Journal: Cell reports

Article Title: Neuronal hyperactivity becomes mTORC1 independent due to transcriptional changes in tuberous sclerosis complex disease models

doi: 10.1016/j.celrep.2025.116664

Figure Lengend Snippet: (A and B) Plots showing the weighted mean firing rate of hiPSC-derived neurons of the indicated genotypes ( TSC2 +/+ blue; TSC2 +/− purple; TSC2 −/− red) with the designated treatments (DMSO, squares; rapamycin, asterisks) over time. The arrows above the plot represent the start of treatment with either DMSO or rapamycin, which began earlier (A) or later (B) during neuronal development. Points represent mean per condition, and error bars represent SEM. (C and D) Weighted mean firing of the indicated genotypes and treatments at the end of recording with either earlier (C) or later (D) rapamycin treatment. (E and F) Bar plot of burst frequency of the indicated genotypes and treatments at the end of recording with either earlier (E) or later (F) rapamycin treatment. (G) Bar plot of the day when the synchrony index reaches half maximal in the indicated genotypes and treatments with early rapamycin treatment. For all bar plots, each dot represents a separate well of neurons across three separate differentiations. Bar plots show mean ± SEM ( n = 16–20 independent wells per genotype per treatment from three separate differentiations; p < 0.05 ANOVA with post hoc Dunnett’s test).

Article Snippet: DMSO Vehicle control, rapamycin (MedChem Express HY-10219) 0.2nM, 2nM, 20nM were added to the media beginning at either day 10 (Chronic Treatment) or 30 (Acute Treatment).

Techniques: Derivative Assay

Journal: Molecular and cellular biology

Article Title: Loss of function mouse models reveal a novel regulatory function for ULK1 in myeloproliferative neoplasms

doi: 10.1080/10985549.2025.2529837

Figure Lengend Snippet: ( A ) Schematic illustration of the Jak2 V617F knock-in MPN transplant mouse model used, treatment regimen, and analyses performed. ( B ) Hemoglobin (Hb) levels, ( C ) hematocrit (HCT) percentage and ( D ) red blood cell (RBC) counts in peripheral blood of recipient mice are shown for each treatment group four weeks post treatment initiation. ( E ) Percentage of Ter119 med CD71 high proerythroblasts (R1), ( F ) Ter119 high CD71 high basophilic erythroblasts (R2) and ( G ) Ter119 high CD71 med late basophilic and polychromatophilic erythroblasts (R3) and Ter119 high CD71 low orthochromatophilic erythroblasts (R4) in the BM of recipient mice four weeks post treatment initiation. ( H ) Spleen weight and percentage of ( I ) R1, ( J ) R2 and ( K ) R3+R4 cells in the spleen of recipient mice four weeks post treatment initiation. ( B-K ) Box plots show distribution of data from 10 mice per group. Statistical analyses were performed using Mann-Whitney test. Statistically significant p -values are reported. See also supplemental figures 6 and 7 . ( L-M ) Cellular viability of JAK2 V617F -positive ( L ) HEL and ( M ) SET-2 cells treated with either DMSO-vehicle control (Ctrl) or with increasing doses of the ULK1 inhibitor SBP-7455 for five days, as indicated, was measured using WST-1 cell viability reagent. Data are expressed as percent cell viability relative to Ctrl-treated cells and represent means ± SEM of ( L ) four and ( M ) three independent experiments. IC50 values are shown. ( N ) Clonogenic capability of HEL cells treated with either vehicle-control (DMSO) or with increasing doses of the ULK1 inhibitor SBP-7455, as indicated. Data are expressed as percent colony formation relative to DMSO-treated cells (control) and represent means ± SEM of three independent experiments. Statistical analysis was performed using Welch’s ANOVA test that accounts for unequal variances followed by Dunnett’s T3 pairwise multiple comparisons test. Statistically significant p -values are reported. Test for linear trend based on the one-way ANOVA model showed a significant decrease in colony formation with increased dose of ULK1 inhibitor ( p <0.0001). See also supplemental figure 8 .

