Journal: Nature Communications

Article Title: Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas

doi: 10.1038/s41467-024-52826-0

Figure Lengend Snippet: A UMAP plot showing 24 clusters of the integrated scRNA-seq dataset from two control spleen samples (WT) and two PTCL-NOS Smarcb1− tumor samples. B Relative abundance of different cell types in murine WT spleens (left), PTCL spleens (middle), and human tumors (right; NB: in order to ensure comparability, the stromal cells were removed before quantification). The pie charts in the lower part show the ratio between B-cells and myeloid cells. C Multiplex immunofluorescence (IF) images of FFPE sections of murine PTCL-NOS Smarcb1− and control spleen samples (WT: upper panels; tumor: lower panels). For better visualization, the white boxed areas ( a to f ) are enlarged (2.5x; scale bar = 100 µm). DAPI (gray) provides a nuclear counterstain, Ezh2 (yellow) defines malignant cells (Ezh2 hi ), B220 (blue) is used as a pan B-cell marker (B220 + ), and Ly6g (pink) as a marker for neutrophils (Ly6g + ). D Quantitative analysis of IF images from ( C ). Four representative regions of interest (ROIs; size: 1500 × 1500 µm) were selected and analyzed for mouse WT and Tumor samples. A Wilcoxon-Mann-Whitney test was calculated to determine if there are differences between WT and Tumor samples for all comparisons (* p = 0.0286). Boxplot settings: middle, median; lower hinge, 25% quantile; upper hinge, 75% quantile; upper/lower whisker, largest/smallest observation less/greater than or equal to upper/lower hinge ±1.5 * IQR. E The heatmap shows the overlap between cluster-specific DEG lists and the cancer hallmark metaprograms. F Signature plots of the programs Cycling, MYC, EMT and Stress in cells from WT (left) and tumor (right) samples. G A split violin plot (left/gray half: WT; right/black half: tumor) illustrates the increase in T-cell exhaustion features (Exhaust.) with a simultaneous decrease in NK cytotoxicity (Cytotox.) markers (e.g., Ncr1/NKp46) as well as infiltration of immunosuppressive myeloid cells in tumor versus WT samples. Source data of B and D are provided as a Source Data file. B Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.

Article Snippet: For multiplexed immunofluorescence analysis, slices of PTCL-NOS Smarcb1− and corresponding murine control spleens were stained in the MACSima imaging system using antibodies against B220 (RA3-6B2, Miltenyi Biotec, APC, 1:50), Ly6G (1A8, Miltenyi Biotec, PE, 1:50) and EZH2 (REA907, Miltenyi Biotec, APC, 1:50).

Techniques: Control, Multiplex Assay, Immunofluorescence, Marker, MANN-WHITNEY, Whisker Assay

Journal: bioRxiv

Article Title: SUN2 mediates epigenetic remodeling to drive mechanotransduction during skin fibrosis

doi: 10.64898/2026.03.19.712957

Figure Lengend Snippet: (A-C) Images and quantification of Ezh2 immunofluorescence in WT and Sun2 KO dermal fibroblasts cultured on soft or stiff substrates. (A) Scale bar = 10 μ m. (B) Quantification of nuclear Ezh2 intensity. N = 2, n soft = 21–37, n stiff = 20–24. Significance was assessed using a two-tailed Mann–Whitney U test. (C) qPCR analysis of Ezh2 mRNA expression in WT or Sun2 KO fibroblasts on soft or stiff substrates. N = 3. Significance was assessed using a two-tailed Mann–Whitney U test. (D-E) Schematic and analysis of WT and Sun2 KO dermal fibroblasts plated on soft or stiff substrates for 24 h, followed by 24 h treatment with the Ezh2 inhibitor GSK343 or DMSO (Day 1), and collection for qPCR (Day 2). N = 3 independent experiments. Statistical significance was assessed using one-way ANOVA. ns, not significant; p < 0.05, * p < 0.01, ** p < 0.001, *** p < 0.0001. (F) Proposed model for SUN2–LINC–PRC2–dependent control of profibrotic gene expression in dermal fibroblasts. In quiescent WT fibroblasts, fibrotic genes are repressed. Upon mechanical stimulation of WT cells, cytoskeletal tension transmitted through LINC complexes promotes lamin stretching and altered Ezh2-driven epigenetic remodeling to activate transcription, repress transcriptional activators, and promote enhancer-licensing. In Sun2 KO dermal fibroblasts,loss of LINC complexes blunts this mechanotransduction despite cytoskeletal activation.

