Journal: NPJ Precision Oncology

Article Title: Venetoclax resistance in preclinical KMT2A-rearranged acute lymphoblastic leukemia models is characterized by high inter- and intra-model heterogeneity

doi: 10.1038/s41698-025-01249-1

Figure Lengend Snippet: A Determination of IC50 concentrations for B-ALL cell lines SEM, RS4;11, REH and NALM-6 using trypan blue staining and subsequent cell counting (proliferation), WST-1 assay (metabolic activity) and annexin V-FITC/propidium iodide staining (apoptosis). Nonlinear fitting of 2-4 individual biological replicates. B Cells were continuously incubated with increasing concentrations of VEN and the metabolic activity was assessed by WST-1 proliferation assay. Dose-response curves of vehicle-incubated cells (gray) and VEN-incubated cells (red) are depicted in joint diagrams. IC50 values were calculated for both settings. NR, not reached.

Article Snippet: Human B—ALL cell lines SEM, RS4;11, REH, and NALM-6 were purchased from DSMZ (Braunschweig, Germany) and maintained at 37 °C and 5% CO 2 in IMDM medium (SEM), Alpha MEM medium (RS4;11) or RPMI medium (REH, NALM-6) supplemented with 10% heat-inactivated fetal calf serum and 100 μg/ml penicillin/streptomycin (all PAN—biotech, Aidenbach, Germany).

Techniques: Staining, Cell Counting, WST-1 Assay, Activity Assay, Incubation, Proliferation Assay

Journal: Nature Communications

Article Title: IKAROS levels are associated with antigen escape in CD19- and CD22-targeted therapies for B-cell malignancies

doi: 10.1038/s41467-025-58868-2

Figure Lengend Snippet: A – C Relative IKAROS and CD19 median levels in B-ALL cell lines (697, NALM6, NALM16, NALM20, REH, RS4;11, SUP-B15) transduced with lentivirus expressing scrambled or short hairpin RNA (shRNA) against IKZF1 ( A ; n from left to right: 20, 20, 8, 25, 25, 12), treated with DMSO or 10 µM lenalidomide ( B ; n = 8), or combining shRNA knockdown with or without lenalidomide treatment ( C , n = 9). Proteins were measured by flow cytometry and normalized to scrambled transduced ( A ), DMSO-treated ( B ), or scrambled transduced and DMSO-treated ( C ) cells. RFI = relative fluorescence intensity. N represents independent biological replicates. D CD19 variance-stabilized transformed (vst) counts in IKAROS WT or KD B-ALL cells. E Accessibility profile of CD19 promoter and gene from one representative IKAROS WT and KD B-ALL cell line pair. Other cell lines and their biological replicates can be found in Supplementary Fig. . F Gene set enrichment analysis (GSEA) results for RNA splicing (GO: 0008380) gene signature in IKAROS WT and KD B-ALL cells. G , H Frequency of intron 10 retention in CD19 mRNA in IKAROS WT or KD B-ALL cells ( G ) or pediatric B-ALL patients treated with 19.BBz CAR T cells , ( n = 11), adult B-ALL patients treated with blinatumomab ( n = 2), and adult LBCL patients treated with 19.28z CAR T cells , ( n = 6) ( H ). I GSEA results for Zheng Cord Blood C6 HSC/MPP gene signature in IKAROS WT and KD B-ALL cells. J Cell type enrichment analysis of genes with differentially accessible promotors in IKAROS WT or IKAROS KD B-ALL cells. K CD22 vst counts in IKAROS WT or KD B-ALL cells. L Relative CD22 median levels in isogenic IKAROS WT or KD B-ALL cells ( n = 7; independent biological replicates). Values were measured by flow cytometry or CyTOF and normalized to IKAROS WT condition. M Paired pre-CART22 and post-CD22 low relapse cohort of leukemic patient samples analyzed by CyTOF. IKAROS median levels in pro-BII-like tumor cells. N represents individual patient samples. Schematic representation of the patient cohort created in BioRender . RNA-seq and ATAC-seq experiments ( D – G , I – K ) were performed in 3 cell lines (NALM6, REH, and SUP-B15) with two biological replicates per cell line. Bar plots in ( A–D ), ( G , H ), and ( K , L ) show mean ± SEM. Boxplots in ( M ) extend from the 25th to the 75th percentiles, with a line in the middle representing the median and whiskers extending from the minimum to the maximum values. Statistical tests used were two-way ANOVA followed by Šidák’s multiple comparisons test ( A – C ); DESeq’s Wald test followed by BH correction ( D ) and ( K ); multivariate analysis of transcript splicing (rMATS) followed by FDR correction ( G ); and two-sided paired t-test ( L ) and ( M ). Not significant (n.s.), P > 0.05.

Article Snippet: 697 (ACC 42), CI (ACC 770), JVM-2 (ACC 12), MHH-CALL4 (ACC 337), NALM16 (ACC 680), NALM20 (ACC 681), and WA-OSEL (ACC 767) were purchased from DSMZ (Braunschweig, Germany).

Techniques: Transduction, Expressing, shRNA, Knockdown, Flow Cytometry, Fluorescence, Transformation Assay, RNA Sequencing