Journal: Cell Reports Medicine

Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression

doi: 10.1016/j.xcrm.2026.102650

Figure Lengend Snippet: Spatial whole-transcriptome profiling of ESPL and ESCC samples (A) Workflow of DSP experimental process. (B) The UMAP plot displaying the clustering results of AOIs from different compartments at multiple stages of ESCC. (C) The heatmap displaying the expression levels of AOI characteristic markers RNA in different compartments. (D) The boxplots showing the expression levels of marker genes in five different compartments at different stages of ESCC. Box plot shows the median and interquartile range, whiskers extend to 1.5 × IQR. DSP, digital spatial profiling; UMAP, uniform manifold approximation and projection; AOI, area of interest; EP, epithelial-cell-enriched; MC, macrophage-cell-enriched; NC, neutrophil-cell-enriched; ST, stroma-enriched; LS, lymphoid structure; CAFs, cancer-associated fibroblasts; ESPL, esophageal squamous precancerous lesion; non-mESCC, non-metastasis esophageal squamous cell carcinoma; mESCC, metastasis esophageal squamous cell carcinoma; mLN, lymph node metastasis tissues.

Article Snippet: KYSE450 human ESCC cell line , Servicebio , STCC11902P.

Techniques: Expressing, Marker

Journal: Cell Reports Medicine

Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression

doi: 10.1016/j.xcrm.2026.102650

Figure Lengend Snippet: Changes in gene expression patterns in the EP compartment during the initiation of ESCC (A) Volcano plot showed significant DEGs during the formation of ESPL. (B) Pathway enrichment analysis of DEGs in ESPL and normal stages. (C) Changes in gene expression across epidermis development and keratinocyte differentiation pathways during ESPL formation. (D) Interaction plot of ESPL-formation-related genes. Each circle represents a protein, and the interactions are connected by solid lines. The types of interactions were shown on the right side of the figure. (E) The four-quadrant plot illustrates the significant differences in gene expression patterns among four distinct types during the initiation of ESCC. (F) The boxplot shows the expression levels of the presented genes across the four patterns during ESCC initiation. Pattern 1 to 4 were tagged in blue, pink, yellow, and purple, respectively. Box plot shows the interquartile, whiskers extend to1.5 × IQR. (G) Pathway enrichment results for genes in the four patterns. (H) The line graph depicts changes in the signature scores of the indicated pathways during the initiation and development of ESCC. DEGs, differentially expressed genes.

Article Snippet: KYSE450 human ESCC cell line , Servicebio , STCC11902P.

Techniques: Gene Expression, Expressing

Journal: Cell Reports Medicine

Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression

doi: 10.1016/j.xcrm.2026.102650

Figure Lengend Snippet: Spatial transcriptome analysis of the TME during ESCC initiation process (A) Quantitative analysis of immune cells in non-EP compartments during the initiation process of ESCC using TME_consense algorithm. (B) Comparison of B, plasma, CD4 + T, and CD8 + T cells during the initiation process of ESCC. (C) Analyze the immune cell changes in non-EP compartments during the initiation process of ESCC using SpatialDecon algorithm. (D) mIF staining of CD20, CD8, and CD4 on tumor tissues in ESCC initiation stages. Scale bar, 200 μm. (E) Comparison of the percentages of CD20-, CD8-, and CD4-positive cells across the ESCC initiation stages. (F) Pathway enrichment analysis of significantly differential expression genes in non-EP compartments during the initial stage of ESCC. (G) The heatmap shows the differential genes in the MC and NC compartments during the initial stage of ESCC. (H) Comparison of the proportion of tumor-associated macrophage and neutrophile cells across the ESCC development. (I) The heatmap shows the differential genes in TLS compartments during the initial stage of ESCC. (J) mIF staining on TLS compartment of ESCC initiation stage. Scale bar, 100 μm. (K) Comparison of the percentages of APOBEC3A-positive cells between ESPL and non-mESCC stages in the TLS. NE, normal epithelia; ESCC, esophageal squamous cell carcinoma; mIF, multiplex immunofluorescence; MC, macrophage-cell-enriched compartment; NC, neutrophil-cell-enriched compartment; TLS, tertiary lymphoid structures. Box plots show the median and interquartile range, whiskers extend to 1.5×IQR. ∗p < 0.05 , ∗∗ p < 0.01,∗∗∗ p < 0.001, p values were calculated using a two-sided Wilcoxon rank-sum test.

