Journal: eLife

Article Title: FGF2-FGFR1 signaling regulates release of Leukemia-Protective exosomes from bone marrow stromal cells

doi: 10.7554/elife.40033

Figure Lengend Snippet: Figure 1. Extracellular vesicles (ECVs) secreted by HS-5 cells are internalized by MOLM14 and K562 cells and protect from treatment with AC220 or imatinib, respectively. HS-5 conditioned media (CM) was collected and separated by ultracentrifugation at 100,000 g into a supernatant (S100) and pellet (P100) fraction containing ECVs. These fractions were incubated with (A) K562 cells ± 1 mM imatinib, or (B) MOLM14 cells ± 10 nM AC220, and Figure 1 continued on next page

Article Snippet: DOI: https://doi.org/10.7554/eLife.40033 14 of 23 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Genetic reagent (homo sapiens) FGF2-2 GenScript CRISPR/Cas nine guide RNA design Genetic reagent (homo sapiens) FGFR1-1 GenScript CRISPR/Cas nine guide RNA design Genetic reagent (homo sapiens) FGFR1-2 GenScript CRISPR/Cas nine guide RNA design Genetic reagent (mus musculus) pMIG with BCR-ABL and GFP murine retrovirus Cell line (homo sapiens) MOLM14 Dr. Yoshinobu Matsuo RRID:CVCL_7916 Cell line (homo sapiens) K562 American Type Culture Collection RRID:CVCL_0004 Cell line (homo sapiens) HS-5 Dr. Beverly Torok-Storb RRID:CVCL_3720 Cell line (homo sapiens) HS-27 Dr. Beverly Torok-Storb RRID:CVCL_0335 Antibody Mouse monoclonal anti-FGFR1 Cell Signaling 9740 Dilution 1:1000 Antibody Rabbit polyclonal anti-FGF2 Santa Cruz Sc-79 Dilution 1:500 Antibody Rabbit monoclonal anti-CD63 ABCAM ab134045 Dilution 1:1000 Antibody Rabbit polyclonal anti-CD9 Santa Cruz Sc-9148 Dilution 1:200 Antibody Mouse monoclonal anti-tsg-101 Santa Cruz Sc-7964 Dilution 1:200 Antibody Mouse monoclonal anti-actin Millipore MAB1501 Dilution 1:5000 Peptide, recombinant protein FGF2 (human) Peprotech Commercial assay or kit Thermo Scientific lentiviral transfection kit Chemical compound, drug quizartinib (AC220) LC labs Chemical compound, drug imatinib LC labs Chemical compound, drug nilotinib SelleckChem Chemical compound, drug PD173074 SelleckChem Chemical compound, drug BGJ-398 SelleckChem Chemical compound, drug doxycycline Fisher Software, algorithm CellProfiler Cell area

Techniques: Incubation

Journal: eLife

Article Title: FGF2-FGFR1 signaling regulates release of Leukemia-Protective exosomes from bone marrow stromal cells

doi: 10.7554/elife.40033

Figure Lengend Snippet: Figure 7. Fgf2 -/- mice survive significantly longer with TKI therapy in a murine BCR-ABL leukemia model. Fgf2 +/+ bone marrow was removed from donor mice and spinoculated with pMIG BCR-ABL retrovirus containing an IRES-GFP marker. The transfected bone marrow was then transplanted into lethally irradiated Fgf2 +/+ or -/- recipients. Mice were treated with 75 mg/kg/day nilotinib by oral gavage starting on day 11 of transplant. (A) Survival curves of untreated and nilotinib-treated Fgf2 +/+ and -/- mice. (B) GFP in peripheral blood was evaluated weekly and at time of euthanasia to quantify disease burden. The average GFP (percent of nucleated cells) is shown and did not differ significantly between groups indicating that all animals developed similar disease burden. Error bars indicate standard deviation. (C) Bone marrow cells from Fgf2 +/+ mice were spinoculated with pMIG BCR- ABL retrovirus containing GFP-IRES. The cells were then incubated with ECVs obtained from Fgf2 +/+ and -/- primary stroma cultured alone or with 500 nM PD173074. The next day the incubated cells were washed three times to remove cytokines and exosomes and plated in cytokine-free methylcellulose ± imatinib. After 8 days, colonies were counted and normalized to untreated condition. Graph shown on right. Error bars indicate standard error of the mean. *p<0.05 and **p<0.005. (D) Lineage-negative bone marrow cells were isolated from Fgf2 +/+ mice and cells were stained with DiO (green) tracer, washed, and immobilized on Poly-D-lysine coated chamber slides. ECVs from bone marrow stroma of Fgf2 +/+ or -/- mice were stained with DiI (red) tracer and added to the cells for a 24 hr incubation. Slides were stained with DAPI (blue) and imaged by confocal fluorescent microscopy. Movie of the z-stack images are included as Figure 7—video 1 and 2. (E) Model of bone marrow stromal FGF2 autocrine signaling and paracrine protection of leukemia cells by FGF2-containing exosomes. Figure 7 continued on next page