Article Snippet: To assess the effects of drug-targeted inhibition of ULK1 on cellular viability of JAK2 V617F -positive leukemic cells, SET-2 cells (20,000 cells/well) or HEL cells (1,500 cells/well) were plated in quadruplicate in 96-well plates and treated with vehicle-control (DMSO), ULK101 (TargetMol), SBI-0206965 (Cayman Chemical) or SBP-7455 (TargetMol) at increasing concentrations, for 5 days.

Techniques: Inhibition, Activity Assay, In Vivo, Knock-In, MANN-WHITNEY, Control

Journal: Molecular and cellular biology

Article Title: Loss of function mouse models reveal a novel regulatory function for ULK1 in myeloproliferative neoplasms

doi: 10.1080/10985549.2025.2529837

Figure Lengend Snippet: ( A-B ) Immunoblotting analysis of the indicated proteins in lysates from non-targeting (NT) control, Atg7 KO and Ulk1 KO Jak2 V617F -positive Ba/F3-EpoR + GFP-LC3-RFP-expressing cells. ( C ) Percentage of autophagy measured as percentage of GFP negative cells assessed by flow cytometry analyses of NT control, Atg7 KO and Ulk1 KO Jak2 V617F -positive Ba/F3-EpoR + GFP-LC3-RFP-expressing cells cultured under normal nutrient conditions (RPMI 1640 media supplemented with 10% FBS and 10 ng/mL of IL-3, no starvation) or under starvation conditions (RPMI 1640 media without serum and IL-3) for 48 hours. Scatter dot plot shows means ± SD. Statistical analysis was performed using Welch’s ANOVA test that accounts for unequal variances followed by Dunnett’s T3 pairwise multiple comparisons test. Statistically significant p -values are reported. ( D-F ) Immunoblotting analysis of the indicated proteins in lysates from ( D ) Cas9-control compared to ULK1 KO HEL cells and from ( E ) HEL cells treated with either DMSO-vehicle control (C), 5μM SBP-7455 (S), 100nM bafilomycin A1 (B) or with the combination of SBP-7455 and bafilomycin A1 (S+B) for 4 hours under either nutrient-starvation conditions (HBSS) or normal complete nutrient-conditions (RPMI). Immunoblots shown are representative of three independent experiments. ( F ) SET-2 cells treated with either DMSO-vehicle control (C), 5μM SBP-7455 (S), 100nM bafilomycin A1 (B) or with the combination of SBP-7455 and bafilomycin A1 (S+B) for 4 hours under either nutrient-starvation conditions (HBSS) or normal complete nutrient-conditions (RPMI). Immunoblots shown are representative of three independent experiments.

Article Snippet: To assess the effects of drug-targeted inhibition of ULK1 on cellular viability of JAK2 V617F -positive leukemic cells, SET-2 cells (20,000 cells/well) or HEL cells (1,500 cells/well) were plated in quadruplicate in 96-well plates and treated with vehicle-control (DMSO), ULK101 (TargetMol), SBI-0206965 (Cayman Chemical) or SBP-7455 (TargetMol) at increasing concentrations, for 5 days.

Techniques: Inhibition, Western Blot, Control, Expressing, Flow Cytometry, Cell Culture

Journal: Molecular and cellular biology

Article Title: Loss of function mouse models reveal a novel regulatory function for ULK1 in myeloproliferative neoplasms

doi: 10.1080/10985549.2025.2529837

Figure Lengend Snippet: ( A-B ) HEL cells were treated with either vehicle (DMSO, Ctrl), 5μM SBI-0206965 (SBI) or 5μM ULK101 for 6 hours followed by RNA-seq and analysis of transcript expression. ( A ) Heatmap of differentially expressed genes between treatment groups (adj. p val. < 0.01). ( B ) MA plot of genes significantly changed by drug-targeted inhibition of ULK1 in HEL cells versus control (adj. p val. < 0.01). In purple are represented up-regulated genes and in green are represented down-regulated genes. ( C and D ) Enriched ontology clusters for genes that are ( C ) increased or ( D ) decreased after drug-targeted inhibition of ULK1 in HEL cells. ( A-D ) Data are from 4 biological replicates per condition. See also supplemental figures 9 – 11 .

