Journal: Nature Communications

Article Title: Nuclear ANLN regulates transcription initiation related Pol II clustering and target gene expression

doi: 10.1038/s41467-025-56645-9

Figure Lengend Snippet: A KYSE150 cells were treated with 0.1 μM THZ1 for 3 h, ANLN (pink) and Pol II (green) clusters were observed with super-resolution imaging. Scale bar, 3 μm. B , C Effect of THZ1 on the number of different types of clusters. n = 42 (Control); n = 45 (THZ1). The error bars indicate the mean ± SDs. Two-tailed Student’s t tests were performed to determine the significance. D Relative fluorescence intensity of protein signals per cell per focal plane. n = 42 (Control); n = 45 (THZ1). The error bars indicate the mean ± SDs. Two-tailed Student’s t tests were performed to determine the significance. E , F Heatmap ( E ) and box plots ( F ) showing expression changes of all protein-coding genes (Total, n = 11376), super-enhancer-associated genes (SE, n = 652), and target genes (TG, n = 84) with or without THZ1 treatment. The error bars indicate the mean ± SDs. Two-tailed Student’s t tests were performed to determine the significance. G KYSE150 cells were treated with 0.1 μM THZ1, the mRNA expression of the indicated target genes was measured. The error bars indicate the mean ± SDs. Two-tailed Student’s t tests were performed to determine the significance. H The indicated cell lines were treated with different concentrations of THZ1 for 48 h, and cell viability was subsequently analyzed by MTS assay. The error bars indicate the mean ± SDs. I ESCC cell lines were treated with low toxicity THZ1 (0.04 μM) or/and F806 (20 μM) for 48 h, and cell viability was measured by MTS assay. n = 3 for each group. The error bars indicate the mean ± SDs. The data are representative of at least three independent experiments with similar results. Source data are provided as a Source Data file.

Article Snippet: ESCC cell lines were established and provided by Dr. Shimada Yutaka (Faculty of Medicine, Kyoto University, Japan) and Dr. Nishihira (Tohoku University School of Medicine, Japan) – .

Techniques: Imaging, Control, Two Tailed Test, Fluorescence, Expressing, MTS Assay

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: Top 20 upregulated protein molecules modulated by CDDO-Me in Ec109 cells

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques:

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: The top ten canonical signaling pathways regulated by CDDO-Me in Ec109 cells analyzed by ingenuity pathway analysis. Abbreviations: CDDO-Me, methyl ester of 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid; eIF2, eukaryotic initiation factor 2; p70S6K, p70S6 kinase; mTOR, mammalian target of rapamycin; RAN, ras-related nuclear protein; Nrf2, nuclear factor (erythroid-derived 2)-like 2.

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques: Protein-Protein interactions, Derivative Assay

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: Representative blots of protein levels of VKORC1, CaMKIIα, NPLOC4, PSME3, and Dynamin 2 in various human ESCC cell lines and normal human esophageal epithelial cell line (Het-1A) were determined using Western blot analysis. β-Actin served as loading controls. Abbreviations: VKORC1, vitamin K epoxide reductase complex subunit 1; CaMKIIα, calcium/calmodulin-dependent protein kinase type II subunit alapha; NPLOC4, nuclear protein localization protein 4 homolog; PSME3, proteasome activator complex subunit 3; ESCC, esophageal squamous cell carcinoma.

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques: Western Blot

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: Mitochondrial dysfunction signaling pathway regulated by CDDO-Me in Ec109 cells. Notes: Ec109 cells were treated with 0.5 μM CDDO-Me for 24 hours and the protein samples were subject to quantitative proteomic analysis. Red indicates an upregulation; green indicates a downregulation. The intensity of green and red molecule colors indicates the degree of down- or upregulation, respectively. Solid arrows indicate direct interaction and dashed arrows indicate indirect interaction. Abbreviations: CDDO-Me, methyl ester of 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid.

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques:

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: mTOR signaling pathway regulated by CDDO-Me in Ec109 cells. Notes: Ec109 cells were treated with 0.5 μM CDDO-Me for 24 hours and the protein samples were subject to quantitative proteomic analysis. Red indicates an upregulation; green indicates a downregulation. The intensity of green and red molecule colors indicates the degree of down- or upregulation, respectively. Solid arrows indicate direct interaction and dashed arrows indicate indirect interaction. Abbreviation: CDDO-Me, methyl ester of 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid; mTOR, mammalian target of rapamycin.