Article Snippet: KYSE450 human ESCC cell line , Servicebio , STCC11902P.

Techniques: Comparison, Clinical Proteomics, Staining, Quantitative Proteomics, Multiplex Assay, Immunofluorescence

Journal: Cell Reports Medicine

Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression

doi: 10.1016/j.xcrm.2026.102650

Figure Lengend Snippet: Characteristic changes in transcription patterns during the progression of ESCC (A) The volcano plot shows significant differences in genes between the early (ESPL and non-mESCC) and advanced (mESCC and mLN) stages of ESCC. (B) Pathway enrichment analysis of differentially expressed genes in the early and advanced stages of ESCC. (C) The gene expression levels associated with significantly enriched pathways throughout the occurrence and development of ESCC. (D) mIF staining of CCND1, LAMB1, and IL-18 on ESCC tissues. Scale bar, 200 μm. (E) Comparison of the percentages of CCND1, LAMB1, and IL-18-positive cells on ESCC tissues. Box plots show the median and interquartile range, whiskers extend to 1.5 × IQR. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, p values were calculated using a two-sided Wilcoxon rank-sum test. (F) The heatmap of gradient-changed DEGs based on pseudotime and ESCC progression of EP.

Article Snippet: KYSE450 human ESCC cell line , Servicebio , STCC11902P.

Techniques: Gene Expression, Staining, Comparison

Journal: Cell Reports Medicine

Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression

doi: 10.1016/j.xcrm.2026.102650

Figure Lengend Snippet: OGT promotes ESCC progression through regulating proliferation, migration, invasion, and apoptosis in vitro and in vivo (A) Representative images of immunohistochemical staining for OGT in cancer and adjacent tissues, magnified at 200× and 400×; scale bars, 100 μm. (B) Paired comparison of OGT IHC scores in tumor and peritumor tissues. p value was calculated using a two-sided Wilcoxon signed-rank test (paired samples, n = 76). (C) Representative WB images of OGT and O-GlcNAc level in all transient transfection groups, including knockdown in KYSE30 and KYSE450 (transfected with siNC, si OGT #1, or si OGT #2) and overexpress in KYSE150 and KYSE410 (transfected with oeVector, oe OGT , or oe OGT and treated with OSMI-1). Images are representative of three independent experiments ( n = 3). (D) OGT and O-GlcNAc level in lentiviral-mediated knockdown KYSE450 and overexpress KYSE150. Representative protein images of three independent experiments were shown ( n = 3). (E and F) Representative images and quantification of plate clone formation assay of lentiviral-mediated knockdown KYSE450 and overexpress KYSE150 cell lines. Data are mean ± SD from three independent experiments ( n = 3). p values were calculated using one-way ANOVA. (G) Cell proliferation measured by the CCK8 assay and relative cell proliferation quantified by OD value at 450 nm of KYSE30, KYSE450, KYSE150, and KYSE410 cell lines. Data are presented as mean ± SD from three independent experiments ( n = 3). p values were calculated using two-way ANOVA with Tukey's multiple-comparisons test. (H) Representative images of cell migration and invasion assays in the KYSE30, KYSE450, KYSE150, and KYSE410 cell lines ( n = 3). Scale bars, 200 μm. (I) Stably transfected shNC/sh OGT KYSE450 cell subcutaneously injected into nude mice. Representative image of xenograft tumors and tumor volume from day 5 to day 30. Data are presented as mean ± SD, n = 5 mice per group. p values were calculated using two-way repeated-measures ANOVA with Sidak's multiple-comparisons test. (J) Bioluminescence imaging of lung metastatic foci at the 7th week in a lung metastasis model. Luciferase activity is measured in photons per cm2 per second per steradian (p/s/cm2/sr). (K) Representative images and quantitative analysis of metastasis nodules on the lung surface. Arrowheads denote the metastasis nodules on the lung surface. (L) Representative images of HE staining of lung metastasis and quantitative analysis of lung metastasis area. Arrowheads denote the metastasis nodules. Scale bars, 200 μm. (J–L) Data are presented as mean ± SD, n = 5 mice per group. p values were calculated using a two-sided Wilcoxon rank-sum test. (M) The results of enriched pathways affected by OGT expression detected across different omics. In the RNA-seq dataset, siOGT cells were defined as the OGT low group, while siNC cells were defined as the OGT-high group. In both the proteomic and glycoproteomic datasets, oeVector cells were defined as the OGT-low group, and oeOGT cells were defined as the OGT-high group. Pathways activated in the OGT-high group are marked in green, while pathways inhibited are marked in red. (N) Comparison of apoptosis rate between KYSE450 siNC and si OGT groups. Data are presented as mean ± SD, n = 3 per group. p values were calculated using unpaired Student's t test. (O) Flow cytometry analysis of cell cycle distribution of KYSE450 cells across siNC and si OGT . ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001. NC, negative control group.