Article Snippet: Primary antibody diluted in blocking solution – SUN2, 1:200 (Abcam, AB124916), YAP, 1:200 (CST, 4912S), LaminA/C (Abcam, AB133256), and/or Ezh2, 1:200 (CST, 5246T) was incubated overnight at 4°C.

Techniques: Immunofluorescence, Cell Culture, Two Tailed Test, MANN-WHITNEY, Expressing, Control, Gene Expression, Activation Assay

Journal: Molecular Nutrition & Food Research

Article Title: AMPK‐Dependent Epigenetic Regulation of Metabolism Mediates the Anti‐Cancer Action of Pterostilbene in Hepatocellular Carcinoma

doi: 10.1002/mnfr.70217

Figure Lengend Snippet: APMK‐dependent PTS epigenetic activation of metabolism‐associated genes is mediated by KDM6A demethylase, but not EZH2 methyltransferase or JMJD3 (KDM6B) demethylase. (A) The level of mRNA, as measured by qRT‐PCR, for EZH2 in liver tissues from the control group (choline‐sufficient diet, CSAA), HCC group (CDAA) and CDAA supplemented with PTS (CDAA+PTS). (B) Phosphorylated EZH2 at Thr311 (phospho‐EZH2, which indicates EZH2 activation) and total EZH2 levels as determined by western blot analysis and normalized by total protein load. The chart depicts the ratio of phospho‐EZH2 to total EZH2, as quantified based on band intensity values. (C and D) Occupancy of KDM6A (C) and JMJD3 (D) at the ALDH1L1 , BHMT , and DMGDH promoter regions in wild‐type HepG2 cells treated with 10 µM PTS for 24 hrs and in HepG2 cells pre‐treated with 10 µM of compound C (CC), an AMPK inhibitor, 24 h prior to PTS exposure. The occupancy was measured by chromatin immunoprecipitation (ChIP) followed by qPCR (qChIP) and compared to control—vehicle‐treated cells (ethanol for PTS; DMSO+ethanol for PTS+CC). Results represent mean ± SEM, * p < 0.05. (E) A scheme shows possible players in AMPK‐dependent decrease in histone H3 lysine 27 trimethylation (H3K27me3) in response to PTS. AMPK may act through the activation of KDM6 demethylases or via the inhibition of EZH2 methyltransferase. Created in BioRender. Boycott, C. (2025) https://BioRender.com/y60b739 .

Article Snippet: After blocking the membranes in EveryBlot Blocking buffer, membranes were incubated overnight at 4°C with the primary polyclonal antibody, anti‐AMPKα (1:1000; 5831, Cell Signaling Technology, Danvers, Massachusetts, USA), anti‐phospho‐AMPKα (Thr172) (1:1000; 2531, Cell Signaling Technology), anti‐EZH2 [Ezh2 (D2C9) XP Rabbit mAb, 1:1000, 5246, Cell Signaling Technology], and anti‐phospho‐EZH2 (Thr311) (1:1000; 27888, Cell Signaling Technology).

Techniques: Activation Assay, Quantitative RT-PCR, Control, Western Blot, Chromatin Immunoprecipitation, Inhibition

Journal: Immunobiology

Article Title: Transcription suppression of GABARAP mediated by lncRNA XIST-EZH2 interaction triggers caspase-11-dependent inflammatory injury in ulcerative colitis.

