Journal: bioRxiv

Article Title: A Single-cell and Spatially Resolved Cell Atlas of Human Esophageal Squamous Cell Carcinoma

doi: 10.1101/2025.06.01.657221

Figure Lengend Snippet: UMAP plots of total fibroblasts labeled by groups ( A ) and samples ( B ). C. Bar plots showing fibroblast subcluster proportions across eight samples. D. GO terms of top 100 specifically expressed genes for each fibroblast subpopulation. E. qPCR and WB analysis of TWIST1 expression levels in BJ cells transfected with TWIST1 overexpression lentivirus after 10 days. F. qPCR and WB analysis of TWIST1 expression levels in BJ cells transfected with si- TWIST1 after 48 h. qPCR analysis of genes POSTN , COL1A1 , COL3A1 , INHBA , COL5A2 after TWIST1 overexpression ( G ) or knockdown ( H ) in BJ cells. *, P < 0.05; **, P < 0.01; ***, P < 0.001. Statistical significance was calculated by Student’s t -test, mean ± SD.

Article Snippet: The following primary antibodies were used in this study: anti-p63 (Proteintech, 12143-1-AP), anti-COL17A1 (Abcam, ab184996), anti-Cytokeratin 15 (Proteintech, 10137-1-AP), anti-EGFR (Proteintech, 18986-1-AP), anti-GAPDH (Proteintech, 10494-1-AP), anti-SMAD2 (Proteintech, 12570-1-AP), anti-pSMAD2 (Abcam, 280888), anti-Activin A (Proteintech, 60352-1-lg), anti-TWIST1 (Proteintech, 25461-1-AP), and anti-Periostin (Abcam, ab215199).

Techniques: Labeling, Expressing, Transfection, Over Expression, Knockdown

Journal: bioRxiv

Article Title: A Single-cell and Spatially Resolved Cell Atlas of Human Esophageal Squamous Cell Carcinoma

doi: 10.1101/2025.06.01.657221

Figure Lengend Snippet: A. UMAP plots showing total fibroblasts labeled by seven fibroblast subpopulations. B. Heatmap showing the mRNA expression of the top five marker genes for seven fibroblast subpopulations. C. Comparison of the tissue preference distribution among seven fibroblast subpopulations in paired samples (n = 3). The Ro/e value indicates tissue preference, with Ro/e > 1 suggesting enrichment in tumor tissues and Ro/e < 1 indicating preference for adjacent notumor tissues. D. Box plots showing the enrichment scores of POSTN + fibroblasts between tumor (n = 95) and normal tissues (n = 13) in ESCC dataset from TCGA database. E. Survival curve of POSTN + fibroblast score in 75 ESCC samples. F. UMAP plots of cell trajectory analysis labeled by fibroblast subpopulations and pseudo-time. G. Trajectory analysis of fibroblasts using scVelo. Heatmap showing the AUC scores ( H ) and mRNA expression ( I ) of the top four TF regulons for each fibroblast subpopulation. J. Feature plots of TF including TWIST1 , SOX4 , TWIST2 , PRDM1 in fibroblasts. K. ROC curve analysis showing the specificity of TF TWIST1 , TWIST2 , SOX4 , and PRDM1 in POSTN + fibroblasts. L. Regulatory network of TF TWIST1 and its selected target genes. M. Violin plots showing the mRNA expression of INHBA , POSTN , COL1A1 , COL3A1 , COL5A2 among fibroblast subpopulations. P < 0.05 (two-sided log-rank test) is considered as a statistically significant difference. ROC, receiver operating characteristic curve.

Article Snippet: The following primary antibodies were used in this study: anti-p63 (Proteintech, 12143-1-AP), anti-COL17A1 (Abcam, ab184996), anti-Cytokeratin 15 (Proteintech, 10137-1-AP), anti-EGFR (Proteintech, 18986-1-AP), anti-GAPDH (Proteintech, 10494-1-AP), anti-SMAD2 (Proteintech, 12570-1-AP), anti-pSMAD2 (Abcam, 280888), anti-Activin A (Proteintech, 60352-1-lg), anti-TWIST1 (Proteintech, 25461-1-AP), and anti-Periostin (Abcam, ab215199).

