Journal: Scientific Reports

Article Title: Neddylation status determines the therapeutic sensitivity of tyrosine kinase inhibitors in chronic myeloid leukemia

doi: 10.1038/s41598-025-04153-7

Figure Lengend Snippet: Neddylation inhibitor blunted the therapeutic function of BCR::ABL1-targeting TKIs. (A, B) K562 cells were treated with imatinib (0.5 µM), nilotinib (0.1 µM), ponatinib (2.5 nM) ( A ), or asciminib (50 nM) ( B ) in the presence or absence of MLN4924 (25 µM) for 24 h. Cell viability was evaluated by CCK8. ( C ) KU812 cells were treated with imatinib in the presence or absence of MLN4924 for 24 h. Cell viability was evaluated by CCK8. ( D ) K562 cells were treated with the indicated TKIs in the presence or absence of MLN4924 (25 µM) for 24 h, cell counting was performed following Hoechst staining. ( E ) K562 cells were treated with imatinib (0.5 µM) in the presence or absence of MLN4924 (25 µM) for 24 h. Cell apoptosis was evaluated by Annexin V/PI staining. ( F ) K562 cells were treated with imatinib (0.5 µM), nilotinib (0.1 µM), or ponatinib (2.5 nM) in the presence or absence of TAS4464 (1 µM) for 24 h. Cell viability was evaluated by CCK8. ( G ) K562 cells were treated with the indicated TKIs in the presence or absence of TAS4464 (1 µM) for 24 h, cell counting was performed following Hoechst staining. ( H ) UBA3 was silenced in K562 cells, followed by imatinib (0.5 µM) treatment for 24 h, cell viability was evaluated by CCK8. Unpaired, two-tailed Student’s t-test. * p < 0.05; ** p < 0.01; *** p < 0.001.

Article Snippet: K562 cells were treated with 0.5 μM imatinib in the presence or absence of 25 μM MLN4924 for 24 h. Cell apoptosis was evaluated using Annexin V-APC/PI Apoptosis Kit (Elabscience, Wuhan, China) following the manufacturer’s protocol.

Techniques: Cell Counting, Staining, Two Tailed Test

Journal: Scientific Reports

Article Title: Neddylation status determines the therapeutic sensitivity of tyrosine kinase inhibitors in chronic myeloid leukemia

doi: 10.1038/s41598-025-04153-7

Figure Lengend Snippet: Neddylation activator sensitizes the function of imatinib. ( A ) K562 cells were treated with imatinib (0.1 µM) in the presence or absence of VII-31 (80 nM) for 24 h. Cell viability was evaluated by CCK8. (B, C) K562 cells were treated with 10 µM cisplatin (CDDP) ( B ) or 0.5 µM doxorubicin ( C ) in the presence or absence of MLN4924 (25 µM) for 24 h. Cell viability was evaluated by CCK8. Data are presented as mean ± SEM. Unpaired, two-tailed Student’s t-test. * p < 0.05; ** p < 0.01; *** p < 0.001.

Article Snippet: K562 cells were treated with 0.5 μM imatinib in the presence or absence of 25 μM MLN4924 for 24 h. Cell apoptosis was evaluated using Annexin V-APC/PI Apoptosis Kit (Elabscience, Wuhan, China) following the manufacturer’s protocol.

Techniques: Two Tailed Test

Journal: Scientific Reports

Article Title: Neddylation status determines the therapeutic sensitivity of tyrosine kinase inhibitors in chronic myeloid leukemia

doi: 10.1038/s41598-025-04153-7

Figure Lengend Snippet: RNA sequencing analysis of the transcriptomal features in CML cells. (A, B) K562 cells were treated with imatinib (0.5 µM) in the presence or absence of MLN4924 (25 µM) for 12 h, RNA sequencing was performed. PCA analysis ( A ) and sample correlation analysis ( B ) were performed. ( C ) GO analysis of the DEGs between imatinib group and imatinib + MLN4924 group. (D-H) Construction of WGCNA network of all RNA sequencing samples: ( D ) Dendrogram of gene topological matrix branch. ( E ) Dendrogram and correlation heatmap of 10 eigengenes in each module. ( F ) Heatmap of correlations between gene modules and each group of RNA-seq samples. The Pearson correlation coefficient (R) between different gene modules and clinical traits were shown in the heatmap. ( G ) Scatter plot of gene significance for selected groups with module membership (MM) in the most significantly positively correlated module. The brown module showed significant positive correlations with both MLN and IMA + MLN groups. ( H ) GO enrichment analysis of genes in blue, red, turquoise, and brown modules.