doi: 10.1016/j.imbio.2024.152796

Figure Lengend Snippet: Fig. 1. XIST is highly expressed in DSS-treated mice and is a possible gene correlated with inflammation. A, LncRNAs that can interact with EZH2 predicted using the RNA Inter tool; B, subcellular localization of XIST in cells predicted in the LncATLAS system. C57BL/6N mice were treated with 3 % DSS for 7 d or not. C, XIST expression in the colon tissue of mice examined by RT-qPCR (n = 6); D, body weight of mice in each group (n = 6); E, the length of colon of mice in each group (n = 6); F, DAI of mice in each group (n = 6); G, mucosal injury and inflammatory infiltration in the mouse colon determined by HE staining (n = 6); H, concentrations of inflammatory cytokines TNF-α, IL-1β, and IL-18 in the mouse colon tissue examined using ELISA kits (n = 6); I, protein levels of occludin, ASC, and cleaved caspase-1 in the mouse colon tissue determined by WB analysis (n = 6); J, concentrations of caspase-1 and caspase-11 in the mouse colon tissue determined using ELISA kits (n = 6). Differences were analyzed by the unpaired t test (C, E, H, and J) or two-way ANOVA (D, F, and I). * p < 0.05 vs. the Control group.

Article Snippet: These membranes were then probed with the antibodies of GABARAP (1:1000, GTX31541, GeneTex Inc., San Antonio, TX, USA), occludin (1:1000, GTX114949, GeneTex), ASC (1:1000, ab307560, Abcam Inc., Cambridge, MA, USA), EZH2 (1:2000, NBP2-17087; Novus Biologicals, Littleton, CA, USA), caspase-11 (1:1000, 21741–1-AP, Proteintech Group, Inc, Wuhan, Hubei, China), cleaved caspase-1 (1:1000, #89332, Cell Signaling Technology, Beverly, MA, USA) and β-actin (1:2000, GTX109639, GeneTex) overnight at 4°C.

Techniques: Expressing, Quantitative RT-PCR, Staining, Enzyme-linked Immunosorbent Assay, Control

Journal: Immunobiology

Article Title: Transcription suppression of GABARAP mediated by lncRNA XIST-EZH2 interaction triggers caspase-11-dependent inflammatory injury in ulcerative colitis.

doi: 10.1016/j.imbio.2024.152796

Figure Lengend Snippet: Fig. 4. XIST recruits EZH2 to regulate GABARAP expression. A, genes exhibiting a significant negative correlation with EZH2 in TCGA-COAD samples in the UALCAN system; B, a negative correlation between GABARAP and EZH2 in in normal colon samples in the GEPIA system; C, the existence of H3K27me3 modifications near the GABARAP promoter analyzed using the mouse H3K27me3 ChIP-seq sample in the ENCODE system; D, GABARAP mRNA expression in mouse colonic mucosal epithelial cells (Procell) after different treatments (PBS/DSS + LPS/KD-NC/KD-XIST) examined by RT-qPCR (n = 3); E, binding relationship between XIST and EZH2 in cells examined by RIP assay (n = 3); F-G, binding between EZH2 (F) and H3K27me3 (G) and the GABARAP promoter in cells examined by ChIP assay (n = 3); H, mRNA and protein levels of EZH2 in mice after different treatments (drinking water/DSS/KD-NC/KD-XIST transfection) determined by RT-qPCR and WB analysis, respectively (n = 6); I mRNA and protein levels of EZH2 in mouse colonic mucosal epithelial cells (Procell) after different treatments (PBS/DSS + LPS/KD-NC/KD- XIST) determined by RT-qPCR and WB analysis, respectively (n = 3); J-K, binding between H3K27me3 (J) and EZH2 (K) and the GABARAP promoter in cells after different treatments (PBS/DSS + LPS/KD-NC/KD-XIST) determined by ChIP assays (n = 3); L-M, mRNA (L) and protein (M) levels of GABARAP in cells transfected with KD-NC/KD-EZH2 determined by RT-qPCR or WB analysis (n = 3); N, binding between H3K27me3 and the GABARAP promoter in cells transfected with KD-NC/ KD-EZH2 examined by ChIP assay (n = 3). Differences were analyzed by the unpaired t test (E, F, G, L, M, and N) or one-way ANOVA (D, H, I, J, and K). * p < 0.05 vs. the IgG/Control/Normal group; # p < 0.05 vs. the KD-NC group.