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques:

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: The effect of knockdown of CaMKIIα on the CDDO-Me induced apoptosis in human ESCC cells. A. Percentages of specific cell populations showed in dot plots and apoptotic cells showed in bar graphs for the silencing of CaMKIIα in Ec109 and KYSE30 cells with or without 0.5 μM CDDO-Me treatment for 24 hours. B. Representative blots of bcl-2, bax, and cleaved caspase-3 for the proteinlysate samples, which were prepared from Ec109 and KYSE30 cells treated with CaMKIIα siRNAs or 0.5 μM CDDO-Me for 24 hours. Abbreviation: CaMKIIα, calcium/calmodulin-dependent protein kinase type II subunit alapha; CDDO-Me, methyl ester of 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid; ESCC, esophageal squamous cell carcinoma; bcl-2, B-cell lymphoma-2; bax, bcl-2 associated X protein; siRNA , small interfering RNA.

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques: Knockdown, Small Interfering RNA

Journal: American Journal of Translational Research

Article Title: The therapeutic response of CDDO-Me in the esophageal squamous cell carcinoma (ESCC) cells is mediated by CaMKIIα

doi:

Figure Lengend Snippet: The effect of knockdown of CaMKIIα on the CDDO-Me induced autophagy in human ESCC cells. A. Percentages of specific cell populations showed in dot plots and autophagic cells showed in bar graphs for the silencing of CaMKIIα in Ec109 and KYSE30 cells with or without 0.5 μM CDDO-Me treatment for 24 hours. B. CDDO-Me-induced autophagic death in the silencing of CaMKIIα in Ec109 and KYSE30 cellsdetermined by confocal microscopy. The level of autophagy was evaluated using a lysosome-specific fluorescence dye. The confocal microscopic images of autophagic Ec109 and KYSE 30 cells (stained in green) are also shown. C. Representative blots of beclin-1 and LC3I/II for the proteinlysate samples, which were prepared from Ec109 and KYSE30 cells treated with CaMKIIα siRNAs or 0.5 μM CDDO-Me for 24 hours. Abbreviation: CaMKIIα, calcium/calmodulin-dependent protein kinase type II subunit alapha; CDDO-Me, methyl ester of 2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid; ESCC, esophageal squamous cell carcinoma; siRNA, small interfering RNA; LC 3, microtubule-associated protein 1A/1B-light chain 3.

Article Snippet: Human ESCC Ec109 cells was obtained from AddexBio Inc. (San Diego, CA, USA), KYSE70 and KYSE30 cells were obtained from Sigma-Aldrich Co (St Louis, MO, USA).

Techniques: Knockdown, Confocal Microscopy, Fluorescence, Staining, Small Interfering RNA

Journal: Cancer Medicine

Article Title: Aberrant DNA hypermethylation reduces the expression of the desmosome-related molecule periplakin in esophageal squamous cell carcinoma

doi: 10.1002/cam4.369

Figure Lengend Snippet: PPL expression was silenced by DNA methylation in ESCC. (A) Typical images of formalin-fixed, paraffin-embedded samples of ESCC, and adjacent noncancerous mucosa (normal) stained with H&E or anti-PPL antibody. (B) PPL transcript levels in paired samples from 13 ESCC samples were determined by RT-PCR. Data indicate expression relative to the mean levels of normal tissues. (C) DNA methylation of PPL as determined by pyrosequencing of paired samples from 17 patients with ESCC. (D) Expression of PPL in ESCC relative to that in normal tissue plotted against the change in DNA methylation (ratio of tumor to normal tissue) in each paired sample. (E) PPL mRNA induction in ESCC cell lines after treatment with 1 or 5 μ mol/L of 5-aza-dC. The fold increase in induction in the treated cells relative to that in the untreated cells is shown for each cell line. Data are shown as mean + SD of duplicated assays. *Difference from untreated cells was statistically significant ( P < 0.05). (F) KYSE270 cells were treated with the indicated concentrations of 5-aza-dC. The levels of methylation of PPL DNA (left Y axis, solid lines) and mRNA (right Y axis, dotted lines) are shown. Data are shown as mean ± SD of triplicated assays. *Difference from untreated cells was statistically significant ( P < 0.05). (G) KYSE270 cells were treated with 5 μ mol/L of 5-aza-dC, and stained with anti-PPL antibody (green) and DAPI for nuclear staining (red). ESCC, esophageal squamous cell carcinoma; PPL, periplakin.

