Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: DKC1 expression is upregulated in UCEC tumors (A) The flow chart of the study (B) The levels of DKC1 mRNA [log2 (TPM+1)] were evaluated and compared between 545 tumors and 35 non-tumorous endometrial tissues in the TCGA UCEC cohort (C) The DKC1 protein levels (Z-value) were evaluated and compared between 100 tumors and 31 non-tumorous endometrial tissues in the CPTCA UCEC cohort (D) The significantly positive correlation between mRNA and protein levels of DKC1 (Z-value) based on (B) and (C) results (E–G) The upregulation of DKC1 expression in UCEC tumors from the Qilu cohort, as determined using immunohistochemistry (IHC). The representative IHC images in (E) showed stronger DKC1 staining in tumors than in adjacent normal glands. Magnifications: ×40 (F) Comparison of IHC scores between tumors and adjacent normal glands in 12 paired samples (G) Comparison of IHC scores in all 30 tumors with 12 normal gland-containing samples.

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Expressing, Immunohistochemistry, Staining, Comparison

Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: The positive correlation between higher DKC1 expression and TERC, telomerase activity and aggressive UCEC tumors (A–F) RNA levels were assessed using log2 (TPM+1). The TCGA cohort of UCEC was analyzed (A) Upregulation of TERC expression in UCEC tumors (B) The positive correlation between DKC1 and TERC expression (C, D) The positive correlation between DKC1 and telomerase activity. Telomerase activity levels were calculated using the telomerase score (Ref. 14) and EXTEND (Ref. 41) algorithms, respectively (E) Significantly higher DKC1 expression in serous and mixed types of UCECs (F) The association between higher DKC1 expression and higher risk of recurrence (G) The association between higher DKC1 expression and higher frequency of metastasis. The GSE120490 UCEC cohort with 145 UCEC patients (100 without and 45 with metastasis) were analyzed (H) Significantly higher DKC1 expression (microarray data) in late-stage UCEC tumors from the GSE23518 cohort (with 10 early and 10 late-stage UCECs).

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Expressing, Activity Assay, Microarray

Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: Higher DKC1 expression predicts UCEC patient survival independently. Patients in the TCGA UCEC cohort were categorized into low and high groups based DKC1 mRNA levels in their tumors (median value as the cutoff) (A, B) Association between DKC1 expression and overall and progression-free survival (OS and PFS) (C, D) Univariate and multivariate COX regression analyses of DKC1 effect on patient OS (C) Univariate and (D) Multivariate (E, F) Univariate and multivariate COX regression analyses of DKC1 effect on patient PFS (E) Univariate and (F) Multivariate (G–I) Nomogram for prediction of UCEC PFS. A total of 349 patients were analyzed by including DKC1 (high vs. low), stage (I/II vs. III/IV) and age (<60 vs. ≥60) (H) The accuracy of the nomogram to predict PFS (Prediction curve vs. observed scenario) (I) The ROC prediction of PFS. ROC showed AUC values 0.67, 0.73 and 0.71 at 1, 3 and 5 years PFS, respectively. RNA levels were calculated using log2 (TPM+1).

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: DKC1 expression is regulated by genomic alterations and female sex hormones but not by telomere length in UCEC tumors and cells. The TCGA cohort of UCEC tumors and UCEC-derived cells were analyzed (A) Differences in DKC1 expression in UCEC tumors carrying different copy numbers (B) Differences in DKC1 copy numbers between endometrial and serous/mixed types of UCEC tumors (C) The mutational landscape of the DKC1 gene in UCEC tumors (D) Up- and downregulation of DKC1 (Top panel) and MYC (Bottom panel) mRNA expression in UCEC-derived Ishikawa cells treated by 17 β-estradiol (left) and 1 nM MPA (right), respectively. *** and ****: P < 0.001 and 0.0001, respectively. Three independent experiments were performed (E) Correlation between DKC1 and estrogen receptor 1 (ESR1) (left) or PGR (right) expression (F) No correlation between DKC1 expression and the ratios of telomere length of UCEC tumors and corresponding patient blood cells. Telomere length of UCEC tumors and corresponding patient blood cells were obtained from reference Barthel FP, et al.

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Expressing, Derivative Assay

Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: Molecular features and pathway enrichments in DKC1-high UCEC tumors. A total of 545 tumors in the TCGA UCEC cohort were analyzed. Robustly increased Ki67 expression (A) , cell cycle score (B) , Stemness score (C) and EMT score (D) in DKC1-high tumors (E) The identification of enriched E2F and MYC targets as the hallmarks in DKC1-high tumors by GSEA analysis (F) The enriched cell cycle and DNA replication pathways in DKC1-high tumors by KEGG analysis.

