Journal: Cell Communication and Signaling : CCS

Article Title: Reprogramming the epigenetic profile improves the B regulatory cell function of patients with recurrent pregnancy loss

doi: 10.1186/s12964-026-02669-7

Figure Lengend Snippet: DNMT1 ubiquitination status and TRIM28-Pol II correlations at the IL10 promoter in Bregs. A – C Ubiquitination levels of DNMT1 at the IL10 promoter in Bregs. ( D ) TRIM28 occupancy at the IL10 promoter in Bregs. E – F Correlation between TRIM28 occupancy and DNMT1 levels. G – H Correlation between DNMT1 occupancy and RNA polymerase II (Pol II) recruitment. I – L B cells transfected with plasmids encoding wild-type (DNMT1p, TRIM28p) or mutant (DNMT1mup, TRIM28mup) proteins. I Quantification of His-DNMT1 by ELISA. J – L Ubiquitination ( J ), K48-linked polyubiquitin chains (K), and proteasomal recruitment ( L ) in His-antibody-precipitated complexes (cross-ELISA). Data are mean ± SD; individual data points represent biological replicates. Statistics: One-way ANOVA with Tukey’s post hoc test ( A – D , I – L ); Pearson’s correlation coefficient ( E – H ). Significance: ** p < 0.01; *** p < 0.001; **** p < 0.0001. Plasmid notation: “p” denotes wild-type plasmid; “mup” denotes catalytically inactive mutant (e.g., DNMT1mup: C1246Y mutation)

Article Snippet: TRIM28 siRNA: Two independent sequences (Santa Cruz, sc-45905: 5′-GCAUGGAACUUCGAGAUCA-3′; sc-45906: 5′-CCUUGAAGAUGU CCUGAAA-3′) + scrambled control (50 nM, Lipofectamine RNAiMAX).

Techniques: Ubiquitin Proteomics, Transfection, Mutagenesis, Enzyme-linked Immunosorbent Assay, Plasmid Preparation

Journal: Cell Communication and Signaling : CCS

Article Title: Reprogramming the epigenetic profile improves the B regulatory cell function of patients with recurrent pregnancy loss

doi: 10.1186/s12964-026-02669-7

Figure Lengend Snippet: SAHA restores the immunosuppressive capacity of RPL Bregs. A Global TRIM28 protein levels in Bregs. B – C Correlation between TRIM28 expression and the immunosuppressive function of Bregs. D SAHA treatment induces TRIM28 upregulation in RPL Bregs. I – M Levels of indicated molecules at the IL10 promoter region in RPL Bregs. N Teff proliferation rate. O Quantification of proliferating Teff cells. P Effects of TRIM28 knockdown (kd) via RNA interference (RNAi). Q - S Bars show the levels of indicated cytokines in culture supernatant. Individual data points represent independent samples; bar graphs show mean ± SD. Statistical analysis: Mann–Whitney U test (A); Pearson correlation coefficient (B–C); one-way ANOVA with Tukey’s post hoc test (I–M, O, P). Significance: * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001. Abbreviations: IgG, isotype control antibody for ChIP experiments; kd, TRIM28 knockdown; cRNAi, control RNAi (scrambled sequence)

Article Snippet: TRIM28 siRNA: Two independent sequences (Santa Cruz, sc-45905: 5′-GCAUGGAACUUCGAGAUCA-3′; sc-45906: 5′-CCUUGAAGAUGU CCUGAAA-3′) + scrambled control (50 nM, Lipofectamine RNAiMAX).