Article Snippet: DOI: https://doi.org/10.7554/eLife.40033 14 of 23 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Genetic reagent (homo sapiens) FGF2-2 GenScript CRISPR/Cas nine guide RNA design Genetic reagent (homo sapiens) FGFR1-1 GenScript CRISPR/Cas nine guide RNA design Genetic reagent (homo sapiens) FGFR1-2 GenScript CRISPR/Cas nine guide RNA design Genetic reagent (mus musculus) pMIG with BCR-ABL and GFP murine retrovirus Cell line (homo sapiens) MOLM14 Dr. Yoshinobu Matsuo RRID:CVCL_7916 Cell line (homo sapiens) K562 American Type Culture Collection RRID:CVCL_0004 Cell line (homo sapiens) HS-5 Dr. Beverly Torok-Storb RRID:CVCL_3720 Cell line (homo sapiens) HS-27 Dr. Beverly Torok-Storb RRID:CVCL_0335 Antibody Mouse monoclonal anti-FGFR1 Cell Signaling 9740 Dilution 1:1000 Antibody Rabbit polyclonal anti-FGF2 Santa Cruz Sc-79 Dilution 1:500 Antibody Rabbit monoclonal anti-CD63 ABCAM ab134045 Dilution 1:1000 Antibody Rabbit polyclonal anti-CD9 Santa Cruz Sc-9148 Dilution 1:200 Antibody Mouse monoclonal anti-tsg-101 Santa Cruz Sc-7964 Dilution 1:200 Antibody Mouse monoclonal anti-actin Millipore MAB1501 Dilution 1:5000 Peptide, recombinant protein FGF2 (human) Peprotech Commercial assay or kit Thermo Scientific lentiviral transfection kit Chemical compound, drug quizartinib (AC220) LC labs Chemical compound, drug imatinib LC labs Chemical compound, drug nilotinib SelleckChem Chemical compound, drug PD173074 SelleckChem Chemical compound, drug BGJ-398 SelleckChem Chemical compound, drug doxycycline Fisher Software, algorithm CellProfiler Cell area

Techniques: Marker, Transfection, Irradiation, Standard Deviation, Incubation, Cell Culture, Isolation, Staining, Microscopy

Journal: Gastric Cancer

Article Title: Targeting yes-associated protein to overcome imatinib resistance in gastrointestinal stromal tumor drug-tolerant persister cells

doi: 10.1007/s10120-025-01657-z

Figure Lengend Snippet: Characterization of imatinib-derived gastrointestinal stromal tumor (GIST) drug-tolerant persister cells (DTPs). A Schematic explanation of DTP generation. B Cell proliferation measured by WST-8 assays at 72 h after imatinib treatment in GIST-T1 parental cells and DTPs. Each value is presented as mean ± SD (n = 6). Two-sided t-test (*** p < 0.001). C Western blot analysis of cKIT, pKIT, YAP and pYAP in nuclear and whole cell lysates of parental cells, DTPs, and regrown cells. D Cell cycle analysis of parental cells and DTPs. E Immunofluorescence staining of YAP/TAZ in parental cells, DTPs, and regrown cells. Scale bar:20 μm

Article Snippet: Cells were treated with imatinib mesylate (Tocris, Bristol, UK), verteporfin (a YAP inhibitor (Selleck chemicals, Houston, TX), or XAV-939 (a tankyrase inhibitor that indirectly suppresses YAP activity; Selleck chemicals, Houston, TX) [ ].

