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Image Search Results
Journal: Cancer cell
Article Title: Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation
doi: 10.1016/j.ccell.2025.03.027
Figure Lengend Snippet: (A) Signal tracks of total RNA-seq in TKO GEMM and ENCODE mouse midbrain H3K4me3 ChIP-seq. Mouse transcript Rmst -207 (ENSMUST000000218678.3, GENCODE vM32) is shown. Curved lines above the TKO signal tracks indicate backsplicings with the thickest line indicating the most abundant isoform. Conservation score calculated by phyloP in 35 vertebrates is downloaded from UCSC genome browser. Human RMST -211 transcript is shown in reverse orientation. Red exons indicate the exons involved in circularization. Vertical gray lines represent short and long repetitive elements annotated in the human upstream intron. Red arrows represent MIRb elements. Schematic of CRISPR-dual guide designs to delete MIRbs is shown. (B) FPKM of circRmst isoforms identified in 4 SKO, 5 DKO and 4 TKO tumors. Wilcoxon rank-sum test. (C) Heatmap of 691 differential circRNAs (FDR <0.05) between 4 SKO and 4 TKO tumors calculated by the Wilcoxon rank-sum test. Color key indicates row Z score for each circRNA. (D) DNA gel electrophoresis of genomic PCR confirming the human downstream MIRb deletion with guide set 2 in SHP77 single cell clones. WT, wild type. HOM, homozygous. Del, deletion. (E) circRMST expression by RT-qPCR. Expressions were normalized first to GAPDH , then to wild-type clones. Unpaired two-tailed Student’s t test. (F) DNA gel electrophoresis of genomic PCR confirming mouse downstream Mirb deletion at cell population level in KP1. (G) circRmst expression at cell population level by RT-qPCR. Expressions were first normalized to Actb , then to cells with deletion ofa gene desert region AAVS. Unpaired two-tailed Student’s t test. All error bars represent SD. * p < 0.05. ** p < 0.01. *** p < 0.001. See also and .
Article Snippet:
Techniques: RNA Sequencing, ChIP-sequencing, CRISPR, DNA Gel Electrophoresis, Single Cell, Clone Assay, Expressing, Quantitative RT-PCR, Two Tailed Test
Journal: Cancer cell
Article Title: Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation
doi: 10.1016/j.ccell.2025.03.027
Figure Lengend Snippet: (A) Schematic of circRMST shRNA design. shRNA knockdown efficiency determined by divergent primers in SHP77 after 3 days of puromycin selection. Relative expression was first normalized to GAPDH , then to shGFP. Unpaired two-tailed Student’s t-test. (B) Representative images of SCLC-A SHP77, H889, and H69 cell lines and NEPC organoid PM155, PM154, and PDX-derived 331R cell line grown in Matrigel after circRMST shRNA treatments. Cells were selected with puromycin for at least 3 days before seeding. Images were taken after 7 days to one month of cell growth. (C) Quantification of colony numbers or organoid diameters. Two biological replicates were quantified. Relative colony numbers were normalized to shGFP. Unpaired two-tailed Student’s t test. (D) In vivo growth curves of SHP77 shRNA xenograft tumors ( n = 7 for each group) in NSG mice. Error bars represent SEM. Two-way ANOVA. (E) Volcano plot showcasing RNA-seq gene expression changes in SHP77 treated with circRMST shRNA 1 compared to shGFP. Significance and fold change were calculated with DESeq2. (F) Lollipop graph of all upregulated GSEA pathways and a selected subset of downregulated pathways in SHP77 circRMST shRNA cells compared to shGFP. Significance is −log 10 (FDR). (G) Western blots of ASCL1 after circRMST knockdowns. (H) Schematic of RMST promoter deletion designs using CRISPR-dual guide system. (I) circRMST expression by RT-qPCR in SHP77 with ΔRMST promoter deletions at cell population level. Relative expression was first normalized to GAPDH , then to ΔAAVS. Unpaired two-tailed Student’s t test. (J) Representative images of SHP77 and H889 growth in Matrigel after ΔRMST deletions. (K) Quantification of colony numbers of SHP77 and H889 in Matrigel. Two biological replicates were quantified. (L) Western blots of ASCL1 after ΔRMST deletions in SHP77 and H889. All error bars represent SD unless otherwise specified. * p < 0.05. ** p < 0.01. *** p < 0.001. See also and .