Techniques: Labeling, Expressing, Marker, Comparison

Journal: Biochemistry and Biophysics Reports

Article Title: High expression of THY1 is a prognostic marker for gastric Cancer: Deciphering its transcriptional regulation as a component of the Epithelial–mesenchymal transition

doi: 10.1016/j.bbrep.2025.102050

Figure Lengend Snippet: Conservation of PRRX1, TWIST1, and SNAI2 binding sites in THY1 regulatory regions. The figure shows the location and conservation of transcription factor binding sites within the THY1 regulatory regions for PRRX1 (A) , TWIST1 (B) , and SNAI2 (C) . At the top of each panel, a schematic representation of the THY1 gene is shown, where +1 marks the transcription start site, and the 3-kb upstream region is defined as the promoter. The first intron begins after the end of exon 1 (+60). Binding sites are labeled with their respective names, and their positions relative to the transcription start site are indicated. Below each schematic, alignment tables show the conservation of binding sites across the evaluated species. Conserved nucleotides are highlighted in gray, whereas nonconserved nucleotides are highlighted in white. The species names are listed on the left, and the nucleotide positions relative to the human sequence are shown above each alignment. The schematics of the gene structure, regulatory regions, and binding site positions are illustrative and not drawn to scale.

Article Snippet: Briefly, chromatin from the HGC-27, AGS, and KATO III cell lines—which was previously prepared and digested with micrococcal nuclease—was incubated with 2 μg of either a TWIST1 antibody (sc-81417, Santa Cruz Biotechnology, TX, USA), a PRRX1 antibody (sc-293386, Santa Cruz Biotechnology, TX, USA), a SNAI2 antibody (#9585, Cell Signaling Technology, MA, USA) or a negative immunoprecipitation control consisting of a normal anti-IgG rabbit antibody (#2729, Cell Signaling Technology, MA, USA).

Techniques: Binding Assay, Labeling, Sequencing

Journal: Biochemistry and Biophysics Reports

Article Title: High expression of THY1 is a prognostic marker for gastric Cancer: Deciphering its transcriptional regulation as a component of the Epithelial–mesenchymal transition

doi: 10.1016/j.bbrep.2025.102050

Figure Lengend Snippet: Chromatin immunoprecipitation analysis of PRRX1, TWIST1 and SNAI2 binding sites in THY1 regulatory regions across gastric cancer cell lines. The bar graphs represent the bound/input (%) values for each binding site evaluated. The y-axis indicates the percentage of DNA recovered (bound) relative to the input DNA, and the x-axis shows the cell lines analyzed: HGC-27 ( THY1 high ), Kato III, and AGS (both THY1 low ). The title of each panel specifies the transcription factor, the binding site name, and its position within the THY1 regulatory regions. (A – C) correspond to PRRX1 binding sites, (D – H) correspond to TWIST1 binding sites, and (I – L) correspond to SNAI2 binding sites. The error bars represent the standard deviations of three replicates. Statistical significance was determined using pairwise Mann‒Whitney U tests with p value correction. For each bound/input (%) analysis, the bound/input (%) value of the control IgG was subtracted from the value of each cell line. The data are shown as the means ± standard deviations. ns: not significant, ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, and ∗∗∗∗p < 0.0001.

Article Snippet: Briefly, chromatin from the HGC-27, AGS, and KATO III cell lines—which was previously prepared and digested with micrococcal nuclease—was incubated with 2 μg of either a TWIST1 antibody (sc-81417, Santa Cruz Biotechnology, TX, USA), a PRRX1 antibody (sc-293386, Santa Cruz Biotechnology, TX, USA), a SNAI2 antibody (#9585, Cell Signaling Technology, MA, USA) or a negative immunoprecipitation control consisting of a normal anti-IgG rabbit antibody (#2729, Cell Signaling Technology, MA, USA).

Techniques: Chromatin Immunoprecipitation, Binding Assay, Control