Journal: Nature Communications

Article Title: A phenopushing platform to identify compounds that alleviate acute hypoxic stress by fast-tracking cellular adaptation

doi: 10.1038/s41467-025-57754-1

Figure Lengend Snippet: a Overview of AH-to-CH phenopushing screening and hit-calling framework. N: Normoxia. AH: Acute hypoxia (1 d). CH: Chronic hypoxia (6 d). D: Distance from the phenotypic profile of a perturbation (a given compound at a given dose) to the centroid of the phenotypic profiles of CH DMSO controls. θ : Angle of deviation from the phenotypic profile of a perturbation relative to the centroid of the phenotypic profiles of CH DMSO controls. The cell icons: Created in BioRender. Wu, A. (2025) https://BioRender.com/q85j552 . b Summary of geometric hit calls in the primary screen. Scatter plot and density map for distance (x-axis) and direction (y-axis) of bioactive compounds. Red solid line and dotted line show cutoffs for distance and angle, respectively. Vehicle (DMSO) controls in N, AH, and CH are shown for reference. Bioactive non-hit compounds (black dots), hits (red dots), and four hit examples (large red dots) are shown. c Screening funnel for AH-to-CH phenopushing hits. d Representative images for DMSO under N, AH, or CH compared to hit examples (highlighted in b) in AH (Temsirolimus, Deforolimus, KU-0063794, WYE-354). The experiment was independently repeated three times with similar results. Source data are provided as a Source Data file.

Article Snippet: Screened compounds included (1) Selleck FDA-approved & Passed Phase I Drug Library (L3800), (2) Selleck Kinase Inhibitor Library (L1200), (3) Selleck Apoptosis Compound Library (L3300), (4) Selleck Epigenetics Compound Library (L1900), (5) Selleck Bioactive Library (L1700), (6) manually curated FDA-approved & Passed Phase I drugs from other vendors, and (7) manually curated bioactive compounds from other vendors.

Techniques:

Journal: Nature Communications

Article Title: A phenopushing platform to identify compounds that alleviate acute hypoxic stress by fast-tracking cellular adaptation

doi: 10.1038/s41467-025-57754-1

Figure Lengend Snippet: a Overview of the ischemia rescue assay. The cell icons: Created in BioRender. Wu, A. (2025) https://BioRender.com/q85j552 . b Scatter plot of hit compound effects on HepG2 survival in ischemia-like stress. Cell survival: normalized to DMSO-treated cells, averaged across all tested well replicates and doses for each drug, and ranked based on their survival rate. Dashed lines: survival of DMSO-treated hypoxia naïve cells (bottom) or DMSO-treated cells pre-exposed to hypoxia for 6 days (top). mTOR/PI3Ki: AH-to-CH phenopushing hits targeting mTOR and/or PI3Ks. BETi: AH-to-CH phenopushing hits targeting BET proteins. Other: AH-to-CH phenopushing hits other than mTOR/PI3Ki and BET proteins. c Normalized cell survival of each tested dose for the top 25 hits shown in b . d Ischemia rescue effect comparison between the most effective tested dose of phenopushing (red) and non-phenopushing, bioactive (blue) compounds. Kernel density estimation used to smooth histograms. Dashed lines: (grey) mean survival of DMSO-treated cells or (red) 3x DMSO survival. Source data are provided as a Source Data file.

Article Snippet: Screened compounds included (1) Selleck FDA-approved & Passed Phase I Drug Library (L3800), (2) Selleck Kinase Inhibitor Library (L1200), (3) Selleck Apoptosis Compound Library (L3300), (4) Selleck Epigenetics Compound Library (L1900), (5) Selleck Bioactive Library (L1700), (6) manually curated FDA-approved & Passed Phase I drugs from other vendors, and (7) manually curated bioactive compounds from other vendors.

Techniques: Rescue Assay, Comparison

Journal: International Journal of Molecular Sciences

Article Title: Pluripotent Stem Cell-Derived Hepatocytes Phenotypic Screening Reveals Small Molecules Targeting the CDK2/4-C/EBPα/DGAT2 Pathway Preventing ER-Stress Induced Lipid Accumulation

doi: 10.3390/ijms21249557

Figure Lengend Snippet: High-throughput screening performance of bioactive compounds in hiPSC-Hep. ( A ) Integrated spot signal (ISS) vs. valid cell count in 2D scatter plot for hiPSC-Hep seeded at 24K (green, Z’ = 0.38), 30K (pink, Z’ = 0.57) and 36K (blue, Z’ = 0.62) per well cell densities. Average of TG/FA treated wells (green squares) and average of BSA-treated cells (blue dots) per screening plate for ( B ) ISS relative values of BODIPY 493/503 fluorescence imaged in the green channel and ( C ) valid cell count relative to values of Hoechst 33342 fluorescence detected in the blue channel. Each data point represents the mean relative ISS from six fields per well and the average of 16 wells per plate. ( D ) Determined Z’ scores (dark green line) and robust Z’ scores (RZ’ light green line) calculation for ISS values in TG/FA vs. BSA treated controls per assay plate.

Article Snippet: We collaborated with AstraZeneca Open Innovation Group and obtained a copy of their annotated library set of 13,000 bioactive compounds.

Techniques: High Throughput Screening Assay, Cell Counting, Fluorescence

Journal: Memórias do Instituto Oswaldo Cruz

Article Title: Past and future of trypanosomatids high-throughput phenotypic screening

doi: 10.1590/0074-02760210402

Figure Lengend Snippet: HCS-based assays employed in trypanosomatid drug discovery

Article Snippet: , L. donovani , Laboratory strain: MHOM/SD/62/1S-cl2D , Intracellular amastigotes , None , Human acute monocytic leukemia (THP-1) cells , Number of host cells (cytotoxicity evaluation) and number of amastigotes per cell , Parasites kDNA and cell nucleus detected by DAPI. Cell boundary was delineated around the nucleus object. , 909 bioactive compounds library from Iconix Biosciences , Primary screening and cytotoxicity evaluation performed in the same assay. A similar method was used to generate the dose-response curves , (96).

Techniques: Infection, Immunostaining, Cytotoxicity Assay, Activity Assay, Luciferase, Proliferation Assay, Imaging, Time-Kill Assay, Derivative Assay, Expressing, Drug discovery, Staining, Labeling, SYBR Green Assay