Journal: European Urology

Article Title: The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer

doi: 10.1016/j.eururo.2015.10.042

Figure Lengend Snippet: ESR1 is upregulated in response to degarelix treatment. (A) Dot plots to show mRNA expression levels of ESR1 in untreated and degarelix-treated prostate cancer (PCa) samples by expression array. (Bi) Using the Gene Set Enrichment Analysis (GSEA) to examine the distribution of known genes with the ESR1 binding motif, shown within their promoter regions, we found that these genes were enriched among genes that degarelix treatment upregulated when they were ranked by their statistical significance. The ESR1 binding motif analysed was described previously . (Bii) This ESR1 binding motif closely matches the validated, experimentally derived ESR1 binding motif shown here. (C) GSEA demonstrates enrichment of factors known to be involved with ESR1 signalling (from the National Cancer Institute BIOCARTA curated database) among genes differentially expressed in response to degarelix ranked by statistical significance. For this analysis, the degree to which the genes were enriched is defined by the running sum statistic called the normalised enrichment score , which was 2.036 (false discovery rate q -value of 0.027; p = 0.024). (D) Representative images of PCa samples stained by immunohistochemistry (IHC) for ESR1 in untreated and degarelix-treated patients with intense nuclear staining seen in the malignant epithelia of the treated but not the untreated samples. Scale bars = 250 μm. (E) IHC ESR1 staining was increased in treated (+) compared with untreated (−) PCa samples in malignant epithelia but not cancer-associated stroma or benign epithelia (samples in triplicate; sample sizes [ n ] indicate the number of subjects [20 or 27] times 3 minus missing or damaged samples on the human tissue microarray; staining intensity 0 [none] to 3 [strong]). Mean intensities from replicate samples for each patient were used to calculate statistical significance when comparing treated and untreated groups (Mann-Whitney test). (F) Graph shows correlation between intensity of staining by IHC for ESR1 and Ki-67. Spearman's ρ correlation coefficient of 0.338 ( p = 0.041).

Article Snippet: We used Gene Set Enrichment Analysis (GSEA) version 2.0.14 (The Broad Institute, Cambridge, MA, USA).

Techniques: Expressing, Binding Assay, Derivative Assay, Staining, Immunohistochemistry, Microarray, MANN-WHITNEY

Journal:

Article Title: Early Expression of Stem Cell-Associated Genes Within The CD8 Compartment After Treatment With a Tumor Vaccine

doi: 10.1016/j.cellimm.2010.07.004

Figure Lengend Snippet: (A) Tumor-bearing and tumor-free mice were generated by the subcutaneous inoculation of 106 AGN2a cells or PBS, respectively, on Day 0. Mice were treated with 250μg of anti-CD25 monoclonal antibody intraperitoneally (Day 3) and/or vaccinated with 2×106 AGN2a-4P vaccine cells given subcutaneously on Days 6. CD8+ splenocytes were collected from 5–6 mice on Day 11 by immunomagnetic cell sorting. RNA was extracted and pooled for gene expression profiling on the Affymetrix GeneChip® Mouse Genome 430 2.0 microarray. GSEA was used to analyze the combined gene expression data of two independent experiments. The “Stemcell_Common_Up” gene set was identified as being enriched in treated tumor-free mice relative to treated tumor-bearing mice. The enrichment profiles of the “Stemcell_Common_Up” gene set are shown for mice given No Treatment (B), Vaccine (C) or Vaccine+anti-CD25 (D). For each enrichment profile, a rank ordered gene list was generated between tumor-free and tumor-bearing mice, in which all genes in the microarray were ordered from highest differential expression in tumor-free (left/red end of bar) to the highest differential expression in tumor-bearing (right/blue end of bar). Black lines represent the location of the “Stemcell_Common_Up” genes in the rank ordered gene list. A summing generates a running enrichment score (green line) which yields the overall enrichment of the gene set at the maximum deviation from zero.

Article Snippet: Importantly, this stem cell-related gene set was not enriched in the CD8 + T cells of non-treated tumor-free mice as compared to non-treated tumor-bearing mice (p=0.749, FDR=0.834, ) indicating that this finding is related to the vaccine-induced immune response and not simply a reflection of the presence or absence of tumor. table ft1 table-wrap mode="anchored" t5 caption a7 P value False Discovery Rate No Treatment 0.749 0.834 Vaccine < 0.001 0.003 Vaccine + Anti-CD25 < 0.001 0.019 Open in a separate window caption a8 Enrichment of the “Stemcell_Common_Up” gene set in tumor-free mice relative to tumor-bearing mice Gene Set Enrichment Analysis (GSEA) was used to examine coordinated changes in the gene expression profile of tumor-free and tumor-bearing mice after undergoing treatment with vaccine ± anti-CD25.

Techniques: Generated, FACS, Gene Expression, Microarray, Quantitative Proteomics

Journal:

Article Title: Early Expression of Stem Cell-Associated Genes Within The CD8 Compartment After Treatment With a Tumor Vaccine

doi: 10.1016/j.cellimm.2010.07.004

Figure Lengend Snippet: The leading edge genes from the “Stemcell_Common_Up” gene set were identified in the comparison of CD8+ T cells from tumor-free and tumor-bearing mice treated with vaccine and anti-CD25. The median expression of the leading edge genes was calculated using GSEA software, and was examined in each treatment group relative to CD8+ T cells from naïve (tumor-free, non-treated) mice. Results were averaged from two independent experiments, normalized and hierarchically clustered using Genesis software [20].

