: anti-NAT10 (#sc-271770, Santa Cruz Biotechnology Inc., USA), anti-p53 (#sc-126), anti-XPC (#sc-30156); anti-XPA (#sc-28353), anti-DDB2 (#sc-25368), and anti-GAPDH (#60004-1, Proteintech, Germany).

Techniques:

Journal: bioRxiv

Article Title: The NAT10 acetyltransferase modulates DNA damage-related factors and global 3D-genome architecture

doi: 10.1101/2025.03.05.641614

Figure Lengend Snippet: Interaction properties between p53-DDB2 and NAT10-DDB2 in human NAT10 wt and NAT10 dn cells were studied using PLA. (A) The panel shows an example of PLA methodology, adapted from BioRender software. In (B) NAT10 wt and (C) NAT10 dn cells, after fixation, the PLA was performed using antibodies to detect the p53-DDB2 or NAT10-DDB2 complexes in both non-irradiated and UVC-irradiated NAT10 wt and NAT10 dn cells. Red dots indicate amplified interaction signals, with cell nuclei counterstained with DAPI, used for visualization of DNA content. NAT10-DDB2 in NAT10 dn acted as a control, showing no external impact on PLA outcomes. This section quantifies PLA signals (dots per nucleus) for (D) the p53-DDB2 complex in non-irradiated and UVC-irradiated NAT10 wt cells, (E) p53-DDB2 in non-irradiated and UVC-irradiated NAT10 dn cells. (F) The UVC irradiation significantly increased NAT10-DDB2 PLA signals in NAT10 wt cells, suggesting enhanced interaction. Non-irradiated cells and cells irradiated by UVC light were analyzed. We used ImageJ software (NIH freeware, USA) to analyze the number of PLA signals. The statistical analysis was performed using GraphPad Prism 9 software (USA) and the nonparametric Mann-Whitney U -test. The asterisk in panel F represents statistically significant differences with a p-value ≤ 0.05 (*).

Article Snippet: Following this, the membranes were blocked with 5% non-fat dry milk for 2 hours and were incubated overnight at 4 °C with specific primary antibodies: anti-NAT10 (#sc-271770, Santa Cruz Biotechnology Inc., USA), anti-p53 (#sc-126), anti-XPC (#sc-30156); anti-XPA (#sc-28353), anti-DDB2 (#sc-25368), and anti-GAPDH (#60004-1, Proteintech, Germany).

Techniques: Software, Irradiation, Amplification, Control, MANN-WHITNEY

Journal: bioRxiv

Article Title: The NAT10 acetyltransferase modulates DNA damage-related factors and global 3D-genome architecture

doi: 10.1101/2025.03.05.641614

Figure Lengend Snippet: (A, B) Animation documents chromatin density inside the cell nucleus (see graphical illustration created by BioRender software). Panel (A) shows cell nucleolus (Nu) and nuclear lamina in dark blue, and panel (B) shows localization of heterochromatin (green) decorating the periphery of cell nucleus and nucleolus, while euchromatin (pale blue) is shown as de-condensed treads inside the cell nucleus. An analysis of the DDB2 nuclear distribution pattern was done using immunohistochemistry in (C) NAT10 wt and NAT10 dn cells. (D) The NAT10 protein (red) was accumulated into tiny, well-visible foci in DAPI-dense (considered as heterochromatin), DAPI-poor (euchromatin, more decondensed) genomic region as well as inside compartment of nucleoli. Panel (E) shows representative images of the DDB2 protein recruitment to UVA-microirradiated chromatin in NAT10 wt and NAT10 dn cells. Microirradiation using a 405 nm laser line was performed, followed by immunofluorescent staining for DDB2 and DNA damage marker γH2A.X. DAPI was used for nuclear counterstaining in blue fluorescence. The scale bar represents 7.5 μm.

Article Snippet: Following this, the membranes were blocked with 5% non-fat dry milk for 2 hours and were incubated overnight at 4 °C with specific primary antibodies: anti-NAT10 (#sc-271770, Santa Cruz Biotechnology Inc., USA), anti-p53 (#sc-126), anti-XPC (#sc-30156); anti-XPA (#sc-28353), anti-DDB2 (#sc-25368), and anti-GAPDH (#60004-1, Proteintech, Germany).

Techniques: Software, Immunohistochemistry, Staining, Marker, Fluorescence

Journal: Scientific reports

Article Title: Validation of a blood biomarker panel for machine learning-based radiation biodosimetry in juvenile and adult C57BL/6 mice.

doi: 10.1038/s41598-024-74953-w

Figure Lengend Snippet: Fig. 1. Intracellular protein biomarker panel MFI in peripheral blood samples 1, 4, and 7, days post 0–4 Gy X-irradiation. Data represent ACTN1, DDB2, and FDXR MFI values in all adult and juvenile mice. Data were natural log (ln) transformed (Y = ln(Y)). Bars represent the ln-transformed mean MFI of each group. Two-way ANOVA were performed to analyze the effect of Day and Dose on biomarker levels in all leukocytes, B-cell and T-cell populations; complete results can be found in Supplementary Table S2. n = 15–18 at each Dose per Day.

Article Snippet: Each of the triplicate samples were then stained intracellularly with one of the following antibodies: FDXR (1:100; Sigma, #HPA044393), ACTN1 (1:100; Cell Signaling Technology, #3134s), or DDB2-FITC (1:100; Cusabio, #CSB-PA846067LC01HU).

Techniques: Biomarker Discovery, Irradiation, Transformation Assay

Journal: Journal of hazardous materials

Article Title: Incense-burning smoke ingredient Auramine enhances lincRNA-p21 expression for chemosensitization in p53-mutated non-small cell lung cancer.

doi: 10.1016/j.jhazmat.2024.135105

Figure Lengend Snippet: Fig. 6. Downregulation of DDB2 is involved in auramine-enhanced apoptosis. (A) Annotation of cell types from 3 datasets of single-cell gene expression profiles in (B). (B) The distribution of TP53 (upper) and DDB2 (bottom) gene expression locus in the single-cell gene expression map. (C) The quantitative results from Fig. 6B. (D) The expression of DDB2 induced by auramine in a dose-dependent manner for 48 h was analyzed by qRT-PCR. (E) The protein level of DDB2 in auramine-treated cells transfected with siRNA against lincRNA-p21 was determined in Western blot analysis. (F, G) Wtp53 A-549 and mutp53 CL1–0 cancer cells were treated with carboplatin (50 μM) combined with auramine (10 μM) for 48 h, and the cell lysates were collected (F) or separated into chromatin-bound and chromatin-free groups by triton extraction assay (G) for Western blot analysis. (H) The cell viability of CL1–0 cancer cells with indicated treatment following the infection with viral shRNA against DDB2 was determined in MTT assays. Data represent at least three experiments and are shown as mean ± SD. *p < 0.05; **p < 0.01; ***p < 0.001 versus control group, Student’s t-test.

Article Snippet: Antibodies against p53 (sc-126, RRID: AB_628082), DDB2 (sc-81246, RRID: AB_2261381), DDB1 (sc-25367, RRID: AB_639050), and XPC (sc74410, RRID: AB_1131407) were purchased from Santa Cruz Biotechnology, Inc., (CA, USA).

Techniques: Gene Expression, Expressing, Quantitative RT-PCR, Transfection, Western Blot, Extraction, Infection, shRNA, Control