Article Snippet: Human ESCC lines KYSE70, KYSE140, KYSE150, KYSE270, KYSE410, and KYSE510 were obtained from the Japanese Collection of Research Bioresources Cell Bank (Osaka, Japan) on 13 August 2013.

Techniques: Expressing, DNA Methylation Assay, Formalin-fixed Paraffin-Embedded, Staining, Reverse Transcription Polymerase Chain Reaction, Methylation

Journal: Cancer Medicine

Article Title: Aberrant DNA hypermethylation reduces the expression of the desmosome-related molecule periplakin in esophageal squamous cell carcinoma

doi: 10.1002/cam4.369

Figure Lengend Snippet: Forced PPL expression induced desmosome-like structures. (A) TEM images were obtained from normal human esophageal mucosa (normal) and mock-transfected or PPL-transfected KTSE270 cells at 10,000× or 30,000× magnification. Desmosomes were frequently found in normal tissues and PPL-transfected cells (arrows). In the images of the mock-transfected cells taken at 10,000× magnification, the arrow indicates adhesion plaque-like structures, which was not identified as a desmosome at higher magnification. (B) Expression of envoplakin (EVPL) in mock- or PPL- transfected KYSE270 cells. EVPL mRNA levels were shown as fold expression of the levels to normal esophageal mucosa (average of 13 mucosa = 1). Data are shown as mean + SD of three assays. (C) Expression of envoplakin (EVPL) in ESCC tissues with paired normal mucosa. PPL, periplakin; ESCC, esophageal squamous cell carcinoma.

Article Snippet: Human ESCC lines KYSE70, KYSE140, KYSE150, KYSE270, KYSE410, and KYSE510 were obtained from the Japanese Collection of Research Bioresources Cell Bank (Osaka, Japan) on 13 August 2013.

Techniques: Expressing, Transfection

Journal: Nature Communications

Article Title: Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma

doi: 10.1038/s41467-019-12846-7

Figure Lengend Snippet: Top recurrent genes harbored somatic variants and somatic CNVs. a Left panel, bar plot shows the proportion of 161 ESCC samples with somatic mutations in the specific genes. Right panel, occurrence of the top 23 ranked somatically mutated genes identified by the cancer panel. Mutation subtypes (Missense, Stopgain, Stoploss, Splice, Frameshift, and Non-frameshift) are denoted by color. b Heatmap of the top recurrent genes associated with the top recurrent somatic CNVs in the 161 ESCC samples. The genes with recurrence of more than 10% are shown here. Mutation subtypes (Gain and Loss) are denoted by color

Article Snippet: In addition, ten ESCC commercial cell lines used in cell viability assay with compounds were purchased from three different cell banks, including European Collection of Authenticated Cell Cultures (ECACC), Japanese Collection of Research Bioresources (JCRB), and RIKEN BRC cell banks.

Techniques: Mutagenesis

Journal: Nature Communications

Article Title: Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma

doi: 10.1038/s41467-019-12846-7

Figure Lengend Snippet: Exploration of the potential biomarkers of drug sensitivity in ESCC. a A schematic diagram exploring potential biomarkers of drug sensitivity in esophageal squamous cell carcinoma. Eight ESCC patient-derived cells (PDCs) were established from an independent cohort of 123 ESCC patients. DNA sequencing was used to detect the mutations and gain/loss in ESCC PDCs. We used the ESCC PDCs for integrated targeted deep sequencing and drug sensitivity evaluation systems to explore potential biomarkers of drug sensitivity. b The mutational landscape was studied in eight ESCC PDCs. c Each circle represents a single drug–gene interaction, and the size is proportional to the number of mutant cell lines screened (range 1–7). An unpaired t test was performed for each drug–gene mutation associations. The top four drug–gene mutation associations sorted by FDR were colored by green (sensitive) and red (resistant)

Article Snippet: In addition, ten ESCC commercial cell lines used in cell viability assay with compounds were purchased from three different cell banks, including European Collection of Authenticated Cell Cultures (ECACC), Japanese Collection of Research Bioresources (JCRB), and RIKEN BRC cell banks.

