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Image Search Results
Journal: Molecular cell
Article Title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders
doi: 10.1016/j.molcel.2026.01.023
Figure Lengend Snippet: (A) RING1 and RNF2 variants (top). Reported variants in ClinVar and cancer-related somatic (COSMIC) mutations in RING1 and RNF2 genes (bottom). Metadome plots (middle) represent the level of predicted intolerance for amino acid change in RING1A and RING1B. For COSMIC, only positions of interest are shown as labels. Circle size represents the number of patients reported. (B) ColabFold predictions of RING1A and RING1B variants in altering interaction with PCGF proteins. (C) WBs of dKO-RING1A/B cells expressing HA-tagged WT and mutant RING1A and RING1B. Vinculin and histone H3 served as loading controls. n = 3 independent experimental replicates. (D) Possible mechanisms of deleterious variants that result in a decrease or absence of H2AK119ub. (E) Partial protein sequence alignments of a subset of RING1B homologs. The conserved RING1B-R70 residue corresponds to C. elegans R181 and is indicated by a star. Conserved zinc-coordinating residues, blue ; required for stabilizing the E2 enzyme-E3 ligase interaction in mammals, red ; required for binding to the nucleosome in mammals, green predicted to be important for the RING1B:PCGF4 interaction, magenta 47; and predicted to mediate β sheet interactions, cyan. * indicates identical residues, and : and. indicate residues with strongly and weakly similar physicochemical properties, respectively. The secondary structure of SPAT-3 and H. sapiens RING1B is shown below. (F) WBs of H2AK119ub in the indicated genotypes. The dilution factor is 1:3. The spat-3(mgw26) allele is a full deletion of the spat-3 coding region. Quantification of H2AK119ub and SPAT-3 isoform A is normalized to loading controls (histone H3/actin) and shown relative to the sample indicated by an asterisk. ND, not detectable. (G) WBs in dKO-RING1A/B cells stably expressing HA-RING1B WT or HA-RING1B R70H . Vinculin and histone H2A and H3 served as fractionation controls. n = 3 independent experimental replicates. (H) Normalized H3K27me3 Cut&Run signal (two independent experimental replicates) in cells treated with 1 μM of vehicle (DMSO) or GSK343 for 72 h. See also and .
Article Snippet:
Techniques: Expressing, Mutagenesis, Sequencing, Residue, Binding Assay, Stable Transfection, Fractionation
Journal: Molecular cell
Article Title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders
doi: 10.1016/j.molcel.2026.01.023
Figure Lengend Snippet: (A) Strategy to generate Rnf2 WT/R70H ESCs by homologous recombination. (B) DEG from WT and two clones of Rnf2 WT/R70H ESCs (log 2 fold > 2, q < 0.01). n = 2 independent experimental replicates. (C) GO of upregulated genes in Rnf2 WT/R70H ESCs. (D) Heatmaps of Ring1b, H3K27me3, and H2AK119ub ChIP-seq (average signal of two independent experimental replicates) in WT and clone #1 of Rnf2 WT/R70H ESCs. (E) Strategy to generate HA and FLAG-tagged Rnf2 alleles by CRISPR-Cas9 in WT and Rnf2 WT/R70H ESCs. (F) Normalized Ring1b WT and Ring1b R70H Cut&Run signals in WT and Rnf2 WT/R70H ESCs. Signal was generated from two biological replicates from two independent WT and Rnf2 WT/R70H clones. HA and FLAG Cut&Run signals were merged (average of 4 replicates) to avoid potential bias from the HA and FLAG antibodies’ efficiency. (G) Anti-FLAG IPs in Rnf2 HA-WT/FLAG-R70H and Rnf2 FLAG-WT/HA-R70H ESCs followed by LC-MS/MS in three independent experimental replicates. Results are normalized to IgG as a negative control. Volcano plot shows proteins enriched or weakened in FLAG-Ring1b R70H compared with FLAG-Ring1b WT from Rnf2 WT/R70H ESCs. (H) Heatmaps of Cbx7 and Pcgf2, Rybp, Mtf2/Pcl2, and Jarid2 ChIP-seq (average signal of two independent experimental replicates) in WT and clone #1 of Rnf2 WT/R70H ESCs. (I) Genome browser screenshots of ChIP-seq from (H). (J) Mutabind2 scores upon the human RING1B R70H variant vs. full length and lacking their IDR, PCGF1-6 using AlphaFold and ColabFold. (K) Full-length Pcgf2 or lacking the IDR used in (L). (L) Anti-HA IPs followed by WBs against HA, Phc1, and Ring1b in WT and Rnf2 WT/R70H ESCs expressing HA-Pcgf2 WT or HA-Pcgf2 ΔIDR . (M) Model of PRC1/2 recruitment in Rnf2 WT/R70H ESCs. See also .
