Journal: Journal of Translational Medicine

Article Title: Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification

doi: 10.1186/s12967-025-06682-1

Figure Lengend Snippet: Machine learning algorithms and hub targets acquisition. ( A ) The identification of potential targets using the randomForest algorithm. The abscissa of the figure is the score of importance, and the ordinate is the gene name. The red line represents the cut-off value. ( B ) Univariate Cox regression analysis of DP subtype signature genes in TCGA BLCA cohort. ( C ) A LASSO model was employed to identify significant genes. The partial likelihood deviance was plotted as a function of log(λ). Vertical lines denote the 1-SE rule for model selection. 27 genes were selected with non-zero coefficients at the optimal λ. ( D ) Venn diagram for identifying hub genes of BLCA. ( E ) Single gene GSEA enrichment analysis for DAD1 based on hallmark gene set. ( F ) Single gene GSEA enrichment analysis for CYP1B1 based on hallmark gene set. ( G ) Single gene GSEA enrichment analysis for REXO2 based on hallmark gene set. ( H ) Correlation between DAD1 and 22 infiltrating immune cells. ( I ) Correlation between CYP1B1 and 22 infiltrating immune cells. ( J ) Correlation between REXO2 and 22 infiltrating immune cells

Article Snippet: The membranes were subsequently incubated overnight at 4 °C with primary antibodies diluted 1:1000 in a solution against specific targets: DAD1 (1:1000; 10531-1-AP, Proteintech, China), CYP1B1 (1:1000; R24037 , Zenbio, China), and REXO2 (1:1000; 15598-1-AP, Proteintech, China).

Techniques: Selection

Journal: Journal of Translational Medicine

Article Title: Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification

doi: 10.1186/s12967-025-06682-1

Figure Lengend Snippet: Malignancy phenotypes and experimental validation of hubgenes. ( A ) Kaplan-Meier of OS with log-rank test in TCGA BLCA cohort, respectively, for the grouping of the median expression of DAD1, CYP1B1, and REXO2. ( B ) The relative expression of different stages for DAD1, CYP1B1, and REXO2, respectively. ( C ) The relative expression of different grades for DAD1, CYP1B1, and REXO2, respectively. Ns represents P-value > 0.05; *, **, ***, **** represents P-value < 0.05. ( D ) Western blotting of DAD1, CYP1B1, and REXO2 proteins in different tumor stages. β-actin was used as the reference protein. ( E ) The bar graphs show the relative expression of DAD1, CYP1B1, and REXO2 proteins in different tumor stages. ( F ) Immunohistochemistry of DAD1 and CYP1B1 proteins in four tumor stages

Article Snippet: The membranes were subsequently incubated overnight at 4 °C with primary antibodies diluted 1:1000 in a solution against specific targets: DAD1 (1:1000; 10531-1-AP, Proteintech, China), CYP1B1 (1:1000; R24037 , Zenbio, China), and REXO2 (1:1000; 15598-1-AP, Proteintech, China).

Techniques: Biomarker Discovery, Expressing, Western Blot, Immunohistochemistry

Journal: Journal of Translational Medicine

Article Title: Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification

doi: 10.1186/s12967-025-06682-1

Figure Lengend Snippet: Machine learning algorithms and hub targets acquisition. ( A ) The identification of potential targets using the randomForest algorithm. The abscissa of the figure is the score of importance, and the ordinate is the gene name. The red line represents the cut-off value. ( B ) Univariate Cox regression analysis of DP subtype signature genes in TCGA BLCA cohort. ( C ) A LASSO model was employed to identify significant genes. The partial likelihood deviance was plotted as a function of log(λ). Vertical lines denote the 1-SE rule for model selection. 27 genes were selected with non-zero coefficients at the optimal λ. ( D ) Venn diagram for identifying hub genes of BLCA. ( E ) Single gene GSEA enrichment analysis for DAD1 based on hallmark gene set. ( F ) Single gene GSEA enrichment analysis for CYP1B1 based on hallmark gene set. ( G ) Single gene GSEA enrichment analysis for REXO2 based on hallmark gene set. ( H ) Correlation between DAD1 and 22 infiltrating immune cells. ( I ) Correlation between CYP1B1 and 22 infiltrating immune cells. ( J ) Correlation between REXO2 and 22 infiltrating immune cells

Article Snippet: The slides were blocked for one hour and then incubated overnight at 4 °C with primary antibodies against DAD1 (1:100; CSB-PA03124A0Rb, CUSABIO, https://www.cusabio.com/ , China) and CYP1B1 (1:100; R24037 , Zenbio, China).

Techniques: Selection

Journal: Journal of Translational Medicine

Article Title: Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification

doi: 10.1186/s12967-025-06682-1

Figure Lengend Snippet: Malignancy phenotypes and experimental validation of hubgenes. ( A ) Kaplan-Meier of OS with log-rank test in TCGA BLCA cohort, respectively, for the grouping of the median expression of DAD1, CYP1B1, and REXO2. ( B ) The relative expression of different stages for DAD1, CYP1B1, and REXO2, respectively. ( C ) The relative expression of different grades for DAD1, CYP1B1, and REXO2, respectively. Ns represents P-value > 0.05; *, **, ***, **** represents P-value < 0.05. ( D ) Western blotting of DAD1, CYP1B1, and REXO2 proteins in different tumor stages. β-actin was used as the reference protein. ( E ) The bar graphs show the relative expression of DAD1, CYP1B1, and REXO2 proteins in different tumor stages. ( F ) Immunohistochemistry of DAD1 and CYP1B1 proteins in four tumor stages

Article Snippet: The slides were blocked for one hour and then incubated overnight at 4 °C with primary antibodies against DAD1 (1:100; CSB-PA03124A0Rb, CUSABIO, https://www.cusabio.com/ , China) and CYP1B1 (1:100; R24037 , Zenbio, China).