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: DKC1 expression is associated with UCEC molecular subtypes and genomic aberrations. A total of 545 tumors in the TCGA UCEC cohort were analyzed (A) The association between DKC1 mRNA expression and molecular subtypes of UCECs (B–F) Comparisons of genomic alterations between DKC1-low and high tumors: Aneuploidy scores (B) , mitochondrial DNA (MTDNA) copies (C) , HRD (D) , MSI (E) and TMB (F) (G) Different frequencies of genomic alterations in important UCEC driver genes between DKC1-low and high tumors.

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma

doi: 10.3389/fcell.2025.1592135

Figure Lengend Snippet: Identification of defective anti-tumor immunity and immunoexclusion microenvironments in DKC1-high tumors. A total of 544 tumors in the TCGA UCEC cohort were analyzed (A) Differences in immune, stromal and estimate scores between DKC1-high and low tumors, as determined using ESTIMATE analysis (B) TIDE analyses for comparison between DKC1-high and low tumors (C) CD274, CTLA4 and VTCN1 expression in DKC1-high and low tumors (D) Cancer immune cycle analyses of DKC1-high and low tumors. *, ** and ***: P < 0.05, 0.01 and 0.001, respectively (E) Differences in MHC scores between DKC1-high and low tumors (F) Prediction of DKC1-high and low tumors to immune checkpoint inhibitor sensitivity. Higher DKC1 expression is associated with lower sensitivity to immune checkpoint inhibitors.

Article Snippet: Slides were blocked using 10% goat serum and incubated with a DKC1 polyclonal antibody (Cat 25420-1-AP, Proteintech, Rosemont, IL) for 2 h at room temperature.

Techniques: Comparison, Expressing

Journal: Journal of Thoracic Disease

Article Title: SH3BGRL2 as a vital tumor suppressor and prognostic factor in human esophageal squamous cell carcinoma

doi: 10.21037/jtd-2025-1878

Figure Lengend Snippet: mRNA and protein expression levels and prognostic significance of SH3BGRL2 in ESCC. (A) Differentially expressed mRNAs between ESCC tumor samples and adjacent normal tissues identified by RNA sequencing (T: tumor tissue; N: normal tissue). (B,C) SH3BGRL2 expression levels in ESCC as analyzed via the GEPIA database (P<0.01) and GEO database (both P<0.05, GSE23400, GSE17351, and GSE45670). (D) Representative tissue microarray images of SH3BGRL2 staining via immunohistochemistry (×200): positive SH3BGRL2 expression in tumor tissues (a) and normal tissues (b) and negative SH3BGRL2 expression in tumor tissues (c) and normal tissues (d). (E) Percentages of SH3BGRL2-positive samples in tumor and nontumor esophageal tissues (31.2% vs. 51.0%; P<0.001). (F,G) Kaplan-Meier curves showing the disease-free survival (F) or overall survival (G) of patients with ESCC and higher SH3BGRL2 expression and in those with lower SH3BGRL2 expression. Error bars represent the standard deviation of the mean. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001 (Student t -test, one-way ANOVA). ANOVA, analysis of analysis; DFS, disease-free survival; ESCC, esophageal squamous cell carcinoma; GEO, Gene Expression Omnibus; GEPIA, Gene Expression Profiling Interactive Analysis; OS, overall survival; SH3BGRL2, SH3 domain binding glutamate rich protein-like 2.

Article Snippet: Standard IHC was performed with a primary antibody against human SH3BGRL2 (#21944-1-AP; Proteintech, Rosemont, IL, USA) at a dilution of 1:200.

Techniques: Expressing, RNA Sequencing, Microarray, Staining, Immunohistochemistry, Standard Deviation, Gene Expression, Binding Assay

Journal: Journal of Thoracic Disease

Article Title: SH3BGRL2 as a vital tumor suppressor and prognostic factor in human esophageal squamous cell carcinoma

doi: 10.21037/jtd-2025-1878

Figure Lengend Snippet: SH3BGRL2 inhibited the proliferation of ESCC PDCs. (A) RNA sequencing and western blot analysis of SH3BGRL2 expression levels in different ESCC PDCs. Western blot assays validated the efficiencies of SH3BGRL2 knockdown in ZEC043, ZEC056, and ZEC145 cells (B,C) and overexpression in ZEC014 cells (D). CCK-8 and colony formation with crystal violet staining assays analyzed cell proliferation in ZEC043, ZEC056, ZEC145 cells (E-H), and ZEC014 cells (I). Each picture represents a well of a 6-well plate. Data are presented as the mean ± standard deviation. *, P<0.05; **, P<0.01; ***, P<0.001 (Student t -test). The grayscale analysis values of western blot bands are listed below the bands. CCK-8, Cell Counting Kit-8; ESCC, esophageal squamous cell carcinoma; OD, optical density; PDC, patient-derived cell line; SH3BGRL2, SH3 domain binding glutamate rich protein-like 2.