Article Snippet: K562 cells were treated with 0.5 μM imatinib in the presence or absence of 25 μM MLN4924 for 24 h. Cell apoptosis was evaluated using Annexin V-APC/PI Apoptosis Kit (Elabscience, Wuhan, China) following the manufacturer’s protocol.

Techniques: RNA Sequencing

Journal: Scientific Reports

Article Title: Neddylation status determines the therapeutic sensitivity of tyrosine kinase inhibitors in chronic myeloid leukemia

doi: 10.1038/s41598-025-04153-7

Figure Lengend Snippet: ABL1 is a novel neddylation substrate. ( A ) The binding of NEDD8 to ABL1 domain was evaluated by co-IP in K562 cells. ( B ) ABL1 structure predicted by an AI large-molecule structure predicting tool ESM-fold. The light-green sites represent K1080, K87, and K756. ( C ) ABL1 structure predicted by AlphaFold3. The orange sites represent K1080, K87, and K756. ( D ) ABL1 structure before and after deneddylation as predicted by ESM-fold. The blue color represents structure after deneddylation of ABL1, the purple color indicates ABL1 bound to a NEDD8 molecule. The pink color represents the NEDD8 molecule. The red site is K1080, the yellow site is K87, the green site is K756. ( E ) ABL1 structure before and after deneddylation as predicted by AlphaFold3. The yellow color indicates ABL1 structure after deneddylation, the pink color represents ABL1 neddylated by one NEDD8 molecule. The purple color represents NEDD8.

Article Snippet: K562 cells were treated with 0.5 μM imatinib in the presence or absence of 25 μM MLN4924 for 24 h. Cell apoptosis was evaluated using Annexin V-APC/PI Apoptosis Kit (Elabscience, Wuhan, China) following the manufacturer’s protocol.

Techniques: Binding Assay, Co-Immunoprecipitation Assay

Journal: Scientific Reports

Article Title: Neddylation status determines the therapeutic sensitivity of tyrosine kinase inhibitors in chronic myeloid leukemia

doi: 10.1038/s41598-025-04153-7

Figure Lengend Snippet: A low neddylation status inhibits the effectiveness of imatinib therapy in murine CML model. (A, B) K562 cells were subcutaneously inoculated into nude mice ( n = 6/group), followed by the administration of imatinib (100 mg/kg), MLN4924 (50 mg/kg), or imatinib plus MLN4924, tumor growth was monitored ( A ), tumor weight was evaluated at the experimental endpoint ( B ). Data are presented as mean ± SEM. Unpaired, two-tailed Student’s t-test. * p < 0.05.

Article Snippet: K562 cells were treated with 0.5 μM imatinib in the presence or absence of 25 μM MLN4924 for 24 h. Cell apoptosis was evaluated using Annexin V-APC/PI Apoptosis Kit (Elabscience, Wuhan, China) following the manufacturer’s protocol.

Techniques: Two Tailed Test

Journal: eLife

Article Title: The acetylase activity of Cdu1 regulates bacterial exit from infected cells by protecting Chlamydia effectors from degradation

doi: 10.7554/eLife.87386

Figure Lengend Snippet:

Article Snippet: Chemical compound, drug , Protein A/G PLUS-Agarose , Santa Cruz Biotechnology , Cat# sc-2203 , Agarose for immunoprecipitations.

Techniques: Sequencing, Transfection, Construct, Transformation Assay, Expressing, Plasmid Preparation, Mutagenesis, FLAG-tag, Ubiquitin Proteomics, Recombinant, Immunoprecipitation, Gene Knockout, Software, Cloning, Cell Analysis