Article Snippet:
Techniques: shRNA, Knockdown, Selection, Expressing, Two Tailed Test, Derivative Assay, In Vivo, RNA Sequencing, Gene Expression, Western Blot, CRISPR, Quantitative RT-PCR
Journal: Cancer cell
Article Title: Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation
doi: 10.1016/j.ccell.2025.03.027
Figure Lengend Snippet: (A) Schematic of circRMST pulldown assays with 3′ biotin labeled DNA probes. (B and C) circRMST pulldown efficiency in SHP77 and H1092. Percentage of input was calculated comparing the pull-down fraction to the input. Unpaired two-tailed Student’s t test. (D) Cytoscape illustration of circRMST protein interactors identified in both SHP77 and H1092 in two biological replicates. SAINT analysis was applied comparing circRMST pulldowns and control pulldowns. All proteins had FDR <0.1. (E) Western blot of circRMST interacting and non-interacting proteins in SHP77 and H1092. (F) Enrichment of SOX2 and NKX2-1 with 1% formaldehyde crosslinked RIP in H889. IgG antibody was used as a negative control. (G) RNA enriched by SOX2 and NKX2-1 crosslinked RIP in H889. Percentage of input was calculated by comparing the IP fraction to the input. All error bars represent SD. ** p < 0.01. See also and .
Article Snippet:
Techniques: Labeling, Two Tailed Test, Control, Western Blot, Negative Control
Journal: Cancer cell
Article Title: Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation
doi: 10.1016/j.ccell.2025.03.027
Figure Lengend Snippet: (A) Western blot of NKX2-1 and SOX2 in SHP77 after 7 days of circRMST shRNA knockdown. SOX2 western was performed in the same experiment as ASCL1 shown in , and the Vinculin blot in serves as the loading control. (B) NKX2-1 protein amounts in 50 μg/mL cycloheximide (CHX) treated SHP77 with and without circRMST knockdown. Relative amounts from two biological replicates were normalized to vinculin and then to time point 0. Paired Student t tests. Error bars represent SD. (C) NKX2-1 protein amounts in SHP77 treated with bafilomycin A1 (BafA) at 200 nM for 24 h after 48 h of circRMST shRNA treatment. Band intensity was quantified by ImageJ, shown below NKX2-1 blots. LC3 was used as a positive control for BafA treatment. (D) Representative images of SHP77 live cells stained with 50 nM Deep Red LysoTracker for 1.5 h (E) Quantification of LysoTracker signal intensity per cell using ImageJ. At least 5 images for each group were quantified. Unpaired two-tailed Student’s t test. (F) Western blot of NKX2-1 with circRMST and HSC70 shRNAs in SHP77. Band intensity was quantified by ImageJ, shown below NKX2-1 blots. (G) Profile plots of SOX2 and NKX2-1 ChIP-seq signals at all peaks called by MACS2 in SHP77 with and without circRMST knockdown. (H) Heatmaps of SOX2 unaltered, downregulated and upregulated peaks in SHP77 circRMST knockdown cells, filtered by FDR < 0.01 and fold change > 2. (I) ChIP-seq signal tracks for SOX2 and NKX2-1 at ASCL1 and INSM1 with and without circRMST knockdown. Yellow region represents significantly differential peaks determined by DiffBind with p value < 0.05. (J) Western blots of CRISPR-Cas9 targeting SOX2 and/or NKX2-1 in SHP77. (K) Overlaps between SOX2 and NKX2-1 cistromes in SHP77. (L) Graphical summary of circRMST function in neuroendocrine tumors. * p < 0.05. ** p < 0.01. *** p < 0.001. See also and .