Article Snippet: Importantly, this stem cell-related gene set was not enriched in the CD8 + T cells of non-treated tumor-free mice as compared to non-treated tumor-bearing mice (p=0.749, FDR=0.834, ) indicating that this finding is related to the vaccine-induced immune response and not simply a reflection of the presence or absence of tumor. table ft1 table-wrap mode="anchored" t5 caption a7 P value False Discovery Rate No Treatment 0.749 0.834 Vaccine < 0.001 0.003 Vaccine + Anti-CD25 < 0.001 0.019 Open in a separate window caption a8 Enrichment of the “Stemcell_Common_Up” gene set in tumor-free mice relative to tumor-bearing mice Gene Set Enrichment Analysis (GSEA) was used to examine coordinated changes in the gene expression profile of tumor-free and tumor-bearing mice after undergoing treatment with vaccine ± anti-CD25.

Techniques: Comparison, Expressing, Software

Journal:

Article Title: Early Expression of Stem Cell-Associated Genes Within The CD8 Compartment After Treatment With a Tumor Vaccine

doi: 10.1016/j.cellimm.2010.07.004

Figure Lengend Snippet: Enrichment of the “Stemcell_Common_Up” gene set in tumor-free mice relative to tumor-bearing mice Gene Set Enrichment Analysis (GSEA) was used to examine coordinated changes in the gene expression profile of tumor-free and tumor-bearing mice after undergoing treatment with vaccine ± anti-CD25. Gene expression data from two independent experiments was combined and analyzed by GSEA. Of the 1360 gene sets used to interrogate the gene expression data, only the “Stemcell_Common _Up” gene set was found to be consistently enriched in vaccinated tumor-free mice relative to tumor-bearing mice receiving the same treatment. Values above represent the p value and False Discovery Rate (FDR) of the enrichment of the “Stemcell_Common _Up” gene set in each treatment group.

Article Snippet: Importantly, this stem cell-related gene set was not enriched in the CD8 + T cells of non-treated tumor-free mice as compared to non-treated tumor-bearing mice (p=0.749, FDR=0.834, ) indicating that this finding is related to the vaccine-induced immune response and not simply a reflection of the presence or absence of tumor. table ft1 table-wrap mode="anchored" t5 caption a7 P value False Discovery Rate No Treatment 0.749 0.834 Vaccine < 0.001 0.003 Vaccine + Anti-CD25 < 0.001 0.019 Open in a separate window caption a8 Enrichment of the “Stemcell_Common_Up” gene set in tumor-free mice relative to tumor-bearing mice Gene Set Enrichment Analysis (GSEA) was used to examine coordinated changes in the gene expression profile of tumor-free and tumor-bearing mice after undergoing treatment with vaccine ± anti-CD25.

Techniques: Gene Expression

Journal: Breast Cancer Research : BCR

Article Title: Key regulators of lipid metabolism drive endocrine resistance in invasive lobular breast cancer

doi: 10.1186/s13058-018-1041-8

Figure Lengend Snippet: Cholesterol synthesis is predicted to be upregulated in long-term estrogen deprivation (LTED) cells. (a, b) Gene set enrichment analysis (GSEA) of ( a ) E2F activation signature and ( b ) cholesterol biosynthesis signature (Reactome Cholesterol Synthesis) in LTED variants. Differential expression (DE) genes used in GSEA were ranked by log2(fold change). c Growth of parental and LTED cells with treatment of 25-hydroxycholesterol (25-HC) and 27-hydroxycholesterol (27-HC). Parental cells were hormone-deprived before being seeded in hormone-deprived media (charcoal-stripped fetal bovine serum, or CSS). Cells were collected after 5-day treatment. Fold growth was compared with control group (data not shown), which was treated with vehicle (ethanol). Plots are representative of at least two independent experiments. Data are mean ± standard deviation (SD) of six replicates. One-way analysis of variance (ANOVA) followed by Dunnett’s post hoc test for multiple comparisons was used to test the significance between 25-HC/27-HC–treated groups to the control groups (data not shown), * P <0.05, ** P <0.01, *** P <0.001. d The activation z-score of sterol regulatory element-binding proteins (SREBPs) in LTED cells. The upstream regulator analysis was performed in individual LTED cell variants separately with Ingenuity Pathway Analysis (IPA) software. DE genes (absolute log2(fold change) > log2(1.5) and adjusted P value of less than 0.001) and their log2(fold change) were used as input. Upstream regulators with z-score of more than 2 were defined as “activated” (labeled in red). Abbreviation: ES enrichment score.

Article Snippet: GseaPreranked function in Gene Set Enrichment Analysis (GSEA) (version 2.2.2, Broad Institute, Cambridge, MA, USA) was performed using the Reactome cholesterol synthesis signature (Additional file : Table S4), downloaded from the Molecular Signature Database (MsigDB, version 6.0, Broad Institute).

Techniques: Activation Assay, Quantitative Proteomics, Control, Standard Deviation, Binding Assay, Software, Labeling