Article Snippet: KYSE450 human ESCC cell line , Servicebio , STCC11902P.

Techniques: Migration, In Vitro, In Vivo, Immunohistochemical staining, Staining, Comparison, Transfection, Knockdown, Tube Formation Assay, CCK-8 Assay, Stable Transfection, Injection, Imaging, Luciferase, Activity Assay, Expressing, RNA Sequencing, Flow Cytometry, Negative Control

Journal: Cell Reports Medicine

Article Title: Spatial omics study reveals molecular-cellular dynamics of tumor ecosystem in esophageal squamous-cell carcinoma initiation and progression

doi: 10.1016/j.xcrm.2026.102650

Figure Lengend Snippet: Changes in TME during the progression of ESCC (A) Abundance of 17 cells estimated by SpatialDecon algorithm in non-EP compartments between the early (ESPL and non-mESCC) and advanced stages (mESCC and mLN) of ESCC. (B) Comparison of proportion of presented cells between the early and advanced stages of ESCC. Box plot shows the median and interquartile range, whiskers extend to 1.5 × IQR. p values were calculated using two-sided Wilcoxon rank-sum test. ∗ p < 0.05, ∗∗∗ p < 0.001, ∗∗∗∗ p < 0.0001. (C) Volcano plot showing the DEGs between early and advanced stages in ST compartment. (D) Volcano plot showing the DEGs between early and advanced stages in MC compartment. (E) Volcano plot showing the DEGs between early and advanced stages in NC compartment. (F) Cell-cell interactions based on significant ligand-receptor pairs in advanced stages of ESCC. (G) Interaction relationships of the ACTIVIN, CHEMERIN, and PERIOSTIN pathways among compartments in advanced ESCC. (H) Cell-cell interactions between ST compartments and other compartments via the ACTIVIN, CHEMERIN, and PERIOSTIN pathways during ESCC initiation and progression. (I) The four-quadrant diagram showed the significant differences in gene expression patterns among three different types in the TLS during the ESCC process. Genes showing continuous increase were marked in red, while genes showing continuous decrease were marked in blue. (J) Volcano plot showed significant differentially expressed genes between the TLS of tumor and the lymph follicles of lymph nodules.

Article Snippet: KYSE450 human ESCC cell line , Servicebio , STCC11902P.