Article Snippet: To assess the effects of drug-targeted inhibition of ULK1 on cellular viability of JAK2 V617F -positive leukemic cells, SET-2 cells (20,000 cells/well) or HEL cells (1,500 cells/well) were plated in quadruplicate in 96-well plates and treated with vehicle-control (DMSO), ULK101 (TargetMol), SBI-0206965 (Cayman Chemical) or SBP-7455 (TargetMol) at increasing concentrations, for 5 days.

Techniques: Inhibition, Activity Assay, Gene Expression, RNA Sequencing, Expressing, Control

Journal: Molecular and cellular biology

Article Title: Loss of function mouse models reveal a novel regulatory function for ULK1 in myeloproliferative neoplasms

doi: 10.1080/10985549.2025.2529837

Figure Lengend Snippet: ( A-E ) Scatter dot plots of PIM1 , ID2 , HES1 , CTR9 and PDCD2 expression in healthy individuals (normal, n = 11) and patients with ET (n = 47), PV (n = 28) and MF (n = 18). Data extracted from GSE5464672. Shown are means ± SEM of Log2 mRNA expression. Statistical analyses were performed using one-way ANOVA followed by Dunnett’s multiple comparisons adjustment comparing each MPN group vs. Normal group. Statistically significant p -values are reported. ( F-J ) mRNA expression of the indicated genes was assessed by qRT-PCR analysis for HEL cells treated for 6 hours with either vehicle (DMSO, Control) or SBP-7455 (SBP), as indicated. Data are means ± SEM from three independent experiments. Fold changes relative to control (dashed line) were calculated for each experimental replicate (SBP/DSMO), and fold changes were compared to FC=1 using a one-sample t-test, p values are reported. See also supplemental figure 12 .

Article Snippet: To assess the effects of drug-targeted inhibition of ULK1 on cellular viability of JAK2 V617F -positive leukemic cells, SET-2 cells (20,000 cells/well) or HEL cells (1,500 cells/well) were plated in quadruplicate in 96-well plates and treated with vehicle-control (DMSO), ULK101 (TargetMol), SBI-0206965 (Cayman Chemical) or SBP-7455 (TargetMol) at increasing concentrations, for 5 days.

Techniques: Inhibition, Expressing, Quantitative RT-PCR, Control

Journal: Molecular and cellular biology

Article Title: Loss of function mouse models reveal a novel regulatory function for ULK1 in myeloproliferative neoplasms

doi: 10.1080/10985549.2025.2529837

Figure Lengend Snippet: ( A-E ) qRT-PCR analysis of the indicated genes mRNA expression in murine c-kit + bone marrow Jak2 V617F/+ VavCre + cells from 3 mice treated for 6 hours with either vehicle (DMSO, Control) or 5μM SBP-7455 (SBP), as indicated. Data are means ± SD across three different mice. Fold changes were calculated relative to gene expression from one randomly selected vehicle control-treated mouse sample. Statistical analyses were performed using two-tailed unpaired t test with Welch’s correction. Statistically significant p -values are reported. ( F-J ) qRT-PCR analysis of the indicated genes mRNA expression in Cas9-control and ULK1 KO HEL cells, as indicated. Data are means ± SD across three independent experiments. Fold changes were calculated relative to gene expression from one randomly selected Cas9 control sample. Statistical analyses were performed using two-tailed unpaired t test with Welch’s correction. Statistically significant p -values are reported. See also supplemental figures 13 – 15 .

Article Snippet: To assess the effects of drug-targeted inhibition of ULK1 on cellular viability of JAK2 V617F -positive leukemic cells, SET-2 cells (20,000 cells/well) or HEL cells (1,500 cells/well) were plated in quadruplicate in 96-well plates and treated with vehicle-control (DMSO), ULK101 (TargetMol), SBI-0206965 (Cayman Chemical) or SBP-7455 (TargetMol) at increasing concentrations, for 5 days.

Techniques: Inhibition, Quantitative RT-PCR, Expressing, Control, Gene Expression, Two Tailed Test