Article Snippet:
Techniques: Homologous Recombination, Clone Assay, ChIP-sequencing, CRISPR, Generated, Liquid Chromatography with Mass Spectroscopy, Negative Control, Variant Assay, Expressing
Journal: Molecular cell
Article Title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders
doi: 10.1016/j.molcel.2026.01.023
Figure Lengend Snippet: (A) Normalized Ring1b WT and Ring1b R70H Cut&Run signals in either WT or Rnf2 WT/R70H NPCs in WT Ring1b peak regions. Two biological replicates from two independent clones. Wilcox test. *** p < 0.001. (B) Normalized H3K27me3 and H2AK119ub Cut&Run signals in either WT or Rnf2 WT/R70H NPCs over all genome. Signal was generated from two biological replicates from two independent clones. Wilcox test. *** p < 0.001. (C) Genome browser screenshots of HA, FLAG, H3K27me3, and H2AK119ub Cut&Run (average signal between replicates) in the cells shown on the left. (D) Anti-FLAG IPs in Rnf2 HA-WT/FLAG-R70H and Rnf2 FLAG-WT/HA-R70H NPCs followed by LC-MS/MS in three independent experimental replicates. Results are normalized to IgG as negative control. Volcano plot shows proteins enriched or weakened in FLAG-Ring1b R70H compared with FLAG-Ring1b WT from Rnf2 WT/R70H NPCs. (E) RNA-seq heatmap of PcG target genes in ESCs that are upregulated in WT NPCs but retained PRC1/2 and are repressed in Rnf2 WT/R70H NPCs. #1 and #2 are two different Rnf2 WT/R70H ESC clones. On the right, GO from each cluster. Deseq2; Wald test (FC > 4), q < 0.05. (F) Simplified genome browser screenshots of Ring1b WT , Ring1b R70H , H3K27me3, and H2AK119ub Cut&Run in WT and Rnf2 WT/R70H NPCs. Ring1b signal in WT NPCs and Ring1b WT and Ring1b R70H signals in Rnf2 WT/R70H NPCs are from merging average signals HA and FLAG Cut&Run two replicates from two clones. (G) Normalized signal of Ring1b WT and Ring1b R70H Cut&Run signals as in (F) around the transcription start site (TSS) of genes from (E). (H) Normalized signal of H3K27me3 and H2AK119ub Cut&Run signals (average from two replicates) as in (F) around the TSS of genes from (E). (I) Normalized ATAC-seq signal (average from two replicates) in WT and Rnf2 WT/R70H ESCs and NPCs around the TSS of genes from (E). See also .
Article Snippet:
Techniques: Clone Assay, Generated, Liquid Chromatography with Mass Spectroscopy, Negative Control, RNA Sequencing
Journal: Molecular cell
Article Title: Unbalanced chromatin binding of Polycomb complexes drives neurodevelopmental disorders
doi: 10.1016/j.molcel.2026.01.023
Figure Lengend Snippet: (A) PCA from ATAC-seq from two independent biological replicates of WT and Rnf2 WT/R70H ESCs and NPCs. (B) Genome browser of ATAC-seq signal (average of two replicates) from WT and Rnf2 WT/R70H ESCs and NPCs. (C) RT-qPCR of pluripotency genes and NPC markers in WT and Rnf2 WT/R70H ESCs and NPCs. n = 3. #1 and #2 represent two clones of Rnf2 WT/R70H ESCs. *** p < 0.005, **** p < 0.001 by ANOVA test. (D) WB of Pax6 in WT and clone #1 of Rnf2 WT/R70H ESCs and NPCs. Vinculin served as a loading control. (E) ATAC-seq peaks reduced in Rnf2 WT/R70H NPCs and HOMER analysis. (F) Normalized expression of genes from (E) in WT and clones #1 and #2 of Rnf2 WT/R70H NPCs. *** p < 0.001. NS, not significant. Wilcox test. (G) ATAC-seq specific peaks in Rnf2 WT/R70H NPCs and HOMER analysis. (H) Normalized expression of genes from (G) in WT and clones #1 and #2 of Rnf2 WT/R70H NPCs. *** p < 0.001. NS, not significant. Wilcox test. (I) ATAC-seq signal in WT and Rnf2 WT/R70H NPCs at Sox2- or Sox3-occupied sites in WT NPCs. Sox2 and Sox3 ChIP from Bergsland et al. (J) Genome browser of ATAC-seq signal from WT and Rnf2 WT/R70H ESCs and NPCs as well as Ring1b WT and Ring1b R70H Cut&Run signal in WT and Rnf2 WT/R70H NPCs. (K) Normalized expression and GO of genes occupied by Ring1b WT and Ring1b R70H and compacted. *** p < 0.001. NS, not significant. Wilcox test. See also .