Techniques: Comparison, Gene Expression

Journal: The Journal of Biological Chemistry

Article Title: Pyrimethamine and a potent analog inhibit NRF2 by suppressing one-carbon metabolism

doi: 10.1016/j.jbc.2025.110659

Figure Lengend Snippet: Pyrimethamine inhibits NRF2 mRNA and protein independently of KEAP1. A . H1299 NQO1-eYFP cells were treated with DMSO vehicle or 10 μM PYR in the presence of PRL295, CDDOme, or sulforaphane. B . Western blot analysis showing dose-dependent effects of PYR on indicated proteins in KYSE70 cells. C . Western blot analysis of PYR (10 μM) time course effects on indicated proteins in KYSE70 cells. Quantitation across biological triplicate experiments is shown below, normalized to VCL (vinculin) (∗ p < 0.05 by one-way ANOVA). D . Western blot analysis of lung and esophageal cancer cells following 48 h treatment with PYR (10 μM). Quantitation across biological triplicate experiments is shown below, normalized to VCL (∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001, and ∗∗∗∗ p < 0.0001 by one-way ANOVA). E – F . Western blots assessing the effects of PYR (10 μM; 48 h) on the indicated proteins in KYSE70, KYSE450, or KEAP1 KO derivatives. Quantitation across biological triplicate experiments is shown below (∗∗∗∗ p < 0.0001 by one-way ANOVA). G . Graph showing NRF2 mRNA fold change in KYSE70 cells following 24 and 48 h treatment with PYR (10 μM). NRF2 expression was normalized to RPL13 A. Data are presented as mean ± SD (∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001) by one-way ANOVA (n ≥ 3 biological replicates per group). H . KYSE70 cells harboring a dox-inducible NRF2 shRNA were treated with the indicated amount of dox for 24 h before qPCR and Western blot analysis for NRF2. NRF2 protein was normalized to VCL; NRF2 mRNA expression was normalized to RPL13A. Data are presented as means ± SD (∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001) by one-way ANOVA (n = 3 biological replicates per group). See also .

Article Snippet: KYSE70, KYSE110, KYSE180, and KYSE450 are from DSMZ (Germany), and KYSE450-KEAP1KO and KYSE70-KEAP1KO cells were generated with CRISPR-Cas9.

Techniques: Western Blot, Quantitation Assay, Expressing, shRNA

Journal: Frontiers in Oncology

Article Title: Integration of single-cell and bulk RNA sequencing to identify unique tumor stem cells and construct novel prognostic markers for assessing ESCA prognosis and drug sensitivity

doi: 10.3389/fonc.2025.1649877

Figure Lengend Snippet: Downregulation of TSPO in ESCC and its role in suppressing tumor cell proliferation. (A) The expression of TSPO across various cancer types, as analyzed from the TCGA and GTEx datasets, reveals a notable reduction in ESCC, which is highlighted for emphasis. (B) The Kaplan–Meier survival curve demonstrates that lower TSPO expression is associated with poorer overall survival outcomes in the TCGA-ESCA cohort of ESCC patients. (C) Western blot analysis reveals TSPO expression levels in normal esophageal epithelial cells (HET-1A) compared to ESCC cell lines (KYSE30, KYSE450, EC1). (D) Western blot results confirm the efficiency of TSPO overexpression (OV-TSPO) in ESCC cells. (E–G) Colony formation assays conducted in KYSE30 (E) , KYSE450 (F) , and EC1 (G) cells indicate that TSPO overexpression significantly inhibits clonogenic ability. (H–J) CCK-8 assays demonstrate a reduction in proliferation in TSPO-overexpressing KYSE30 (H) , KYSE450 (I) , and EC1 (J) cells, with statistical significance indicated as *** P < 0.001. (K) Western blot analysis of key apoptotic and DNA damage-related proteins (PPARα, c-PARP, Bcl-2, Noxa, and γH2AX) in TSPO-overexpressing ESCC cells. β-actin was used as the loading control. All data were representative of at least three independent experiments (n = 3; error bar, SD). Statistical significance: P < 0.05 (*), P < 0.01 (**), P < 0.001 (**), P < 0.0001 (****).

Article Snippet: KYSE30 and KYSE450 cells were cultured in RPMI-1640 medium (Solarbio, China), and EC1 cells were maintained in DMEM medium (Solarbio, China), both supplemented with 10% fetal bovine serum (FBS; Solarbio, China), 100 U/mL penicillin, and 100 μg/mL streptomycin.

Techniques: Expressing, Western Blot, Over Expression, CCK-8 Assay, Control