Techniques: Biomarker Discovery, Expressing, Western Blot, Immunohistochemistry

Journal: Journal of Translational Medicine

Article Title: Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification

doi: 10.1186/s12967-025-06682-1

Figure Lengend Snippet: Machine learning algorithms and hub targets acquisition. ( A ) The identification of potential targets using the randomForest algorithm. The abscissa of the figure is the score of importance, and the ordinate is the gene name. The red line represents the cut-off value. ( B ) Univariate Cox regression analysis of DP subtype signature genes in TCGA BLCA cohort. ( C ) A LASSO model was employed to identify significant genes. The partial likelihood deviance was plotted as a function of log(λ). Vertical lines denote the 1-SE rule for model selection. 27 genes were selected with non-zero coefficients at the optimal λ. ( D ) Venn diagram for identifying hub genes of BLCA. ( E ) Single gene GSEA enrichment analysis for DAD1 based on hallmark gene set. ( F ) Single gene GSEA enrichment analysis for CYP1B1 based on hallmark gene set. ( G ) Single gene GSEA enrichment analysis for REXO2 based on hallmark gene set. ( H ) Correlation between DAD1 and 22 infiltrating immune cells. ( I ) Correlation between CYP1B1 and 22 infiltrating immune cells. ( J ) Correlation between REXO2 and 22 infiltrating immune cells

Article Snippet: The membranes were subsequently incubated overnight at 4 °C with primary antibodies diluted 1:1000 in a solution against specific targets: DAD1 (1:1000; 10531-1-AP, Proteintech, China), CYP1B1 (1:1000; R24037 , Zenbio, China), and REXO2 (1:1000; 15598-1-AP, Proteintech, China).

Techniques: Selection

Journal: Journal of Translational Medicine

Article Title: Pathway-based cancer transcriptome deciphers a high-resolution intrinsic heterogeneity within bladder cancer classification

doi: 10.1186/s12967-025-06682-1

Figure Lengend Snippet: Malignancy phenotypes and experimental validation of hubgenes. ( A ) Kaplan-Meier of OS with log-rank test in TCGA BLCA cohort, respectively, for the grouping of the median expression of DAD1, CYP1B1, and REXO2. ( B ) The relative expression of different stages for DAD1, CYP1B1, and REXO2, respectively. ( C ) The relative expression of different grades for DAD1, CYP1B1, and REXO2, respectively. Ns represents P-value > 0.05; *, **, ***, **** represents P-value < 0.05. ( D ) Western blotting of DAD1, CYP1B1, and REXO2 proteins in different tumor stages. β-actin was used as the reference protein. ( E ) The bar graphs show the relative expression of DAD1, CYP1B1, and REXO2 proteins in different tumor stages. ( F ) Immunohistochemistry of DAD1 and CYP1B1 proteins in four tumor stages

Article Snippet: The membranes were subsequently incubated overnight at 4 °C with primary antibodies diluted 1:1000 in a solution against specific targets: DAD1 (1:1000; 10531-1-AP, Proteintech, China), CYP1B1 (1:1000; R24037 , Zenbio, China), and REXO2 (1:1000; 15598-1-AP, Proteintech, China).

Techniques: Biomarker Discovery, Expressing, Western Blot, Immunohistochemistry

Journal: Scientific Reports

Article Title: Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia

doi: 10.1038/s41598-020-66224-1

Figure Lengend Snippet: PRMT5 inhibition impairs stress response pathways and sensitizes cells to PARP inhibitors. ( a ) Reactome pathway analysis of the expression changing genes common to both cell lines. Emapplot showing top 15 categories of enrichment, with dot-size representing number of genes in the category and color representing adjusted p-value. ( b ) Ingenuity Pathway Analysis (IPA) depicts enriched or depleted pathways in differential expression data between control and EPZ015666-treated cells (pval < 0.05 and z-score > |1|). ( c ) Western blot for BRCA1 in control and EPZ015666-treated cells (left panel). Tubulin served as loading control. Quantification of BCRA1 abundance in control and EPZ015666-treated cells relative to tubulin with error bars representing SD from three biological replicates (right panel). ( d ) IncuCyte Caspase-3/7 assay depicts representative pictures showing the induction of apoptosis in HG-3 cells treated as indicated after 0 and 48 h (left panel). Right panel shows summary graphs of the induction of apoptosis over time and with the indicated treatments (error bars represent SD from three biological replicates).

Article Snippet: Membranes were blocked in 5% BSA or 3% dry milk powder in TBS + 0.5% Tween-20 and incubated with the following primary antibodies overnight: rabbit polyclonal PRMT5 (Epigentek; A-3005); rabbit polyclonal DAD1 (Novus; IMG-5615); rabbit polyclonal OXA1L (Biozol; LS-C334623); rabbit polyclonal MXD4 (ThermoFisher; PA5-40596); mouse monoclonal c-Myc (ThermoFisher; 13-2500); rabbit polyclonal BRCA1 (Cell Signaling; 9010); mouse monoclonal GAPDH (Abcam; ab8265), mouse monoclonal alpha-tubulin (Sigma; T5168).

Techniques: Inhibition, Expressing, Quantitative Proteomics, Control, Western Blot