Article Snippet:
Techniques: Quantitative RT-PCR, Clone Assay, Control, Expressing
Journal: Molecular Cancer Research
Article Title: The Opposing Effect of Hypoxia-Inducible Factor-2α on Expression of Telomerase Reverse Transcriptase
doi: 10.1158/1541-7786.mcr-07-0065
Figure Lengend Snippet: FIGURE 4. HIF-2a occupancy on the hTERT promoter, recruitment of p300, and changes in histone H3 acetylation in A498 and U251 cells under hypoxic conditions. A. Schematic presentation of the hTERT promoter and locations of the ChIP PCR amplicons relative to the translational start codon (ATG). The putative HREs in region a are indicated (16). Region b was also found to interact with HIF-1a according to Anderson et al. (10). B. The ChIP assay for the presence of HIF-2a, p300, and histone H3 acetylation at the hTERT promoter in hypoxia-treated A498 and U251 cells. The precipitated DNA was subject to PCR analysis using the primer pairs specific to the hTERT promoter regions a and b. Input is sonicated chromatin without immunoprecipitation, but reverse cross-linked and purified together with ChIP samples. HRE, hypoxia-responsive element; H and N, the cells were cultured under hypoxic and normal oxygen conditions, respectively. Ab, no antibody controls. H3-Ac, the antibody against acetylated histone H3.
Article Snippet: The membranes were probed with the specific
Techniques: Sonication, Immunoprecipitation, Purification, Cell Culture
Journal: The Journal of biological chemistry
Article Title: Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-Tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation.
doi: 10.1074/jbc.M512786200
Figure Lengend Snippet: FIGURE 5. Anti-polyubiquitin staining of affinity-purified PHF-Tau. Following SDS- PAGE separation of MC1 affinity-purified PHF-Tau on a 10% polyacrylamide gel, Western blot was performed with an anti-polyubiquitin antibody. Immunoreactivity was visual- ized by enhanced chemiluminescence (left panel). Secondary antibody (goat anti-mouse IgG-horseradish peroxidase) control for nonspecific immunoreactivity is also depicted (right panel).
Article Snippet: Blots were incubated with a
Techniques: Staining, Affinity Purification, SDS Page, Western Blot, Control
Journal: The Journal of biological chemistry
Article Title: Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-Tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation.
doi: 10.1074/jbc.M512786200
Figure Lengend Snippet: FIGURE 6. Relative quantification of Lys-6, Lys-11, and Lys-48 polyubiquitin linkages by SRM. Polyubiquitin linkages at Lys-6 (A), Lys-11 (B), and Lys-48 (C) of ubiquitin (ubiquitinated and unmodified peptides) were quantified by specific precursor-to-product ion transition monitoring (Table 4). D shows chromatograms for all three ubiquitinated peptides on the same scale for visual comparison of the relative peak areas.
Article Snippet: Blots were incubated with a
Techniques: Quantitative Proteomics, Ubiquitin Proteomics, Comparison
Journal: Cytometry. Part A : the journal of the International Society for Analytical Cytology
Article Title: Flow Cytometric Detection of Circulating Osteosarcoma Cells in Dogs.
doi: 10.1002/cyto.a.23847
Figure Lengend Snippet: Figure 1. Canine OSA cell lines OVC-cOSA-31 (A) and OVC-cOSA-75 (B), gated as indicated, were highly positive for intracellular Col I (center panel) and variably positive for OC (right panel). Blue = anti-rat CD4 control antibody; red = Col I or OC antibody. [Color figure can be viewed at wileyonlinelibrary.com]
Article Snippet: The following isotype- and fluorochrome-matched antibodies were used as negative controls in all assays: (1)
Techniques: Control
Journal: Cytometry. Part A : the journal of the International Society for Analytical Cytology
Article Title: Flow Cytometric Detection of Circulating Osteosarcoma Cells in Dogs.
