Journal: bioRxiv

Article Title: Fibroblasts neurotrophin signaling sustains pathological vascular maturation in rheumatoid arthritis

doi: 10.64898/2026.03.12.711120

Figure Lengend Snippet: (A) Quantiication of a–smooth muscle actin (aSMA) staining in synovial organoids treated with neurotrophins (NGF, BDNF, NT3).(B) Cell viability assay of entrectinib and larotrectinib across a range of concentrations (0-100 uM). Values are presented as mean, with P values indicated (two-tailed student’s t-test). (C) Representative aSMA staining images of synovial organoids treated with neurotrophin receptor agonists. (D) Quantiication of aSMA staining following treatment with neurotrophin receptor agonists (LM22B-10 and 7,8dihydroxylavone).(E) Representative aSMA staining images of synovial organoids treated with neurotrophin receptor antagonists. (F) Quantiication of aSMA staining following treatment with neurotrophin receptor antagonists (DAPT, GNF5837, GW441756, and ANA-12). Values are presented as mean ± standard deviation (SD). Individual data points represent biological replicates, with P values indicated on the graphs. Statistical analysis was performed using one-way ANOVA for comparisons among multiple groups. Post hoc pairwise comparisons were conducted using t tests with Bonferroni correction to control multiple comparisons.

Article Snippet: Small-molecule inhibitors, including GW-441756 (#2238, Tocris, TrkA inhibitor), ANA12 (#4781, Tocris, TrkB inhibitor), GNF 5837 (#4559, Tocris TrkA/BC inhibitor), Entrectinib (Cat. No.: HY-12678, MedChemExpress) Larotrectinib (Cat. No.: HY-12866, MedChemExpress) were used at concentrations of 1, 5, and 10 μM respectively.

Techniques: Staining, Viability Assay, Two Tailed Test, Standard Deviation, Control

Journal: bioRxiv

Article Title: Fibroblasts neurotrophin signaling sustains pathological vascular maturation in rheumatoid arthritis

doi: 10.64898/2026.03.12.711120

Figure Lengend Snippet: (A) Synovial tissue explant were embedded in Matrigel and treated with the NOTCH inhibitor DAPT. Organoids were fixed and stained for a-smooth muscle actin (aSMA) to visualize mural cells. (B) Spatial transcriptomic (Xenium) analysis of synovial explants treated with DAPT, showing expression of PECAM1 (red), NOTCH3 (green), and (B’) NGF (blue). (C) Representative images of synovial explants treated with entrectinib or larotrectinib, showing aSMA staining to visualize mural cells. Scale bar, 650 µm. (D) RNAscope images showing expression of RGS5 (yellow), ACTA2 (red), and MYH11 (green), overlaid with DAPI (blue), following entrectinib or larotrectinib treatment. For MYH11 staining either serial section or different sections were used. (E) Quantification of aSMA-positive vascular structures per tissue section following entrectinib or larotrectinib treatment. (F) Quantification of integrated aSMA staining density in synovial explants treated with entrectinib or larotrectinib.(G) Quantification of PECAM1-positive vascular structures per tissue section from 20x images following entrectinib or larotrectinib treatment. Scale bar, 150 µm. All images were acquired at 20x magnification and cropped to the same scale. Values are presented as mean ± standard deviation (SD). Individual data points represent biological replicates. Statistical analysis was performed using a two-tailed Student’s t test for comparisons between two groups and one-way ANOVA for comparisons among multiple groups. Post hoc pairwise comparisons were conducted using t tests with Bonferroni correction to control for multiple comparisons.

Article Snippet: Small-molecule inhibitors, including GW-441756 (#2238, Tocris, TrkA inhibitor), ANA12 (#4781, Tocris, TrkB inhibitor), GNF 5837 (#4559, Tocris TrkA/BC inhibitor), Entrectinib (Cat. No.: HY-12678, MedChemExpress) Larotrectinib (Cat. No.: HY-12866, MedChemExpress) were used at concentrations of 1, 5, and 10 μM respectively.