Article Snippet:
Techniques: Western Blot, shRNA, Knockdown, Control, Positive Control, Staining, Two Tailed Test, ChIP-sequencing, CRISPR
Journal:
Article Title: G βγ -independent constitutive association of G αs with SHP-1 and angiotensin II receptor AT 2 is essential in AT 2 -mediated ITIM-independent activation of SHP-1
doi: 10.1073/pnas.192404199
Figure Lengend Snippet: AT2 receptor mediates SHP-1 activation. (A) N1E-115, and COS-7 cells were incubated with 0.1 μM Ang II for various periods of time before immunoprecipitation with polyclonal anti-SHP-1 antibodies. The phosphatase activities measured as described in the experimental section were expressed as percentage of basal activity of mock-transfected COS-7 cells. Results are means ± SEM of at least three independent experiments performed in duplicate. (B) Immunodetection of physical interaction between AT2 and SHP-1. Cell lysates (500 μg of protein) or immunocomplexes using anti-SHP-1 and anti-HA antibodies were prepared from COS-7 cells cotransfected with HA–AT2 and SHP-1. After separation on 10% SDS/PAGE, immunoblotting were performed with antibodies as indicated in the figure. (C) Quantitation of the relative extent of SHP-1/AT2 association. The amount of SHP-1 immunoprecipitated by anti-HA antibodies and the amount of AT2 immunoprecipitated by anti-SHP-1 antibodies, as assessed by densitometric scanning (arbitrary units) were normalized to the similarly quantitated amount of AT2 and SHP-1, respectively, recovered in each immunoprecipitate. The mock background were substracted.
Article Snippet: After centrifugation at 15,000 × g for 15 min, the resulting supernatant (1–1.5 mg of proteins) was incubated for 3 h at 4°C with either 10 μl of monoclonal
Techniques: Activation Assay, Incubation, Immunoprecipitation, Activity Assay, Transfection, Immunodetection, SDS Page, Western Blot, Quantitation Assay
Journal:
Article Title: G βγ -independent constitutive association of G αs with SHP-1 and angiotensin II receptor AT 2 is essential in AT 2 -mediated ITIM-independent activation of SHP-1
doi: 10.1073/pnas.192404199
Figure Lengend Snippet: (A) Ang II analogs induce SHP-1 activity. COS-7 cells transfected with HA-AT2 and SHP-1, CHO-K1 cells transfected with HA-AT2, and N1E-115 cells were incubated with Ang II (0.1 μM) and [Sar1]Ang II (0.1 μM), and [Sar1,Ile4,Ile8]Ang II (50 μM) for 5 min before immunoprecipitation with anti-SHP-1 antibodies. (B) Ang II (0.1 μM) induces SHP-1 activity in N1E-115 cells transfected with or without Gβ1γ2 and βARK. Each data point represents the mean ± SE of two duplicate determinations. *, P < 0.01 with comparison to Gβ1γ2 and βARK.
Article Snippet: After centrifugation at 15,000 × g for 15 min, the resulting supernatant (1–1.5 mg of proteins) was incubated for 3 h at 4°C with either 10 μl of monoclonal
Techniques: Activity Assay, Transfection, Incubation, Immunoprecipitation
Journal:
Article Title: G βγ -independent constitutive association of G αs with SHP-1 and angiotensin II receptor AT 2 is essential in AT 2 -mediated ITIM-independent activation of SHP-1
doi: 10.1073/pnas.192404199
Figure Lengend Snippet: AT2 receptor mutants mediate SHP-1 activation. (A) COS-7 cells cotransfected with SHP-1 and HA-tagged AT2 wild type (WT), or D141A–R142L or D90A mutants were incubated with Ang II (0.1 μM) for 5 min before immunoprecipitation with anti-SHP-1 antibodies. The SHP-1 activities were measured in duplicate. *, P < 0.01 between wild type and D141A–R142L in the presence of Ang II. (B) Immunodetection of receptor-SHP-1 association in the presence or absence of 0.1 μM of Ang II. Each data point represents the mean ± SE of at least two duplicate determinations. (C) Quantitation of the relative extent of SHP-1/AT2 association. The amount of SHP-1 immunoprecipitated by anti-HA antibodies as assessed by densitometric scanning (arbitrary units) were normalized to the similarly quantitated amount of AT2 receptors recovered in each immunoprecipitate. The mock background were substracted.