doi: 10.1002/cyto.a.23847
Figure Lengend Snippet: Figure 8. Cytomorphology of OSA cells. Cytocentrifuge preparations of (A) cultured OVC-cOSA-31 cells (400×); (B) normal dog blood leukocytes spiked with primary OSA tumor aspirate cells, fixed, and permeabilized (arrow on OSA cell, 400×); (C) CTC sorted based on Col I positivity from blood of dog with a primary OSA (1,000×); (D) cell directly aspirated from a primary OSA (1,000×) with neutrophil (arrow); (E) primary OSA cells aspirated from tumor and sorted based on Col I positivity (1,000×); (F) OVC-cOSA-31 cells sorted from spiked normal dog blood (1,000×). All slides were Wright stained. Immunofluorescence of Col I-FITC positive; (G) OVC-cOSA-31 cells; and (H) CTC cells sorted from blood of a dog with OSA. Nuclei are stained with DAPI (1,000×). [Color figure can be viewed at wileyonlinelibrary.com]
Article Snippet: The following isotype- and fluorochrome-matched antibodies were used as negative controls in all assays: (1)
Techniques: Cell Culture, Staining
Journal: International journal of molecular sciences
Article Title: L-Type Amino Acid Transporter 1 Regulates Cancer Stemness and the Expression of Programmed Cell Death 1 Ligand 1 in Lung Cancer Cells.
doi: 10.3390/ijms222010955
Figure Lengend Snippet: Figure 1. LAT1 expression increases in pemetrexed-resistant NSCLC cells. (A) The primary or secondary tumorspheres were cultured from A549 and A400 cells according to the protocol described in the Materials and Methods section. Pictures
Article Snippet: The
Techniques: Expressing, Cell Culture
Journal: International journal of molecular sciences
Article Title: L-Type Amino Acid Transporter 1 Regulates Cancer Stemness and the Expression of Programmed Cell Death 1 Ligand 1 in Lung Cancer Cells.
doi: 10.3390/ijms222010955
Figure Lengend Snippet: Figure 2. Knockdown of LAT1 reduces CSC activity and Akt/mTOR activation in NSCLC cells. (A) The knockdown of LAT1 in A400 and H1299 cells was performed by lentiviral delivery of LAT1-specific shRNAs (shSLC7A5#1 or shSLC7A5#2) and 100 nM of LAT1-specific siRNA oligonucleotides, respectively, for 48 h. The CSC activity was determined by tumorsphere cultivation. The inserted scale bars indicate 100 µm in length. *** p< 0.001. (B) The mRNA expressions of cancer stemness genes (BMI1/SOX2/Oct4) and SLC7A5 were determined by real-time RT-PCR. * p < 0.05; ** p < 0.01; *** p < 0.001. (C) The protein expressions of phosphor-mTORser2481, mTOR, phosphor-Aktser473, Akt, and LAT1 were determined by Western blot analysis. GAPDH was used as a protein-loading control. The inserted numbers present relative expression folds in comparison to shLacZ or the control siRNA group.
Article Snippet: The
Techniques: Knockdown, Activity Assay, Activation Assay, Quantitative RT-PCR, Western Blot, Control, Expressing, Comparison
Journal: International journal of molecular sciences
Article Title: L-Type Amino Acid Transporter 1 Regulates Cancer Stemness and the Expression of Programmed Cell Death 1 Ligand 1 in Lung Cancer Cells.
doi: 10.3390/ijms222010955
Figure Lengend Snippet: Figure 3. Inhibition of LAT1 activity by JPH203 suppresses CSC activity and Akt/mTOR activation in NSCLC cells. (A) The CSC activity of A400 and H1299 cells was determined by tumorsphere cultivation, and pictures were presented at 100× magnification. The quantitative data were presented as relative percentages to the tumorsphere number of the 0.1% DMSO treated group (0 µM). The inserted scale bars indicate 100 µm in length * p < 0.05; ** p < 0.01. (B) The protein expressions of phosphor-mTORser2481, mTOR, phosphor-Aktser473, Akt, and LAT1 were determined by Western blot analysis. GAPDH was used as a protein-loading control. The inserted numbers presented are relative expression folds in comparison to the 0.1% DMSO treated group (0 µM) after normalization with the internal control of GAPDH. (C) The protein expression of BMI1 or SOX2 was determined by Western blot. The inserted numbers indicated relative expression levels as compared to DMSO group after normalization to the internal control of GAPDH. (D) The CSC activity of A400 cells under JPH203 treatment with or without 100 µM LLME cotreatment was determined by tumorsphere cultivation and pictures were presented at 200× magnification. The quantitative data were presented as relative percentages of the tumorsphere number of the 0.1% DMSO without LLME treatment group. The inserted scale bars indicate 100 µm in length. * p < 0.05; ** p < 0.01. (E) The protein expressions of phosphor-mTORser2481, mTOR, phosphor-Aktser473, Akt, and LAT1 in A400 and H1299 cells in the presence of LLME were determined by Western blot analysis. GAPDH was used as a protein-loading control. The inserted numbers are presented as relative expression folds in comparison to the cells without LLME treatment group after normalization to GAPDH. (F) The CSC activity of H1299 cells under JPH203 treatment with or without the overexpression of the myr-Akt vector was determined by tumorsphere cultivation, and pictures were presented at 100× magnification. The inserted scale bars indicate 100 µm in length. The quantitative data were presented as relative percentages of the tumorsphere number of the control vector transfected and 0.1% DMSO treatment group. The overexpression of myr-Akt (upper panel) was determined by Western blot analysis. ** p < 0.01. ns, not significant.
