Journal: Computers in biology and medicine

Article Title: GILEA: In silico phenome profiling and editing using GAN Inversion.

doi: 10.1016/j.compbiomed.2024.108825

Figure Lengend Snippet: Fig. 2. Reconstruction visualization of GILEA and quantitative comparison of drug responses between the baseline [7] and 𝑑𝖫𝖤𝖠(Proposed). a (VERO) and f (HRCE): The reconstructed samples obtained by GILEA. b (VERO) and g (HRCE): The quantitative comparison between the hit score [7] and 𝑑𝖫𝖤𝖠with the latent representations of all concentrations. c (VERO) and h (HRCE): The violin plot of overall comparison between the hit score [7] and 𝑑𝖫𝖤𝖠. d (VERO) and i (HRCE): The quantitative comparison between the hit score [7] and 𝑑𝖫𝖤𝖠with the latent representations of optimal drug concentration. e (VERO) and j (HRCE): The hierarchical clustering of top 50 drug compounds (if exist) w.r.t. the 5 largest eigenvalues of the latent representations of optimal drug concentration.

Article Snippet: For VERO and HRCE cell-lines, Remdesivir and GS-441524 are consistently identified as effective compounds w.r.t. individual fluorescent channels as well as all channels, which supports the clinical utility of Remdesivir approved by U.S. Food and Drug Administration (FDA).2 Meanwhile, the heterogeneous effects of Chloroquine and Hydroxychloroquine are also revealed in our refined analysis.

Techniques: Comparison, Concentration Assay

Journal: Computers in biology and medicine

Article Title: GILEA: In silico phenome profiling and editing using GAN Inversion.

doi: 10.1016/j.compbiomed.2024.108825

Figure Lengend Snippet: Fig. 4. Identification of drug-concentration dependent effects and visual interpretation for key drugs of interest in the HRCE cell-line. a, The proposed 𝑑𝖫𝖤𝖠of different drug concentrations for individual and all fluorescent channels. Here, we report the mean 𝑑𝖫𝖤𝖠(with standard deviation) averaged on 4 randomly sampled cell collections. b, The PCA plots and phenotypic transitions driven by manipulating the largest (top) and 5 largest (bottom) principal component(s). The bounding box indicates the reconstructed image.

Article Snippet: For VERO and HRCE cell-lines, Remdesivir and GS-441524 are consistently identified as effective compounds w.r.t. individual fluorescent channels as well as all channels, which supports the clinical utility of Remdesivir approved by U.S. Food and Drug Administration (FDA).2 Meanwhile, the heterogeneous effects of Chloroquine and Hydroxychloroquine are also revealed in our refined analysis.

Techniques: Concentration Assay, Standard Deviation

Journal: BMC Cancer

Article Title: Preclinical efficacy of dual mTORC1/2 inhibitor AZD8055 in renal cell carcinoma harboring a TFE3 gene fusion

doi: 10.1186/s12885-019-6096-0

Figure Lengend Snippet: Cell viability, cytotoxicity and cell cycle progression in TfRCC cell lines treated with mTOR inhibitors. a , b Cell viability, as measured by MTT assay for TfRCC cell lines and the benign renal epithelial cell line HRCE after 72 h of treatment with up to 1000 nM concentrations of the dual mTORC1/2 inhibitor, AZD8055 ( a ), or selective mTORC1 inhibitor, sirolimus ( b ). Viability in TfRCC cells was suppressed by approximately 80–90% with AZD8055 and 30–50% with sirolimus relative to the untreated (0 nM drug) condition. Both drugs inhibited growth to a greater degree in TfRCC cells than in benign renal cells. c , d Cell cytotoxicity, as measured by LDH release by UOK120 and UOK146 TfRCC cell lines after 48 h of treatment with 1 μM of AZD8055 ( c ) or sirolimus ( d ). Only slight cytotoxicity in UOK120 cells and no cytotoxicity in UOK146 cells was observed after AZD8055 treatment, while sirolimus treatment had no cytotoxic effect. Multi protein inhibitor LY294002 [100 μM] was used as a positive control. e , f Relative fraction of cells in S-phase of the cell cycle, as measured by BrdU incorporation in UOK120 ( e ) and UOK146 ( f ) cell lines treated for 24 h with low (50 nM) and high (500 nM) concentrations of AZD8055 or sirolimus. Dose-dependent reductions in S-phase in both cell lines with either drug mirror the magnitude of reductions observed in cell viability ( a , b ), supporting a predominantly cytostatic mechanism of growth inhibition for both drugs. * p < 0.05; ** p < 0.01; *** p < 0.001; NS = non-significant

Article Snippet: RCC4 was obtained from ECACC General Cell Collection (Salisbury, UK; Cat Nr. 03112702) and the human renal cortical epithelial (HRCE) cell line was obtained from ATCC (Manassas, VA; Cat Nr. PCS-400-011).

Techniques: MTT Assay, Positive Control, BrdU Incorporation Assay, Inhibition