Techniques: Staining, Expressing, RNAscope, Standard Deviation, Two Tailed Test, Control

Journal: bioRxiv

Article Title: Fibroblasts neurotrophin signaling sustains pathological vascular maturation in rheumatoid arthritis

doi: 10.64898/2026.03.12.711120

Figure Lengend Snippet: Pathological synovial vascular maturation in rheumatoid arthritis (RA) is actively sustained despite immunosuppressive therapy and persists independently of clinical remission. Spatial transcriptomic analyses reveal continued expansion of capillary, arteriolar, and mural cell populations, identifying the vasculature as a treatment-resistant disease compartment. Mechanistically, endothelial cells direct mural cell specification through NOTCH3-dependent induction of fibroblast-derived neurotrophin signaling. Pharmacologic inhibition of NOTCH or TRK signaling reduces mural cell activation and vascular density, with FDA-approved TRK inhibitors larotrectinib and entrectinib markedly attenuating pathological vascular maturation in human RA synovial explants. Together, this model identifies a NOTCH3-neurotrophin axis that sustains pathological synovial vascular maturation and represents a therapeutic target in treatment refractory RA.

Article Snippet: Small-molecule inhibitors, including GW-441756 (#2238, Tocris, TrkA inhibitor), ANA12 (#4781, Tocris, TrkB inhibitor), GNF 5837 (#4559, Tocris TrkA/BC inhibitor), Entrectinib (Cat. No.: HY-12678, MedChemExpress) Larotrectinib (Cat. No.: HY-12866, MedChemExpress) were used at concentrations of 1, 5, and 10 μM respectively.

Techniques: Derivative Assay, Inhibition, Activation Assay

Journal: eLife

Article Title: Patient-specific Boolean models of signalling networks guide personalised treatments

doi: 10.7554/eLife.72626

Figure Lengend Snippet: List of selected nodes, their corresponding genes and drugs that were included in the drug analysis of the models tailored for TCGA patients and LNCaP cell line.

Article Snippet: chemical compound, drug , NMS-E973, an Hsp90 inhibitor , MedChemExpress , HY-17547 , .

Techniques:

Journal: eLife

Article Title: Patient-specific Boolean models of signalling networks guide personalised treatments

doi: 10.7554/eLife.72626

Figure Lengend Snippet: ( A ) Real-time cell electronic sensing (RT-CES) cytotoxicity assay of Hsp90 inhibitor, 17-DMAG, that uses the Cell Index as a measurement of the cell growth rate (see the Material and Methods section). The yellow dotted line represents 17-DMAG addition. The brown dotted lines are indicative of the cytotoxicity assay results at 24 hours ( B ), 48 hours ( C ) and 72 hours ( D ) after 17-DMAG addition. ( E ) RT-CES cytotoxicity assay of Hsp90 inhibitor, NMS-E973. The yellow dotted line represents NMS-E973 addition. The brown dotted lines are indicative of the cytotoxicity assay results at 24 hours ( F ), 48 hours ( G ) and 72 hours ( H ) after NMS-E973 addition.

Article Snippet: chemical compound, drug , NMS-E973, an Hsp90 inhibitor , MedChemExpress , HY-17547 , .

Techniques: Cytotoxicity Assay

Journal: eLife

Article Title: Patient-specific Boolean models of signalling networks guide personalised treatments

doi: 10.7554/eLife.72626

Figure Lengend Snippet:

Article Snippet: chemical compound, drug , NMS-E973, an Hsp90 inhibitor , MedChemExpress , HY-17547 , .

Techniques: Software, Mutagenesis

Journal: Cell Reports Medicine

Article Title: Entrectinib inhibits NLRP3 inflammasome and inflammatory diseases by directly targeting NEK7

doi: 10.1016/j.xcrm.2023.101310

Figure Lengend Snippet:

Article Snippet: Entrectinib , TargetMol , Cat#T3678.