Article Snippet: These membranes were then probed with the antibodies of GABARAP (1:1000, GTX31541, GeneTex Inc., San Antonio, TX, USA), occludin (1:1000, GTX114949, GeneTex), ASC (1:1000, ab307560, Abcam Inc., Cambridge, MA, USA), EZH2 (1:2000, NBP2-17087; Novus Biologicals, Littleton, CA, USA), caspase-11 (1:1000, 21741–1-AP, Proteintech Group, Inc, Wuhan, Hubei, China), cleaved caspase-1 (1:1000, #89332, Cell Signaling Technology, Beverly, MA, USA) and β-actin (1:2000, GTX109639, GeneTex) overnight at 4°C.

Techniques: Expressing, ChIP-sequencing, Quantitative RT-PCR, Binding Assay, Transfection, Control

Journal: Immunobiology

Article Title: Transcription suppression of GABARAP mediated by lncRNA XIST-EZH2 interaction triggers caspase-11-dependent inflammatory injury in ulcerative colitis.

doi: 10.1016/j.imbio.2024.152796

Figure Lengend Snippet: Fig. 5. Upregulation of EZH2 or knockdown of GABARAP aggravates inflammatory injury in mice with UC. A, GABARAP mRNA expression in the colon tissue of mice following different treatments (Drinking water/3% DSS/KD-NC/KD-XIST) examined by RT-qPCR (n = 6). UC mice transfected with KD-XIST were further administered KD-GABARAP/KD-NC or oe-EZH2/oe-NC. B, mRNA expression of EZH2 and GABARAP in the mouse colon tissues examined by RT-qPCR (n = 6); C, copies of viral particles in mouse colon tissues determined by qPCR analysis (n = 6); D, protein levels of occludin, ASC, and cleaved caspase-1 in the mouse colon tissue determined by WB analysis (n = 6); E, concentrations of caspase-1 and caspase-11 in the mouse colon tissue determined using ELISA kits (n = 6); F, body weight of mice in each group (n = 6); G, the length of colon of mice in each group (n = 6); H, DAI of mice in each group (n = 6); I, mucosal injury and inflammatory infiltration in the mouse colon determined by HE staining (n = 6); J, concentrations of TNF-α, IL-1β, and IL-18 in the mouse colon tissue examined using ELISA kits (n = 6). Differences were analyzed by the one-way (A, C, E, G, and J) or two-way (B, D, F, and H) ANOVA. * p < 0.05 vs. the KD-XIST + KD-NC group; & p < 0.05 vs. the KD-XIST + oe-NC group; @ p < 0.05 vs. the Control group; # p < 0.05 vs. the KD-NC group.

Article Snippet: These membranes were then probed with the antibodies of GABARAP (1:1000, GTX31541, GeneTex Inc., San Antonio, TX, USA), occludin (1:1000, GTX114949, GeneTex), ASC (1:1000, ab307560, Abcam Inc., Cambridge, MA, USA), EZH2 (1:2000, NBP2-17087; Novus Biologicals, Littleton, CA, USA), caspase-11 (1:1000, 21741–1-AP, Proteintech Group, Inc, Wuhan, Hubei, China), cleaved caspase-1 (1:1000, #89332, Cell Signaling Technology, Beverly, MA, USA) and β-actin (1:2000, GTX109639, GeneTex) overnight at 4°C.

Techniques: Knockdown, Expressing, Quantitative RT-PCR, Transfection, Enzyme-linked Immunosorbent Assay, Staining, Control

Journal: Immunobiology

Article Title: Transcription suppression of GABARAP mediated by lncRNA XIST-EZH2 interaction triggers caspase-11-dependent inflammatory injury in ulcerative colitis.