Techniques: Expressing, Knockdown, MANN-WHITNEY, Control, Sequencing

Journal: Cell Communication and Signaling : CCS

Article Title: Reprogramming the epigenetic profile improves the B regulatory cell function of patients with recurrent pregnancy loss

doi: 10.1186/s12964-026-02669-7

Figure Lengend Snippet: SAHA Rescues Pregnancy Outcomes in RPL Mice via TRIM28-DNMT1-IL10 Axis. A Representative uterine horns (Day 12.5 p.c.): black arrows = resorbed embryos; red arrows = healthy embryos. B Fetal resorption rates. C – D Decidual Breg TRIM28 ( C ) and DNMT1 ( D ) mRNA levels (RT-qPCR). E Decidual Breg Il10 promoter methylation (bisulfite pyrosequencing). F Decidual Breg IL-10 secretion (ELISA). G - H Decidual Breg suppressive effects (Teff co-culture). Data of bar graphs are presented as mean ± SD. Each dot in bars presents one sample. Statistics: One-way ANOVA + Tukey’s test. ** p < 0.01, *** p < 0.001, **** p < 0.0001

Article Snippet: TRIM28 siRNA: Two independent sequences (Santa Cruz, sc-45905: 5′-GCAUGGAACUUCGAGAUCA-3′; sc-45906: 5′-CCUUGAAGAUGU CCUGAAA-3′) + scrambled control (50 nM, Lipofectamine RNAiMAX).

Techniques: Quantitative RT-PCR, Methylation, Enzyme-linked Immunosorbent Assay, Co-Culture Assay

Journal: bioRxiv

Article Title: A non-canonical EZH2/TRIM28 epigenetic axis drives heparan sulfate remodeling and melanoma metastasis

doi: 10.64898/2026.01.21.700969

Figure Lengend Snippet: (A) Immunoprecipitation of EZH2 in A375 wild-type cells and LC-MS/MS proteomics reveals canonical PRC2 proteins and other known EZH2 interactors (table inset). STRING-DB analysis of top hits reveals the EZH2 interactome (right). (B) Endogenous TRIM28 in A375 cells was immunoprecipitated and immunoblotted to detect EZH2. (C) Western blot validating shRNA-mediated knockdown of TRIM28 in A375 cells (shTRIM28). (D) qPCR analysis revealing that SULF1 mRNA expression is decreased upon stable knockdown of TRIM28 . (E) Number of DEGs in the RNA-seq data (FDR p-value ≤ 0.01, |FC| ≥ 2). The number of significantly up- and down-regulated genes for shEZH2 and shTRIM28 is included in the inset table. (F) Venn diagram showing overlap of up- and down-regulated genes in shEZH2 and shTRIM28 RNA-seq datasets (FDR p-value ≤ 0.01, |FC| ≥ 2). (G) Pathway enrichment analysis of overlapping DEGs between shEZH2 and shTRIM28 populations (FDR p-value ≤ 0.01, |FC| ≥ 2). (H) Heatmap of expression z-scores for a subset of co-activated DEGs shared between shEZH2 and shTRIM28 cells relative to shCTRL controls. Red represents higher expression and blue indicates lower expression. Data are presented as mean ± SD (n = 3 independent biological replicates, n = 4 independent biological replicates for RNA-seq experiments), ***p<0.001, **p<0.01, *p<0.05 by two-sided t-test.

Article Snippet: Membranes were probed with primary antibodies against EZH2 (Cell Signaling Technology, #5246; 1:1000), EZH2 (Active Motif, #39076, 1:200), TRIM28 (Cell Signaling Technology, #85322; 1:1000), SUZ12 (Cell Signaling Technology, #3737; 1:1000), EED (Cell Signaling Technology, #85322; 1:1000), H3K27me3 (Cell Signaling Technology, #9733; 1:1000), Histone H3 (Cell Signaling Technology, #3638; 1:1000), or β-actin (Cell Signaling Technology, #3700; 1:5000) at 4°C overnight.