Article Snippet: After centrifugation at 15,000 × g for 15 min, the resulting supernatant (1–1.5 mg of proteins) was incubated for 3 h at 4°C with either 10 μl of monoclonal
Techniques: Activation Assay, Incubation, Immunoprecipitation, Immunodetection, Quantitation Assay
Journal:
Article Title: G βγ -independent constitutive association of G αs with SHP-1 and angiotensin II receptor AT 2 is essential in AT 2 -mediated ITIM-independent activation of SHP-1
doi: 10.1073/pnas.192404199
Figure Lengend Snippet: Role of Gα proteins in AT2-mediated SHP-1 activity. (A) Immunodetection of physical association of Gas with AT2 or SHP-1 in COS-7 cells cotransfected with HA-AT2, SHP-1 and Gαs genes. (B) Immunodetection of AT2-SHP-1 and Gαs-SHP-1 associations in the presence or absence of Gαs peptides. (C) SHP-1 activities induced by 0.1 μM Ang II in N1E-115 cells in the presence of Gαs peptides and Gαs mutants. Gαs peptides are: GiP, IKNNLKDCGLF; rGiP, NGIKCLFNDKL (Randomized peptide of Gi); GqP, LQLNLKEYNAV; rGqP: LAYQVNKLNLE (Randomized peptide of Gq); GsP, QRMHLRQYELL; rGsP: QQRLEMYLRHL (Randomized peptide of Gs); G13P, LHDNLKQLMLQ; rG13P, MQLDNKLQLHL (Randomized peptide of G13). Data for rGiP, rGqP, and rG13P peptides are not included in C. Here caGαs and dnGαs represent constitutively active Gαs mutant R201C and dominant negative mutant A366S-G226A-E268A, respectively. Each data point represents the mean ± SE of at least two duplicate determinations. *, P < 0.01 compared with mock-transfected N1E-115 cells; ¶, P < 0.01 compared with mock-transfected N1E-115 cells.
Article Snippet: After centrifugation at 15,000 × g for 15 min, the resulting supernatant (1–1.5 mg of proteins) was incubated for 3 h at 4°C with either 10 μl of monoclonal
Techniques: Activity Assay, Immunodetection, Mutagenesis, Dominant Negative Mutation, Transfection
Journal:
Article Title: G βγ -independent constitutive association of G αs with SHP-1 and angiotensin II receptor AT 2 is essential in AT 2 -mediated ITIM-independent activation of SHP-1
doi: 10.1073/pnas.192404199
Figure Lengend Snippet: Functional domains of SHP-1 and the ITIMs.
Article Snippet: After centrifugation at 15,000 × g for 15 min, the resulting supernatant (1–1.5 mg of proteins) was incubated for 3 h at 4°C with either 10 μl of monoclonal
Techniques: Functional Assay
Journal: Nature chemical biology
Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.
doi: 10.1038/nchembio.1636
Figure Lengend Snippet: Figure 1 | Engineering and characterization of receptor-based Axl antagonists. (a) Axl’s extracellular domain consists of two Ig-like domains containing high- and low-affinity Gas6 binding sites, followed by two fibronectin type III domains. Binding of Gas6 to Axl leads to receptor dimerization and activation of downstream signaling. Axl decoy receptors sequester Gas6, preventing activation of the Axl signaling cascade. (b) Overlaid flow cytometry dot plots representing binding of yeast-displayed wild-type Axl Ig1 (red) and unsorted Axl Ig1 library (blue) to 10 nM Gas6 (y axis) and expression levels on the yeast cell surface (x axis). (c) Flow cytometry histograms of the initial Axl library and intermediate sort products compared to wild-type Axl Ig1 (gray), measuring binding to 0.5 nM Gas6 (top row) and persistent Gas6 binding after a 30-h incubation with excess competitor (bottom row). MYD1 is also included for comparison. For clarity, only the gated population of yeast expressing Axl is shown. AU, arbitrary units. (d) Binding affinities of wild-type Axl Ig1, MYD1 and Axlnb to Gas6 as determined by KinExA. (e) Binding affinities to Gas6 of every permutation of the four mutations found in MYD1. Raw KinExA data and associated error values can be found in Supplementary Figures 2 and 3.