Article Snippet: The
Techniques: Inhibition, Activity Assay, Activation Assay, Western Blot, Control, Expressing, Comparison, Over Expression, Plasmid Preparation, Transfection
Journal: International journal of molecular sciences
Article Title: L-Type Amino Acid Transporter 1 Regulates Cancer Stemness and the Expression of Programmed Cell Death 1 Ligand 1 in Lung Cancer Cells.
doi: 10.3390/ijms222010955
Figure Lengend Snippet: Figure 4. LAT1 activity participates in PD-L1 expression on NSCLC cells. (A,B). The knockdown of LAT1 by lentiviral delivery of LAT1-specific shRNAs (shSLC7A5#1 or shSLC7A5#2) for A400 cells or by transfection of LAT1-specific siRNA oligonucleotides (si-SLC7A5) for H1299 cells was confirmed by Western blot analysis (A). The cell surface expressions of PD-L1 were determined by Western blot (A) or FACS analysis (B), respectively. The FACS data was analyzed by FlowJo software. The inserted numbers in (A) represent the relative expression levels of PD-L1 or LAT1 in comparison to the sh-LacZ or si-NC (indicated as 0 nM) control group, respectively, after normalization with GAPDH. Blue peaks and red peaks in (B) represent an isotype control and an anti-PD-L1 antibody, respectively. siNC, negative control siRNA. (C,D) The PD-L1 total protein and cell surface expressions of A400 and H1299 cells under JPH203 treatment were determined by Western blot (C) and FACS analysis (D), respectively. The inserted numbers in (A) present the relative expression levels of PD-L1 or LAT1 in comparison to the 0.1% DMSO control group (0 µM) after normalization with GAPDH. Blue peaks and red peaks in (D) represent an isotype control and an anti-PD-L1 antibody, respectively.
Article Snippet: The
Techniques: Activity Assay, Expressing, Knockdown, Transfection, Western Blot, Software, Comparison, Control, Negative Control
Journal: International journal of molecular sciences
Article Title: L-Type Amino Acid Transporter 1 Regulates Cancer Stemness and the Expression of Programmed Cell Death 1 Ligand 1 in Lung Cancer Cells.
doi: 10.3390/ijms222010955
Figure Lengend Snippet: Figure 6. LAT1+/PD-L1+ enriches CSC activity of NSCLC cells. (A) The cell surface expressions of LAT1 and PD-L1 on A549 and H1299 cells were determined by FACS with fluorescence-labeled antibodies. (B) Three populations of NSCLC cells (PD-L1−/LAT1−, PD-L1+/LAT1−, PD-L1+/LAT1+) were isolated by FACS cell sorting, and their CSC activities were measured by tumorsphere cultivation. Pictures were presented at 100× magnification and the inserted scale bars indicate 100 µm in length. The data were presented as relative percentages of the tumorsphere number of PD-L1−/LAT1−cells. * p < 0.05. (C) The expressions of cancer stemness proteins (BMI1, c-MYC, EZH2, OCT4), phosphor-mTORser2481, mTOR, phosphor-Aktser473, and Akt were determined by Western blot. The inserted numbers indicated relative expression levels in comparison to PD-L1−/LAT1−cells after normalization to GAPDH. (D) The overall survival curves of NSCLC patients in the TCGA database regarding expression levels of CD274 and the two-gene signature of CD274 and SLC7A5 using median level as the cutoff criteria were analyzed using the GEPIA2 webtool [18].
Article Snippet: The
Techniques: Activity Assay, Labeling, Isolation, FACS, Western Blot, Expressing, Comparison