Techniques: Derivative Assay, DNA Sequencing, Sequencing, Mutagenesis

Journal: Nature Communications

Article Title: Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma

doi: 10.1038/s41467-019-12846-7

Figure Lengend Snippet: Validation of the biomarkers in PDCs and commercial cell lines. a The copy number variations (CNVs) of CDKN2A and CDKN2B were shown in eight ESCC PDCs and their corresponding tumor tissue. b Fifty percent growth inhibitory concentrations (IC50s) of palbociclib and ribociclib (LEE011) in eight ESCC PDCs with CDKN2A or CDKN2B loss or with no CNV of CDKN2A and CDKN2B . c The CNVs of CDKN2A and CDKN2B were illustrated in ten commercial cell lines. d IC50s of palbociclib and ribociclib in ten ESCC commercial cell lines with CDKN2A or CDKN2B loss or with no CNV of CDKN2A and CDKN2B . Error bars correspond to the standard deviation of IC50s. The comparisons between different groups of compound IC50s were performed using Student’s t test

Article Snippet: In addition, ten ESCC commercial cell lines used in cell viability assay with compounds were purchased from three different cell banks, including European Collection of Authenticated Cell Cultures (ECACC), Japanese Collection of Research Bioresources (JCRB), and RIKEN BRC cell banks.

Techniques: Biomarker Discovery, Standard Deviation

Journal: Nature Communications

Article Title: Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma

doi: 10.1038/s41467-019-12846-7

Figure Lengend Snippet: Validation of the biomarkers of drug sensitivity in vitro. a , b ZEC127 ( CDKN2A / 2B loss) and ZEC118 ( CDKN2A / 2B no CNV) were used to evaluate the sensitivity of CDK4/6 inhibitors (palbociclib and ribociclib) using colony formation assays. Three experiments were averaged, and error bars correspond to the standard deviation of colony numbers. The colony number differences between different dose groups of inhibitors were compared using a Student’s t test and * p < 0.01 and ** p < 0.001. c Mutations of cell cycle checkpoint genes including CDKN2A , CDKN2B , MYC , CCND1 , CDK4 , RB1 , TP53 , CHEK1 , and CCNE1 were detected in eight ESCC PDCs using targeted deep sequencing. d Z -score analysis of the expression level of cell cycle checkpoint genes in the eight ESCC PDCs, which carried either CDKN2A or CDKN2B loss, or neither

Article Snippet: In addition, ten ESCC commercial cell lines used in cell viability assay with compounds were purchased from three different cell banks, including European Collection of Authenticated Cell Cultures (ECACC), Japanese Collection of Research Bioresources (JCRB), and RIKEN BRC cell banks.

Techniques: Biomarker Discovery, In Vitro, Standard Deviation, Sequencing, Expressing

Journal: Nature Communications

Article Title: Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma

doi: 10.1038/s41467-019-12846-7

Figure Lengend Snippet: An ESCC PDX model to confirm the biomarkers of drug sensitivity. a Hematoxylin and eosin staining (HE) results of tumor tissue derived from an ESCC patient are shown. Magnification (right) is ×400. b The expression levels of p15 and p16 were detected by immunohistochemistry (IHC) staining in the FFPE tumor tissues of this ESCC patient. Magnification (right) is ×400. c Change in tumor volume following treatment with palbociclib in three doses in patient-derived xenografts (PDXs)-Z16062301 (28 days) (mean ± s.e.m., n = 10). Error bars correspond to standard error of the mean of tumor volume. * p < 0.01, Student’s t test, palbociclib 0 mg/kg compared with palbociclib 75 mg/kg; * p < 0.01, Student’s t test, palbociclib 75 mg/kg compared with palbociclib 150 mg/kg. d General picture of PDXs-Z16062301 after intragastric administration. e IHC staining of FFPE tumor tissue from PDXs treated with different dosages of palbociclib was used to detect the expression of p15, p16, and Ki67. The imaging results of IHC staining with the magnification of ×200 are shown

Article Snippet: In addition, ten ESCC commercial cell lines used in cell viability assay with compounds were purchased from three different cell banks, including European Collection of Authenticated Cell Cultures (ECACC), Japanese Collection of Research Bioresources (JCRB), and RIKEN BRC cell banks.

Techniques: Staining, Derivative Assay, Expressing, Immunohistochemistry, Imaging