Journal: EBioMedicine

Article Title: Integrative proteogenomic analyses of human tumours identifies ADNP as a novel oncogenic mediator of cell cycle progression in high-grade serous ovarian cancer with poor prognosis

doi: 10.1016/j.ebiom.2019.11.009

Figure Lengend Snippet: Patterns of pathway activity in HGSOC. (a) Patterns of pathway activity ( n = 62) were determined for each sample ( n = 488) in the TCGA high-grade serous ovarian cancer cohort and plotted relative to the previously described molecular subtypes. Expression signatures ( y -axis) are median centered and clustered by complete linkage hierarchical clustering (b) ANOVA test followed by Tukey pairwise comparison was used to demonstrate statistically significant difference in signature score across the molecular subtypes. (c) Principal Component Analysis (PCA) was used to demonstrate the spatial distribution of subtypes based on the expression patterns of the 62 signature scores. Subtype colouring is the same as in (a). (d) Pearson Correlation coefficient (r-values) for the top 10 most strongly and consistently correlated pathways are shown relative to the Poor Prognosis Signature (PPS) for the TCGA cohort.

Article Snippet: To assess the essentiality of ADNP relative to the PPS signature score, ovarian cancer cell line shRNA abundance data was acquired from the Broad Institute Project Achilles dataset .

Techniques: Activity Assay, Expressing, Comparison

Journal: EBioMedicine

Article Title: Integrative proteogenomic analyses of human tumours identifies ADNP as a novel oncogenic mediator of cell cycle progression in high-grade serous ovarian cancer with poor prognosis

doi: 10.1016/j.ebiom.2019.11.009

Figure Lengend Snippet: Identification of essential genes associated with PPS activity. (a) A subset of 39 genes from the 131 candidate genes were found to be consistently associated with PPS score in the TCGA, Tothill and Yoshihara datasets. (b) mRNA expression (red indicates high mRNA expression; green corresponds to low mRNA expression) of 39 candidate genes in TCGA datasets. (c-d) Analysis of data from a genome-wide RNAi screen in 29 ovarian cancer cell lines ( n = 29) identified (c) ADNP and (d) AKAP8L as being essential for cell viability relative to the PPS score (Spearman rank correlation). (e) ADNP ( p = 0.02; HR: 1.2) but not AKAP8L ( p = 0.77; HR: 0.96) copy number status corresponds with overall survival in the TCGA cohort (log-rank test). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: To assess the essentiality of ADNP relative to the PPS signature score, ovarian cancer cell line shRNA abundance data was acquired from the Broad Institute Project Achilles dataset .

Techniques: Activity Assay, Expressing, Genome Wide

Journal: EBioMedicine

Article Title: Integrative proteogenomic analyses of human tumours identifies ADNP as a novel oncogenic mediator of cell cycle progression in high-grade serous ovarian cancer with poor prognosis

doi: 10.1016/j.ebiom.2019.11.009

Figure Lengend Snippet: ADNP is a putative oncogene associated with PPS score. (a) ADNP copy number, mRNA, protein expression is positively correlated with PPS in the TCGA and CPTAC cohorts (FDR-corrected Spearman rank correlation). (b-c) ADNP mRNA expression (top quartile vs bottom quartile) corresponds with poor overall survival in the (b) Tothill cohort ( p = 0.02; HR: 1.9) and (c) Yoshihara cohort ( p = 0.04; HR: 1.7) by log-rank test. (d) ADNP mRNA expression (red indicates high mRNA expression; green corresponds to low mRNA expression) was found to be strongly associated with a panel of proliferation and proliferation-associated gene expression signatures in the TCGA cohort ( n = 488) by Spearman rank correlation, (e) ADNP mRNA expression correlates with cell cycle protein expression ( p < 0.05 for all proteins) based on RPPA analysis of 338 samples from the TCGA study by Spearman rank correlation.

Article Snippet: To assess the essentiality of ADNP relative to the PPS signature score, ovarian cancer cell line shRNA abundance data was acquired from the Broad Institute Project Achilles dataset .

Techniques: Expressing, Gene Expression

Journal: Radiation Oncology Journal

Article Title: PA1 cells containing a truncated DNA polymerase β protein are more sensitive to gamma radiation

doi: 10.3857/roj.2021.00689

Figure Lengend Snippet: Cell cycle analysis by flow-cytometry. (A) Analysis of the cell cycle of PA1 cells after 48 hours of γ-radiation treatment. Cells were arrested in the G2/M phase with increasing doses of radiation. (B) The graph showed significantly more cells were arrested in the G2/M phase in the case of 10 Gy and 15 Gy of radiations (n = 3; ** p < 0.001). (C) PA1PolβΔ cells after 48 hours of γ-radiation treatment. (D) In the case of the PA1PolβΔ cell cycle, the G2/M phase was arrested in significantly more cells in every dose of radiations (n = 3; ** p < 0.001).

Article Snippet: PA1 cells were obtained from the National Centre for Cell Science, Pune, India.

Techniques: Cell Cycle Assay, Flow Cytometry

Journal: Radiation Oncology Journal

Article Title: PA1 cells containing a truncated DNA polymerase β protein are more sensitive to gamma radiation

doi: 10.3857/roj.2021.00689

Figure Lengend Snippet: Apoptosis analysis by Annexin V-FITC/PI using flow-cytometry after 48 hours of treatment. All results are expressed as mean ± standard deviation three individual experiments, and error bar indicating standard deviation ( * p < 0.05, ** p < 0.001). (A) Control cells, i.e., non-treated cells, are mostly live cells. (B) PA1 and PA1PolβΔ cells were treated with a 5 Gy dose. (C) PA1 and PA1PolβΔ cells were treated with a 10 Gy dose. (D) PA1 and PA1PolβΔ cells were treated with a 15 Gy of dose.

Article Snippet: PA1 cells were obtained from the National Centre for Cell Science, Pune, India.

Techniques: Flow Cytometry, Standard Deviation, Control