Journal: European urology

Article Title: Impact of Immune and Stromal Infiltration on Outcomes Following Bladder-sparing Trimodality Therapy for Muscle-invasive Bladder Cancer

doi: 10.1016/j.eururo.2019.01.011

Figure Lengend Snippet: Multivariable models for DSS in the TMT cohort for T-cell–inflamed signature score and interferon-gamma signature scores

Article Snippet: Genomic subtyping classifier (GSC) [ 15 ], immune content signature [ 18 ], hallmark of IFN-gamma response [ 19 ], and stromal signatures [ 17 ] were retrieved from the Decipher GRID database (GenomeDx Inc.).

Techniques:

Journal: European urology

Article Title: Impact of Immune and Stromal Infiltration on Outcomes Following Bladder-sparing Trimodality Therapy for Muscle-invasive Bladder Cancer

doi: 10.1016/j.eururo.2019.01.011

Figure Lengend Snippet: An interferon-gamma (IFNg) gene expression signature is associated with outcomes in the TMT cohort but not in the NAC cohort. (A) Heat map showing expression of a subset of genes from an IFNg gene expression signature [19] across tumors from the TMT cohort. Kaplan-Meier curves for disease-specific survival (DSS) and overall survival (OS) by IFNg expression scores in (B and C) the TMT cohort and (D and E) the NAC cohort. Log-rank p values and the number of patients at risk are shown. (F) Notched box plots showing the IFNg expression scores across GSC subtypes in the TMT cohort. GSC = genomic subtyping classifier; NAC = neoadjuvant chemotherapy; TMT = trimodality therapy.

Article Snippet: Genomic subtyping classifier (GSC) [ 15 ], immune content signature [ 18 ], hallmark of IFN-gamma response [ 19 ], and stromal signatures [ 17 ] were retrieved from the Decipher GRID database (GenomeDx Inc.).

Techniques: Gene Expression, Expressing

Journal: Cancers

Article Title: FOXD1 Repression Potentiates Radiation Effectiveness by Downregulating G3BP2 Expression and Promoting the Activation of TXNIP -Related Pathways in Oral Cancer

doi: 10.3390/cancers12092690

Figure Lengend Snippet: FOXD1 knockdown induces the downregulation of the E2F signaling axis and the upregulation of TXNIP -associated interferon responses and p53 activation in oral cancer cells. ( A ) The enrichment score (ES) derived from the correlation among the IFN-α/γ-response gene sets and the queried Pearson’s correlation coefficient (r) is plotted (green curve). FDR denotes the false discovery rate. ( B , C ) The constructs of firefly luciferase gene adjacent to the IFN-stimulated response element (ISRE) and IFN-gamma activation site (GAS) response element (upper inserts) and the histograms for the results of luciferase-based promoter activity assays in HSC4 cell variants. ( D ) Scatchard plot for the expression of FOXD1 and PD-L1 gene ( CD274 ) in the primary tumors from GSE42734 oral cancer patients. ( E ) The mRNA levels of PD-L1 detected by RT-PCR (upper) and Q-PCR (lower) in parental (PT) HSC4 cells and HSC4 cells transfected with non-silencing (NS) control shRNA or FOXD1 shRNA. ( F ) The enrichment score (ES) derived from the correlation among the E2F target/p53 pathway gene sets and the queried Pearson’s correlation coefficient (r) is plotted (green curve). ( G ) Western blot analyses for phosphorylated Rb, total Rb and GAPDH protein in HSC4 cell variants. GAPDH was used as an internal control of protein loading. ( H ) The constructs of firefly luciferase gene adjacent to the 10-4 cyclin E promoter (upper insert) and the histograms for the results of luciferase-based promoter activity assays in HSC4 cell variants. ( I ) The illustration for that TXNIP gene is included in the upregulated genes after FOXD1 knockdown, IFN-α/γ-response gene sets and p53 pathway gene set. ( J ) The mRNA levels of TXNIP detected by RT-PCR (upper) Q-PCR (lower) in parental (PT) HSC4 cells and HSC4 cells transfected with non-silencing (NS) control shRNA or FOXD1 shRNA. ( K ) Scatchard plot for the expression of FOXD1 and TXNIP in the primary tumors from GSE42734 oral cancer patients. In D and K , Spearman correlation test was used to evaluate the statistical significance. In B , C , E , H and J , non-parametric Friedman test was used to estimate the statistical significances. * p value < 0.05, ** p value < 0.01, *** p value < 0.001.

Article Snippet: Luciferase reporter vectors containing IFN-stimulated response element (ISRE) and IFN-gamma activation site (GAS) response element were purchased from Promega.

Techniques: Activation Assay, Derivative Assay, Construct, Luciferase, Activity Assay, Expressing, Reverse Transcription Polymerase Chain Reaction, Transfection, shRNA, Western Blot