Article Snippet: After the appropriate incubation time, reactions were flowed over
Techniques: Binding Assay, Activation Assay, Flow Cytometry, Expressing, Incubation, Comparison
Journal: Nature chemical biology
Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.
doi: 10.1038/nchembio.1636
Figure Lengend Snippet: Figure 2 | Structural basis for high-affinity binding. (a) Gas6–MYD1 co-complex showing overall architecture and 2:2 stoichiometry. (b) MYD1 Ig1 (orange) and Gas6 LG1 (gray) domains showing the location of the four mutations in MYD1 with respect to the major binding site, which lies at the interface of these two domains. (c) Analysis of the wild-type structure (PDB code 2C5D) reveals steric crowding between the side chains of T457Gas6 and V92Axl. The V92A mutation alleviates this crowding in the MYD1 co-complex and facilitates local reorganization of side chains around V92A, exemplified by R48 and Q94. This in turn creates an elongated groove on MYD1 at the binding interface that allows reorientation of T457 on Gas6. (d) Reorientation of T457 results in capping of the N terminus of helix A. The wild-type (WT, green) and MYD1 (gray) structures are overlaid for comparison. (e) Capping stabilizes helix A, as seen by B-factor analysis (Online Methods).
Article Snippet: After the appropriate incubation time, reactions were flowed over
Techniques: Binding Assay, Mutagenesis, Comparison
Journal: Nature chemical biology
Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.
doi: 10.1038/nchembio.1636
Figure Lengend Snippet: Figure 4 | MYD1 Fc inhibits Axl activation and downstream signaling in skov3.ip cells. (a) Wild- type (WT) Axl Fc and MYD1 Fc, but not Axlnb Fc, can inhibit Gas6-mediated Axl activation in vitro. (b) Inhibition of Axl activation leads to reduced levels of phosphorylated Akt and Erk1/2 and an increase in the epithelial marker e-cadherin. For full (uncut) blots, see Supplementary Figure 11.
Article Snippet: After the appropriate incubation time, reactions were flowed over
Techniques: Activation Assay, In Vitro, Inhibition, Marker
Journal: Nature chemical biology
Article Title: An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis.
doi: 10.1038/nchembio.1636
Figure Lengend Snippet: Figure 5 | Sequestration of Gas6 by MYD1 Fc inhibits metastasis. (a) Amount of free Gas6 in serum of mice 12 h after administration of a single dose of MYD1 Fc. (b) Kinetics of Gas6 sequestration (black) and MYD1 Fc clearance (red) following a 1 mg per kg body weight dose of MYD1 Fc. (c) Using the off-rates of the Gas6-Axl Fc interactions (Fig. 3b), dissociation of Gas6 bound to either wild-type Axl Fc (red) or MYD1 Fc (blue) is plotted over time. The in vivo clearance of the Axl decoy receptors as measured in c is overlaid in black. Two mice were analyzed for each data point in b and c. (d–f) Tumor burden in in vivo models of metastatic human ovarian cancer. The number of visible metastases in animals treated with Axlnb Fc, wild-type Axl Fc or MYD1 Fc was counted in the skov3.ip (d) and OVCAR (f) tumor models. Representative images of mice from each treatment group in the skov3.ip model are shown, and arrows indicate disease (e). In both models, animals were administered 10 mg per kg body weight of the indicated protein twice weekly. (g) Lung metastases in the 4T1 luciferase breast cancer model, as quantified by ex vivo bioluminescent imaging. Mice received intravenous injections of the indicated treatment twice weekly. (h) Representative bioluminescent images of lungs and spleens from each treatment group; scale bar, 1 cm. Error bars represent ± s.d., n = 6–12 mice per group; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.