Techniques: Derivative Assay, Western Blot, Cell Cycle Assay, Immunofluorescence, Staining

Journal: Gastric Cancer

Article Title: Targeting yes-associated protein to overcome imatinib resistance in gastrointestinal stromal tumor drug-tolerant persister cells

doi: 10.1007/s10120-025-01657-z

Figure Lengend Snippet: Evaluation of YAP in patient samples A immunohistochemistry (IHC) staining for YAP in GIST patient samples with or without preoperative imatinib treatment. Scale bar:50 μm. B Proportion of YAP-positive tumor cell nuclei in 26 untreated or imatinib-resistant cases and 17 imatinib-responsive cases. Each value is presented as mean ± SEM. Mann–Whitney U test (**p < 0.01)

Article Snippet: Cells were treated with imatinib mesylate (Tocris, Bristol, UK), verteporfin (a YAP inhibitor (Selleck chemicals, Houston, TX), or XAV-939 (a tankyrase inhibitor that indirectly suppresses YAP activity; Selleck chemicals, Houston, TX) [ ].

Techniques: Immunohistochemistry, MANN-WHITNEY

Journal: Gastric Cancer

Article Title: Targeting yes-associated protein to overcome imatinib resistance in gastrointestinal stromal tumor drug-tolerant persister cells

doi: 10.1007/s10120-025-01657-z

Figure Lengend Snippet: Effects of YAP inhibitors on DTPs. A Western blot analysis of YAP and pYAP in nuclear and whole-cell lysates of parental cells, DTPs, and DTPs treated with verteporfin or XAV-939. B Immunofluorescence staining of YAP/TAZ in DTPs treated with verteporfin or XAV-939. Scale bar:20 μm. C Cell proliferation measured by WST-8 assays at 72 h after verteporfin or XAV-939 treatment in parental cells and DTPs. Each value is presented as mean ± SD (n = 6). Two-sided t-test (* p < 0.05, ** p < 0.01, *** p < 0.001). ( D ) Caspase 3/7 assay of the DTPs at 8 h after treatment with DMSO, imatinib, verteporfin or XAV-939, respectively. Each value is presented as mean ± SD (n = 4). Two-sided t-test (* p < 0.05)

Article Snippet: Cells were treated with imatinib mesylate (Tocris, Bristol, UK), verteporfin (a YAP inhibitor (Selleck chemicals, Houston, TX), or XAV-939 (a tankyrase inhibitor that indirectly suppresses YAP activity; Selleck chemicals, Houston, TX) [ ].

Techniques: Western Blot, Immunofluorescence, Staining

Journal: Gastric Cancer

Article Title: Targeting yes-associated protein to overcome imatinib resistance in gastrointestinal stromal tumor drug-tolerant persister cells

doi: 10.1007/s10120-025-01657-z

Figure Lengend Snippet: Effects of combination therapies of imatinib and YAP inhibitors. A Proliferation of cells treated with the following therapies, followed by drug washout: (1) vehicle, (2) verteporfin for 3 d, (3) XAV-939 for 3 d, (4) imatinib for 12 d, (5) imatinib for 9 d followed by a combination of imatinib and verteporfin for 3 d, and (6) imatinib for 9 d followed by a combination of imatinib and XAV-939 for 3 d. Each value is presented as mean ± SD (n = 6). Tukey–Kramer honestly significant difference test (** p < 0.01, *** p < 0.001). B Cell cycle assay of DTPs treated with the indicated therapies and incubated for 8 d after drug washout: (1) imatinib for 3 d, (2) imatinib and verteporfin for 3 d, and (3) imatinib and XAV-939 for 3 d. Each value is presented as mean ± SD (n = 3). Two-sided t-test (*** p < 0.001). C Annexin V-FITC/DAPI apoptosis assay in parental cells and DTPs treated with the indicated therapies for 8 h. Parental cells: (1) vehicle, (2) imatinib, (3) verteporfin, (4) XAV-939. DTPs: (5) vehicle, (6) imatinib, (7) imatinib and verteporfin, and (8) imatinib and XAV-939

Article Snippet: Cells were treated with imatinib mesylate (Tocris, Bristol, UK), verteporfin (a YAP inhibitor (Selleck chemicals, Houston, TX), or XAV-939 (a tankyrase inhibitor that indirectly suppresses YAP activity; Selleck chemicals, Houston, TX) [ ].