Techniques: Immunoprecipitation, Liquid Chromatography with Mass Spectroscopy, Western Blot, shRNA, Knockdown, Expressing, RNA Sequencing

Journal: bioRxiv

Article Title: A non-canonical EZH2/TRIM28 epigenetic axis drives heparan sulfate remodeling and melanoma metastasis

doi: 10.64898/2026.01.21.700969

Figure Lengend Snippet: Profile plots showing genome-wide localization of (A) TRIM28, (B) EED, and (C) H3K27me3 relative to annotated gene bodies in A375 wild-type cells (hg38 genome, TSS: transcription start site, TES: transcription end site). Genome browser tracks showing TRIM28, EED, and H3K27me3 ChIP-seq signal at the SULF2 (D) and SULF1 (E) loci. (F) Venn diagram showing overlap between genes positively regulated by EZH2 and TRIM28 (RNA-seq) and genes bound by TRIM28 (ChIP-seq). (G) ChIP–qPCR assessing TRIM28-dependent enrichment of EZH2 at the SULF1 locus in control and TRIM28-depleted A375 melanoma cells. Data are presented as mean ± SD (n = 3 independent biological replicates), ***p<0.001, **p<0.01, *p<0.05 by two-sided t-test.

Article Snippet: Membranes were probed with primary antibodies against EZH2 (Cell Signaling Technology, #5246; 1:1000), EZH2 (Active Motif, #39076, 1:200), TRIM28 (Cell Signaling Technology, #85322; 1:1000), SUZ12 (Cell Signaling Technology, #3737; 1:1000), EED (Cell Signaling Technology, #85322; 1:1000), H3K27me3 (Cell Signaling Technology, #9733; 1:1000), Histone H3 (Cell Signaling Technology, #3638; 1:1000), or β-actin (Cell Signaling Technology, #3700; 1:5000) at 4°C overnight.

Techniques: Genome Wide, ChIP-sequencing, RNA Sequencing, ChIP-qPCR, Control

Journal: bioRxiv

Article Title: A non-canonical EZH2/TRIM28 epigenetic axis drives heparan sulfate remodeling and melanoma metastasis

doi: 10.64898/2026.01.21.700969

Figure Lengend Snippet: (A) Study design of an A375 melanoma xenograft model in NSG mice to assess primary tumor growth and metastatic dissemination of SULF1-deficient cells. (B) Total primary tumor volume measured longitudinally (mm³). Mice were euthanized upon reaching a humane endpoint defined as total tumor burden ≥ 2000 mm³, followed by excision of primary tumors and collection of organs for metastatic analysis (n = 10 mice per group; data are presented as mean ± SEM and represent total tumor volume per mouse, p = 0.0022). (C) Contingency analysis showing the number of mice with detectable metastases, as assessed by ex vivo bioluminescence imaging, in any of the indicated organs (lungs, liver, brain, bone, or lymph nodes) (n = 10 mice per group). (D) Contingency plot depicting the number of mice with observed metastases in the lung. Inset: representative image of a shCTRL-injected mouse lung showing luminescence signal from A375 cells is included as an inset. (E-F) Quantification of tumor necrosis expressed as necrotic area (red) relative to total tumor area, determined by H&E staining and QuPath and confirmed by a pathologist (n = 10 mice per group, data represent an average of total tumor necrotic area per mouse). (G) RNA-seq data from the TCGA-SKCM cohort comparing EZH2 , TRIM28 , and SULF1 expression in primary melanoma tumors (n = 103) versus metastatic melanoma tumors (n = 369). Data are presented as mean ± SEM, ***p<0.001, **p<0.01, *p<0.05, unless otherwise stated above. Statistical significance was determined using two-sided tests as indicated (tumor growth: mixed-effects model for repeated measures; metastasis incidence: chi-squared test; tumor necrosis: two-sided t-test).

Article Snippet: Membranes were probed with primary antibodies against EZH2 (Cell Signaling Technology, #5246; 1:1000), EZH2 (Active Motif, #39076, 1:200), TRIM28 (Cell Signaling Technology, #85322; 1:1000), SUZ12 (Cell Signaling Technology, #3737; 1:1000), EED (Cell Signaling Technology, #85322; 1:1000), H3K27me3 (Cell Signaling Technology, #9733; 1:1000), Histone H3 (Cell Signaling Technology, #3638; 1:1000), or β-actin (Cell Signaling Technology, #3700; 1:5000) at 4°C overnight.

Techniques: Ex Vivo, Imaging, Injection, Staining, RNA Sequencing, Expressing