Article Snippet: After the appropriate incubation time, reactions were flowed over
Techniques: In Vivo, Luciferase, Ex Vivo, Imaging
Journal: Nature Communications
Article Title: GBP2 condensates promote ferroptosis to sensitize anti-PD-L1 immunotherapy in melanoma
doi: 10.1038/s41467-025-67690-9
Figure Lengend Snippet: A B16-OVA cells treated with IFN-γ (10 ng/mL, 12 h) were immunoprecipitated with anti-GBP2 for mass spectrometry (MS); SHP1 was selected. B IP assay shows endogenous GBP2 interact with SHP1 in B16-OVA and A375 cells. C sgCtrl and GBP2 −/− of B16-OVA and A375 cells were treated with IFN-γ (10 ng/mL, 12 h), followed by SHP1 knockdown using siRNA for 24 h; cell lysates were analyzed by western blot. D Representative live-cell imaging of B16-OVA cells expressing GBP2-mCherry stimulated with 10 ng/ml IFN-γ for 6 h, and transfected with SHP1-mEGFP plasmid for 36 h. The line plots show GBP2-mCherry and SHP1-mEGFP colocalization of areas. E Western blot analysis of B16-OVA GBP2 −/− and A375 GBP2 −/− cells treated with 10 ng/ml IFN-γ for 12 h, followed by transfection with vector, GBP2-FL, or GBP2 ΔIDR plasmids for 24 h. F , G Representative live-cell imaging and high-resolution confocal demonstrated colocalization of GBP2-mCherry with SHP1-mEGFP, but not GBP2ΔIDR, upon IFN-γ stimulation. H In vitro kinase assays revealed enhanced STAT1 phosphorylation in the presence of GBP2 condensates. I , J In vitro phase separation assays compared condensate formation between GBP2-WT, GBP2ΔIDR, and GBP2-MBP, confirming IDR-dependent condensate activity and STAT1 phosphorylation enhancement. K GBP2 −/− B16-OVA cells expressing GBP2-FL or GBP2ΔIDR (1 × 10 6 ) were subcutaneously injected into C57BL/6 mice and treated with anti–PD-L1 antibody (200 μg/mouse) or IgG every 3 days. L Lipid ROS in CD45⁻ tumor cells were quantified by flow cytometry. M Tumors from GBP2-FL and GBP2ΔIDR groups were immunoprecipitated with anti-SHP1 and analyzed by western blot. N Representative immunofluorescence images of GBP2 in GBP2-FL and GBP2ΔIDR tumors treated with anti–PD-L1 (n = 3). All p value < 0.05 as statistic difference. n = 3 independent experiments ( B – J , M , N ); n = 6 independent experiments ( K , L ). The data are represented as mean ± SD. p value by unpaired two-tailed t-test ( L ) or two-way ANOVA ( K ). Source data are provided as a file.
Article Snippet: The PVDF membranes were blocked with 5% fat-free milk and incubated overnight at 4 °C with the appropriate primary antibodies: GBP2 (11854-1-AP, Proteintech, USA), p-STAT1 (#9167, CST, USA), STAT1 (#14994, CST, USA), SLC7A11 (#98051, CST, USA), SLC3A2 (15193-1-AP, Proteintech, USA), ACSL4 (22401-1-AP, Proteintech, USA), PD-L1 (17952-1-AP, Proteintech, USA), HMGB1 (10829-1-AP, Proteintech, USA),
Techniques: Immunoprecipitation, Mass Spectrometry, Knockdown, Western Blot, Live Cell Imaging, Expressing, Transfection, Plasmid Preparation, In Vitro, Phospho-proteomics, Activity Assay, Injection, Flow Cytometry, Immunofluorescence, Two Tailed Test