Techniques: Cell Cycle Assay, Incubation, Apoptosis Assay

Journal: Gastric Cancer

Article Title: Targeting yes-associated protein to overcome imatinib resistance in gastrointestinal stromal tumor drug-tolerant persister cells

doi: 10.1007/s10120-025-01657-z

Figure Lengend Snippet: Antitumor effects of verteporfin in a GIST xenograft mouse model. A GIST-T1 cells were transplanted subcutaneously and treated with the following therapies: (1) vehicle (n = 4), (2) verteporfin for 3 d (n = 4), (3) imatinib for 12 d (n = 4), and (4) imatinib for 9 d followed by a combination of imatinib and verteporfin for 3 d (n = 4). Treatment was initiated when tumor volume reached approximately 500 mm 3 (day 0). B Body weight and ( C ) tumor volume were measured every day until day 35. Each value is presented as mean ± SD (n = 4). Two-sided t-test (* p < 0.05, ** p < 0.01, *** p < 0.001). D Representative YAP-stained tumor sections from each treatment group. Scale bar: 25 μm. E Proportion of YAP positive nuclei. Each value is presented as mean ± SEM (n = 3), Tukey–Kramer honestly significant difference test (* p < 0.05, ** p < 0.01). F Apoptosis analysis by TUNEL staining from each treatment group. Scale bar: 100 µm

Article Snippet: Cells were treated with imatinib mesylate (Tocris, Bristol, UK), verteporfin (a YAP inhibitor (Selleck chemicals, Houston, TX), or XAV-939 (a tankyrase inhibitor that indirectly suppresses YAP activity; Selleck chemicals, Houston, TX) [ ].

Techniques: Staining, TUNEL Assay

Journal: bioRxiv

Article Title: Functional drug susceptibility testing based on biophysical measurements predicts patient outcome in glioblastoma patient-derived neurosphere models

doi: 10.1101/2020.08.05.238154

Figure Lengend Snippet: (A) Imatinib and ponatinib drug responses observed in Ba/F3 BCR-ABL. For Ba/F3 BCR-ABL, there is a significant reduction in mean cell mass after 8 hours exposure to 1.4 μM imatinib (one-sided Wilcoxon rank-sum p < 10 −3 ) and to 100 nM ponatinib (one-sided Wilcoxon rank-sum p < 10 −3 ). Minimum 2200 cells measured per condition. (B) Imatinib and ponatinib drug responses observed in Ba/F3 BCR-ABL T315I. As expected, for Ba/F3 BCR-ABL T315I, there is only a significant reduction in mean mass after 8 hours exposure to 100 nM ponatinib (one-sided Wilcoxon rank-sum p < 10 −3 ), but not to 1.4 μM imatinib (one-sided Wilcoxon rank-sum p > 0.99). Minimum 2200 cells measured per condition. (C) Ba/F3 BCR-ABL imatinib dose-response curve measured using the SMR mass assay, given as Hellinger distance ± bootstrap standard error. (D) Ba/F3 BCR-ABL T315I imatinib dose-response curve measured using the SMR mass assay, given as Hellinger distance ± bootstrap standard error. (E) Gefitinib and osimertinib drug responses observed in PC9, an EGFR-mutant (Del-E746-A750) lung adenocarcinoma cell line expected to be sensitive to both EGFR inhibitors. For PC9, there is a large reduction in mean cell mass in response to 24 hours exposure to either 1 μM gefitinib (16% reduction, one-sided Wilcoxon rank-sum p < 10 −3 ) or to 100 nM osimertinib (16% reduction; one-sided Wilcoxon rank-sum p < 10 −3 ). Minimum 3000 cells measured per condition. (F) Gefitinib and osimertinib drug responses observed in PC9-GR4, expected to be resistant to gefitinib but not to the second-generation EGFR inhibitor osimertinib. For PC9-GR4, there is only a small reduction in cell mass in response to 24 hours exposure to 1 μM gefitinib (6% reduction, one-sided Wilcoxon rank-sum p < 10 −3 ), but a larger reduction in response to 100 nM osimertinib (34% reduction; one-sided Wilcoxon rank-sum p < 10 −3 ). Minimum 3000 cells measured per condition. (G) Time response for the PC9 cell line after exposure to EGFR inhibitors, given as Hellinger distance ± bootstrap standard error. (H) Time response for the PC9-GR4 cell lines after exposure to EGFR inhibitors, given as Hellinger distance ± bootstrap standard error.