doi: 10.1016/j.imbio.2024.152796

Figure Lengend Snippet: Fig. 6. Upregulation of EZH2 or knockdown of GABARAP increases inflammatory injury in mouse colonic mucosal epithelial cells. Mouse colonic mucosal epithelial cells (Procell) were transfected with KD-NC/KD-XIST and the additional KD-GABARAP/KD-NC or oe-EZH2/oe-NC, followed by DSS and LPS challenge. A, GABARAP and EZH2 mRNA expression in cells examined by RT-qPCR (n = 3); B, viability of cells examined by MTT assay (n = 3); C, apoptosis of cells examined by TUNEL assay (n = 3); D-F, concentrations of TNF-α (D), IL-1β (E), and IL-18 (F) in cells examined using ELISA kits (n = 3); G, concentrations of caspase-1 and caspase-11 in cells examined using ELISA kits (n = 3); H, protein level of cleaved-caspase-1 in cells determined by WB analysis (n = 3). Differences were analyzed by the one-way (B-H) or two-way (A) ANOVA. * p < 0.05 vs. the KD-XIST + KD-NC group; # p < 0.05 vs. the KD-XIST + oe-NC group.

Article Snippet: These membranes were then probed with the antibodies of GABARAP (1:1000, GTX31541, GeneTex Inc., San Antonio, TX, USA), occludin (1:1000, GTX114949, GeneTex), ASC (1:1000, ab307560, Abcam Inc., Cambridge, MA, USA), EZH2 (1:2000, NBP2-17087; Novus Biologicals, Littleton, CA, USA), caspase-11 (1:1000, 21741–1-AP, Proteintech Group, Inc, Wuhan, Hubei, China), cleaved caspase-1 (1:1000, #89332, Cell Signaling Technology, Beverly, MA, USA) and β-actin (1:2000, GTX109639, GeneTex) overnight at 4°C.

Techniques: Knockdown, Transfection, Expressing, Quantitative RT-PCR, MTT Assay, TUNEL Assay, Enzyme-linked Immunosorbent Assay

Journal: Immunobiology

Article Title: Transcription suppression of GABARAP mediated by lncRNA XIST-EZH2 interaction triggers caspase-11-dependent inflammatory injury in ulcerative colitis.

doi: 10.1016/j.imbio.2024.152796

Figure Lengend Snippet: Fig. 8. Graphical abstract. LncRNA XIST is upregulated in UC models. It recruits EZH2, which suppresses GABARAP transcription by binding to its promoter, consequently activating the caspase-11-dependent inflammatory cascade and UC development.

Article Snippet: These membranes were then probed with the antibodies of GABARAP (1:1000, GTX31541, GeneTex Inc., San Antonio, TX, USA), occludin (1:1000, GTX114949, GeneTex), ASC (1:1000, ab307560, Abcam Inc., Cambridge, MA, USA), EZH2 (1:2000, NBP2-17087; Novus Biologicals, Littleton, CA, USA), caspase-11 (1:1000, 21741–1-AP, Proteintech Group, Inc, Wuhan, Hubei, China), cleaved caspase-1 (1:1000, #89332, Cell Signaling Technology, Beverly, MA, USA) and β-actin (1:2000, GTX109639, GeneTex) overnight at 4°C.

Techniques: Binding Assay

Journal: Oncology Reports

Article Title: MicroRNA-218 promotes cisplatin resistance in oral cancer via the PPP2R5A/Wnt signaling pathway

doi: 10.3892/or.2017.5899

Figure Lengend Snippet: Suppression of miR-218 promotes cisplatin sensitivity in resistant oral cancer cells. (A) The tumor cells were transfected with anti-miR-218 or its control (anti-NC), and total RNA was extracted for qRT-PCR. (B and C) UM1 and Cal27 cells transfected with anti-miR-218 or its control were treated with cisplatin (2.5 µg/ml). The cell viability was assayed using the CCK-8 method. (D and E) Apoptosis was quantitated by flow cytometry. (F) The protein expression levels of chemoresistance-related proteins, including EZH2, ABCG2, MRP1, P-glycoprotein and TopoIIβ, were determined by western blotting. β-tubulin served as a loading control. (G) The expression levels of the chemoresistance-related proteins were quantitated. Data represent the mean ± SD of 3 independent experiments; *P<0.05, **P<0.01.

Article Snippet: The antibody against EZH2 was purchased from OriGene (Rockville, MD, USA).

Techniques: Transfection, Control, Quantitative RT-PCR, CCK-8 Assay, Flow Cytometry, Expressing, Western Blot