Article Snippet: Standard IHC was performed with a primary antibody against human SH3BGRL2 (#21944-1-AP; Proteintech, Rosemont, IL, USA) at a dilution of 1:200.

Techniques: RNA Sequencing, Western Blot, Expressing, Knockdown, Over Expression, CCK-8 Assay, Staining, Standard Deviation, Cell Counting, Derivative Assay, Binding Assay

Journal: Journal of Thoracic Disease

Article Title: SH3BGRL2 as a vital tumor suppressor and prognostic factor in human esophageal squamous cell carcinoma

doi: 10.21037/jtd-2025-1878

Figure Lengend Snippet: SH3BGRL2 suppressed the growth of ESCC PDCs in vivo . (A) Representative images of BALB/c nude mice subcutaneously injected with vector control (upper row) or SH3BGRL2 knockdown ZEC-145 cells (lower row). (B) Analysis of tumor volume of mice measured weekly (n=8 per group). (C) Analysis of tumor weight of xenograft tumors 4 weeks after tumor inoculation (n=8 per group). Data are presented as the mean ± standard deviation. *, P<0.05 (Student t -test and Chi-squared test). ESCC, esophageal squamous cell carcinoma; PDC, patient-derived cell line; SH3BGRL2, SH3 domain binding glutamate rich protein-like 2.

Article Snippet: Standard IHC was performed with a primary antibody against human SH3BGRL2 (#21944-1-AP; Proteintech, Rosemont, IL, USA) at a dilution of 1:200.

Techniques: In Vivo, Injection, Plasmid Preparation, Control, Knockdown, Standard Deviation, Derivative Assay, Binding Assay

Journal: Journal of Thoracic Disease

Article Title: SH3BGRL2 as a vital tumor suppressor and prognostic factor in human esophageal squamous cell carcinoma

doi: 10.21037/jtd-2025-1878

Figure Lengend Snippet: SH3BGRL2 inhibited the EGR1 expression of ESCC cells. (A) Differentially expressed genes between SH3BGRL2-silenced and vector control ZEC145 cells. (B) Elevated mRNA expression of EGR1 in SH3BGRL2-silenced ZEC145 and vector control cells, as indicated in orange borders. (C) Transcription factors associated with differentially expressed genes between SH3BGRL2-silenced and vector control ZEC145 cells. Results show the significant enrichment of the C2H2 zinc finger transcription factor family (zf-C2H2). X-axis: the number of genes in each transcription factor family. (D) The significant negative correlation between EGR1 and SH3BGRL2 expression in ESCC tissues as analyzed via TCGA database (P<0.001). (E) Quantitative reverse transcription-PCR confirmed that EGR1 mRNA expression was increased in SH3BGRL2-knockdown cells (P<0.001). (F,G) Protein expression of EGR1 in SH3BGRL2-silenced ZEC145 cells and SH3BGRL2-overexpressing ZEC014 cells and corresponding vector control cells. Data are presented as the mean ± standard deviation. The grayscale analysis values of western blot bands are listed below the bands. **, P<0.01; ***, P<0.001 (Student t -test). EGR1, early growth response 1; ESCC, esophageal squamous cell carcinoma; SH3BGRL2, SH3 domain binding glutamate rich protein-like 2; TCGA, The Cancer Genome Atlas; TPM, transcripts per million.

Article Snippet: Standard IHC was performed with a primary antibody against human SH3BGRL2 (#21944-1-AP; Proteintech, Rosemont, IL, USA) at a dilution of 1:200.

Techniques: Expressing, Plasmid Preparation, Control, Reverse Transcription, Knockdown, Standard Deviation, Western Blot, Binding Assay

Journal:

Article Title: Comparison of Classical Serotyping and PremiTest Assay for Routine Identification of Common Salmonella enterica Serovars ▿ †

doi: 10.1128/JCM.01405-08

Figure Lengend Snippet: Typical microarray results obtained by PT. The boxed microarray spots are used by the PT software (version 4.2) to calculate a PT signature that is used as serovar identifier. (A to F) Strains identified correctly only if purified DNA was assayed; (G) a strain yielding the correct result when crude material was assayed; (H) incorrect identification by PT; (I and J) a single PT signature matching two possible serovars; (K) a strain found to be nontypeable by classical serotyping and identified as Salmonella serovar Paratyphi B by PT; (L) uncommon serovar yielding a PT signature not recognized by the system. ST, serotyping; NT, nontypeable; Purif., purified.

Article Snippet: The array images are generated with a dedicated microarray reader (Array Tube reader; ClonDiag) connected to a standard computer running software customized for PT data analysis (version 4.2).

Techniques: Microarray, Software, Purification