Article Snippet: After 24 hours, cells were dosed with imatinib (Santa Cruz Biotechnology), ponatinib (Santa Cruz Biotechnology), or a vehicle control (0.2% DMSO).

Techniques: Mass Assay, Mutagenesis

Journal: bioRxiv

Article Title: Loss of endothelial ALK1 signaling induces the emergence of a KIT+ angiogenic endothelial cluster driving brain arteriovenous malformations

doi: 10.1101/2025.06.05.657957

Figure Lengend Snippet: A , Experimental timeline of tamoxifen and KIT inhibitor administration in Alk1iECKO and control mice. B, D, F , CD31 immunostaining of the PNVP of P8 Alk1iECKO mice injected with imatinib ( B ), masitinib ( D ), and KIT blocking antibody ( F ), along with their corresponding vehicle controls. C, E, G , Quantification of vessel diameter in the PNVP of P8 Alk1iECKO mice injected with the indicated inhibitor. Each dot represents one mouse. Error bars represent means ± s.e.m, *P<0.05, **P<0.01, ***P<0.001, Mann-Whitney test, Welch’s t test or Unpaired t test (B, D, F) were performed.

Article Snippet: Imatinib Mesylate (100 mg/kg, Selleckchem, S1026), Masitinib Mesylate (100mg/Kg, Cerdalane, E0814), KIT blocking antibody (500 µg, InVivo MAb anti-mouse c-Kit, BioxCell, BE0293-5MG-A) were administered intraperitoneally at P6, 3 hours following tamoxifen injection, and again at P7.

Techniques: Control, Immunostaining, Injection, Blocking Assay, MANN-WHITNEY

Journal: bioRxiv

Article Title: Loss of endothelial ALK1 signaling induces the emergence of a KIT+ angiogenic endothelial cluster driving brain arteriovenous malformations

doi: 10.1101/2025.06.05.657957

Figure Lengend Snippet: A , C , CD31 immunostaining of the PNVP of P8 Alk1l/l mice injected with imatinib (A), and masitinib (C), along with their corresponding vehicle controls. B, D , Quantification of vessel diameter in the PNVP of P8 Alk1l/l mice injected with the indicated inhibitor. Each dot represents one mouse. Error bars represent means ± s.e.m, Mann-Whitney test or Unpaired t test (B, D) were performed. D , Schematic model illustrating how 48 hours of Alk1 deletion induces the emergence of angiogenic 1 ECs in both PNVP and INVP. In the PNVP, angiogenic 1 ECs further differentiate into angiogenic 2 ECs, which drive AVM formation. Both angiogenic populations express KIT, with angiogenic 2 showing stronger expression. Pharmacological inhibition of KIT effectively prevents AVM development in this model. Each dot represents one mouse.

Article Snippet: Imatinib Mesylate (100 mg/kg, Selleckchem, S1026), Masitinib Mesylate (100mg/Kg, Cerdalane, E0814), KIT blocking antibody (500 µg, InVivo MAb anti-mouse c-Kit, BioxCell, BE0293-5MG-A) were administered intraperitoneally at P6, 3 hours following tamoxifen injection, and again at P7.

Techniques: Immunostaining, Injection, MANN-WHITNEY, Expressing, Inhibition