Techniques: Recombinant, LDH Cytotoxicity Assay, Enzyme-linked Immunosorbent Assay, Software

Journal: Cancer letters

Article Title: PI3K inhibitor idelalisib enhances the anti-tumor effects of CDK4/6 inhibitor palbociclib via PLK1 in B-cell lymphoma.

doi: 10.1016/j.canlet.2024.216996

Figure Lengend Snippet: Fig. 6. Combination of palbociclib and idelalisib showed potent antitumor effects in vivo. A. Efficacy of combination treatment in vivo. NOD/SCID mice bearing xenografts were treated with vehicle (grey), PAL (10 mg/kg, yellow), IDE (25 mg/kg, blue), or the combination (red) daily by gavage. Tumor growth curve shown change of tumor volumes, which were measured third per week by caliper (mean ± SD, n = 5 for each group, V = (length × width2)/2 mm3), and the waterfall plot shown specific tumor volume in each group at indicated days of treatment. **p < 0.01, compared with control group; ##p < 0.05, ##p < 0.01, compared with single drugs (One-Way ANOVA). B. Representative H&E, Tunel, and IHC analysis of Ki-67 and PLK1 staining images of OCI-Ly8 xenografts. The combination treatment induced more apoptotic cells quantified by TUNEL assay. Nucleus was stained with DAPI (blue), and green points indicate the TUNEL-positive nucleus (second line). Ki-67 and PLK1 positive cells (stained in brown) were decreased in the combination treatment group. Scale bars: 50 μm. C. Statistics data represent of positive cells of Tunel, Ki-67 and PLK1 for each group. Data were presented by mean ± SD. *p < 0.05, **p < 0.01, ***p < 0.001, compared with control group; ##p < 0.05, ###p < 0.001, compared with PAL (One-Way ANOVA). See also Fig. S6.

Article Snippet: Palbociclib (#HY-50767A) and idelalisib (#HY-13026) were purchased from MedChemExpress (MCE, Monmouth Junction, NJ, USA), and PLK1 inhibitor onvansertib (#T6247) were purchased from TopScience (Target Mol, Shanghai, China).

Techniques: In Vivo, Control, TUNEL Assay, Staining

Journal: Molecular Medicine Reports

Article Title: DNA-PKcs PARylation regulates DNA-PK kinase activity in the DNA damage response

doi: 10.3892/mmr.2019.10640

Figure Lengend Snippet: Olaparib treatment promotes the autophosphorylation of DNA-PKcs. (A) The effect of olaparib on the phosphorylation of DNA-PKcs in response to IR. HeLa cells were treated with 10 µM olaparib for 24 h and irradiated with 8 Gy IR. After 1, 2, 4 and 8 h, the expression of phosphorylated DNA-PKcsSer2056 and DNA-PKcsThr2609 was detected by western blotting. (B) HeLa cells were treated with 1 or 10 µM olaparib for 24 h, and the cells were irradiated with 8 Gy IR. After 1 h, the expression of phosphorylated DNA-PKcs/S2056 was detected by western blotting. The effects of olaparib on the formation of γH2AX and DNA-PKcs/S2056 foci were detected by immunofluorescence staining in 8 Gy-irradiated HeLa cells. (C) The dynamic changes in γH2AX foci in 8 Gy-irradiated HeLa cells (magnification ×100). (D) The dynamic changes in γH2AX foci in 8 Gy-irradiated HeLa cells. (E) The dynamic changes in DNA-PKcs/S2056 foci in 8 Gy-irradiated HeLa cells. *P<0.05 and **P<0.01 vs. DMSO treatment. DNA-PKcs, DNA-dependent protein kinase catalytic subunit; IR, irradiation; γH2AX, γ-histone family member 2AX; PARP1, poly(ADP-ribose) polymerase 1.

Article Snippet: The chemical inhibitor olaparib (cat. no. AZD2281), the PARP1 inhibitor UPF1069 (cat. no. S8038), the PARP1 inhibitor NMS-P118 (cat. no. S8363) and DNA-PK inhibitor NU7441 (cat. no. S2638) were purchased from Selleck Chemicals.

Techniques: Phospho-proteomics, Irradiation, Expressing, Western Blot, Immunofluorescence, Staining