Journal: bioRxiv

Article Title: TET2 loss promotes premalignant survival and clonal selection in MYC-driven B cell lymphoma

doi: 10.64898/2026.03.20.712678

Figure Lengend Snippet: (A) GO-term analysis of RNA-seq data from FACS-sorted IgM + immature-like B cells from the comparison of premalignant EµMyc Tet2 −/− (n=5) versus EµMyc (n=6) mice. DEGs (adjusted p-value<0.05 and absolute log 2 (fold change)>1) were subjected to MSigDB Hallmark 2020 in Enrichr. The bar graph depicts the top enriched pathways ranked by p-value, with the number of DEGs contributing to each term indicated in italics at the end of each bar. (B) Volcano plot comparing transcriptional profiles, with a specific focus on apoptotic/BCL2-family gene panel from the RNA-seq analysis described in (A). Significance was defined as adjusted p-value<0.05 and absolute log 2 (fold change)>0.5. Downregulated genes in EµMyc Tet2 −/− subsets are shown in blue; upregulated genes are shown in red; apoptotic/BCL2-family genes, which are not differentially expressed in dark grey, and all other genes in bright grey. (C) Flow cytometric analysis determining the fraction of BCL2 + cells and MFI within the BCL2 + gate in IgM + immature-like B cells (B220 + CD19 + IgM + IgD − ) ( EµMyc : n=6, EµMyc Tet2 −/− : n=4). (D) MFI of BCL-XL and MFI of MCL1 in IgM + immature-like B cells, quantified by flow cytometry ( EµMyc : n=8, EµMyc Tet2 −/− : n=4). (E) Flow cytometric analysis determining the fraction of BIM hi cells and representative histograms for the BIM staining in the IgM + immature-like B cell compartment ( EµMyc : n=8, EµMyc Tet2 −/− : n=4). (F) Flow cytometric assessment determining the fraction of BCL2 + BIM hi cells and representative dot plots of the BCL2 + BIM hi population in IgM + immature-like B cells ( EµMyc : n=3, EµMyc Tet2 −/− : n=4). (G) Cell survival kinetics assessed in vitro for IgM + immature-like B cells (DAPI + B220 + CD19 + IgM + IgD − ) from EµMyc (n=3) and EµMyc Tet2 −/− (n=3) mice, at 0, 2, 6, and 10 hours of culture. Assessment of mitochondrial apoptotic sensitivity via cytochrome c release of IgM + immature-like B cells (ZombieDye − B220 + CD19 + IgM + IgD − cytochromec − ) treated with (H) 30 µM ABT-199/Venetoclax and (I) 1 µM S63845. For both treatments, cytochrome c release in DMSO controls and treated samples is shown as a line plot (left) and as a bar graph (right), depicting the fold change relative to DMSO ( EµMyc : n=3, EµMyc Tet2 −/− : n=4). Bar plots show median with interquartile range. Statistical significance was assessed using unpaired t-test (A-F, H, I), or two-way ANOVA (G) with Holm-Šidák correction for multiple comparisons. Normality was evaluated using the Shapiro-Wilk test. MFI = mean fluorescence intensity, ns = not significant, *p<0.05, **p<0.005.

Article Snippet: Briefly, 30 μM ABT-199/Venetoclax, (MedChemExpress, HY-15531) 1 μM S63845 (MedChemExpress, HY-100741), 20 μM Alamethicin (MedChemExpress, HY-N6708) and 1% dimethyl sulfoxide (DMSO; Merck, D5879) were diluted to 2X the desired final concentration in 25 μl of 0.002% digitonin (Merck, D141) prepared in MEB buffer (Mannitol Experimental Buffer: 10 mM HEPES (Merck, H0887) pH 7.5, 150 mM mannitol (Merck, M9647), 150 mM KCl, 1 mM EGTA (Merck, E3889), 1 mM EDTA (Merck, ED4S), 0.1% BSA (Sigma-Aldrich, 12659), 5 mM succinate (Merck, S3674)).

Techniques: RNA Sequencing, Comparison, Flow Cytometry, Staining, In Vitro, Fluorescence

Journal: bioRxiv

Article Title: Centrosome architecture and m6A-dependent gating of p53 surveillance after whole-genome doubling

doi: 10.64898/2026.02.25.707964

Figure Lengend Snippet: (A) Representative high-content images of Cal51 mScarlet-MDM2 wild-type (WT) and CEP83 -/- cells treated with DMSO or ZM, and of Cal51 mScarlet-MDM2 WT cells treated with ZM in the presence of increasing concentrations of Emricasan. Nuclear mScarlet fluorescence is displayed as binary labeling: nuclei exceeding a predefined fluorescence threshold are pseudo-colored in yellow, whereas nuclei below threshold are shown in blue. Scale bar: 200 μm. (B) Representative high-content images of Cal51 cells treated with staurosporine (STS), ABT-737 (ABT), or the combined treatment (STS + ABT), in the presence of increasing concentrations of Emricasan. Effector caspase activity was assessed using the CellEvent reporter and is displayed as binary nuclear labeling, with CellEvent-positive nuclei shown in yellow and negative nuclei in blue. Scale bar: 200 μm. (C) Dose-response curves for six caspase inhibitors (Emricasan, QVD, LJ2a, LJ3a, LJ3b, and Belnacasan) measured using two high-content assays performed under distinct treatment conditions. Nuclear mScarlet fluorescence was quantified in Cal51 mScarlet-MDM2 cells treated with ZM, whereas effector caspase activity was quantified in Cal51 cells treated with STS + ABT using the CellEvent reporter. Data represent 3 biological replicates, each with 3 technical replicates (n = 9). (D) Table summarizing IC 50 values for the indicated caspase inhibitors obtained from the two assay conditions shown in (C). ND, not determined. (E) Immunoblot analysis of Cal51 cells treated with ZM or with STS + ABT in the presence of vehicle (DMSO), Emricasan, QVD, or LJ2a (10 μM each).

Article Snippet: The following compounds were used: 2 μM ZM-447439 (MCE®, HY-10128), 1 μM Staurosporine (MCE®, HY-15141), 1 μM ABT-737 (MCE®, HY-50907), 100 nM BI2536 (MCE®, HY-50698), Nutlin-3a (MCE®, HY-10029), 20 μg/Ml Cycloheximide (Thermo Scientific Chemicals, 357420010), 10 μM 3MB-PP1 (Cayman Chemical, 17860), Belnacasan (MCE®, HY-13205), Emricasan (MCE®, HY-10396), Q-VD-OPh (MCE®, HY-12305), 2.5 μM STM2457 (Cayman Chemical, 34280), 2.5 μM ( ) or 10 μM ( ) UZH2 (TargetMol®, T40357), 2.5 μM STC-15 (MCE®, HY-156677), 2.5 μM STM3006 (MCE®, HY-156773), 1 μM NU7441 (Selleckchem, S2638), LJ2a, LJ3a and LJ3b (gift from Dr. Etienne Jacotot, Paris Cité University, Inserm).

Techniques: Fluorescence, Labeling, Activity Assay, Western Blot