Journal: Molecular Therapy Oncology

Article Title: CDKN2A copy number alteration in bladder cancer: Integrative analysis in patient-derived xenografts and cancer patients

doi: 10.1016/j.omton.2024.200818

Figure Lengend Snippet: In silico analysis of CDKN2A copy number loss in the bladder tumor molecular background and chemotherapy response (A) CDKN2A copy number status of BlCa cell lines in the DepMap portal ( https://depmap.org/portal/ ). (B) Boxplots presenting the correlation of CDKN2A copy number loss (HD/LOH) with mRNA and protein expression across BlCa cells. (C) Spearman correlation of CDKN2A mRNA and protein levels in BlCa cells. (D–L) Correlation of CDKN2A CNA with area under the dose-response curve (AUC) and IC50 values of BlCa cell lines for gemcitabine (D and E), methotrexate (G and H), and vinblastine (J and K). The p values were calculated by Mann-Whitney U test (B, E, H, and K) and Spearman analysis (C, D, G, and J) . Shown are indicative dose-response curves of BlCa cells with CDKN2A copy number loss (e.g., RT4, RT112, KU1919, and SW780) compared to WT cells (e.g., 5637, HT1376, and TCCSUP) for gemcitabine (F), methotrexate (I), and vinblastine (L). (M) Dot plot of GSEA Hallmark analysis of the CDKN2A-related enriched gene sets in the TCGA-BLCA and Lindgren et al. cohorts. The size of the dots represents the number of genes, and the color of the dots represents the false discovery rate (FDR) q value. (N) Enrichment plots for the top four gene sets enriched in GSEA Hallmark analysis in the TCGA-BLCA and Lindgren et al. cohorts.

Article Snippet: CNA and mRNA expression profiling as well as response data to gemcitabine, methotrexate, and vinblastine of BlCa cell lines were obtained through the DepMap portal ( https://depmap.org/portal ) of the Broad Institute.

Techniques: In Silico, Expressing, MANN-WHITNEY

Journal: BMC Cancer

Article Title: A novel metabolic subtype with S100A7 high expression represents poor prognosis and immuno-suppressive tumor microenvironment in bladder cancer

doi: 10.1186/s12885-023-11182-w

Figure Lengend Snippet: Metabolic-gene-based stratification of TCGA-BLCA patients. A NbClust analysis of BLCA metabolic-gene-based subtypes. B Silhouette analysis of clustering results. C UMAP visualization of metabolic subtypes in the TCGA cohort for the expression of metabolic genes. D Correlations between metabolic subtypes and clinicopathological features in BLCA. E , F Barplot showing the percentage of pathological stages ( E ) and vital status ( F ) in the MRS1 and MRS2 groups. G , H Kaplan-Meier analysis in term of OS ( G ) and PFS ( H ) in TCGA cohort

Article Snippet: BLCA cell line RT4 (Cat. KG089) was obtained from KeyGEN (Nanjing, China).

Techniques: Expressing

Journal: BMC Cancer

Article Title: A novel metabolic subtype with S100A7 high expression represents poor prognosis and immuno-suppressive tumor microenvironment in bladder cancer

doi: 10.1186/s12885-023-11182-w

Figure Lengend Snippet: Metabolic phenotypes predicted molecular subtypes and clinical therapy. A Correlations between metabolic phenotypes and molecular subtypes using seven different algorithms (CIT, Lund, MDA, TCGA, Baylor, UNC, and consensus) and BLCA signatures. B , C Mutational profiles of chemotherapy-related genes in the MRS1 and MRS2 groups in the TCGA cohort. D Comparison of oncogenic pathways associated with therapeutic-targets between the MRS1 and MRS2 groups. * p < 0.05, ** p < 0.01, *** p < 0.0001. E Left: UMAP visualization the expression distribution of PD-L1 (CD274). Right: Comparison the expression values of PD-L1 between the MRS1 and MRS2 groups. F Stacked histogram showing the percentage of MRS1 and MRS2 groups in CR/PR and PD/SD in GSE176307 cohort. CR: complete remission; PR: partial remission; PD: progression disease; SD: stable disease

Article Snippet: BLCA cell line RT4 (Cat. KG089) was obtained from KeyGEN (Nanjing, China).

Techniques: Comparison, Biomarker Discovery, Expressing

Journal: BMC Cancer

Article Title: A novel metabolic subtype with S100A7 high expression represents poor prognosis and immuno-suppressive tumor microenvironment in bladder cancer

doi: 10.1186/s12885-023-11182-w

Figure Lengend Snippet: S100A7 was up-regulated in MRS1-tumor cells. A The interactions between MRS1-tumor cells and MRS1-T cells. B The interactions between MRS1-tumor cells and MRS1-macrophages. C Comparison of metastasis characteristics between the MRS1- and MRS2-tumor cells. D Venn plot showing the shared up-regulated genes in the MRS1-tumor cells and patients with the MRS1 phenotype. For TCGA-BLCA and GSE13057 cohort, the R package “limma” was applied. Genes with adjusted P-value< 0.05 and FC ≥ 1.5 were identified the DEGs of the MRS1 group. For single cell transcriptional dataset, “FindAllMarkers” function was used to identify the specific genes of MRS1- and MRS2-tumor cells. Genes with adjusted P-value< 0.05, FC ≥ 1.5, pct.1 ≥ 0.4 & pct.2 ≤ 0.1 were identified as the DEGs of the MRS1-tumor cells. E , F Kaplan-Meier analysis in term of OS of S100A7 in the TCGA-BLCA ( E ) and the GSE13057 ( F ) cohorts. All patients were categorized into two groups based on the median of the S100A7 expression. G Correlation between S100A7 and metastatic characteristics in the scRNA-seq dataset of MRS1 and MRS2-tumor cells. H , I Correlation between S100A7 and metastatic characteristics in the TCGA-BLCA ( H ) and GSE13507 cohorts ( I )

Article Snippet: BLCA cell line RT4 (Cat. KG089) was obtained from KeyGEN (Nanjing, China).

Techniques: Comparison, Expressing

Journal: BMC Cancer

Article Title: A novel metabolic subtype with S100A7 high expression represents poor prognosis and immuno-suppressive tumor microenvironment in bladder cancer

doi: 10.1186/s12885-023-11182-w

Figure Lengend Snippet: Validation of expression and prognostic value of S100A7 in the recruited TMA cohort. A Representative images revealing S100A7 expression in tumor and paratumor tissues using anti-S100A7 staining. Magnification, 200×. B Expression levels of S100A7 in tumor and paratumor tissues. C Kaplan-Meier analysis of S100A7 in term of OS in the TMA cohort. D Association between S100A7 expression and clinicopathological features in BLCA. E Representative images revealing PD-L1 expression in the high- and low-S100A7 groups. Magnification, 200×; ( F ) Correlation between S100A7 and PD-L1 expression

Article Snippet: BLCA cell line RT4 (Cat. KG089) was obtained from KeyGEN (Nanjing, China).

Techniques: Biomarker Discovery, Expressing, Staining