Hypoxia inducible pathway Measured in Cell-Based System Using Imaging - 2030-03_Activator_Dose_DryPowder_Activity_Set3
Assay Overview: High content cell imaging assay on human osteosarcoma U2OS cells over-expression GFP-HIF1alpha to identify compounds inducing hypoxia inducible factor (HIF) expression and nuclear translocation. The small molecules inducing an increased nuclear fluorescent mediated by GFP-HIF1alpha will be considered as active. ..more
BioActive Compounds: 59
Keywords: nuclear translocation and GFP
Assay Overview: High content cell imaging assay on human osteosarcoma U2OS cells over-expression GFP-HIF1alpha to identify compounds inducing hypoxia inducible factor (HIF) expression and nuclear translocation. The small molecules inducing an increased nuclear fluorescent mediated by GFP-HIF1alpha will be considered as active.
Expected Outcome: Confirmation that compounds inducing transcriptional activation of hypoxia responsive element (primary screen) are also acting through induction of HIF expression and nuclear transcription. Compounds increasing the presence of GFP-HIF1alpha in the nucleus measured by fluorescent microscopy (average nuclear intensity) to 30% the level of the positive control with an EC50 below 33 uM will be considered as actives.
U2OS HIF1a-GFP High Content Imaging Screen assay:
The U2OS-human HIF1a-GFP cell line (Thermo Scientific, Cat No.066_02) (http://www.thermoscientific.com/wps/portal/ts/products/detail?navigationId=L10770&categoryId=82097&productId=11961949) is propagated in DMEM media (Invitrogen, SKU No.11995) supplemented with 10% heat inactivated fetal bovine serum (Invitrogen, Cat. No. 16140089), 1% penicillin/streptomycin/glutamine (Invitrogen, 10378-016) and 0.5 mg/ml Geneticin (Invitrogen, 10131-027) at 37C in carbon dioxide incubators (Thermo Scientific) with 5% carbon dioxide, 21% oxygen, and 95% humidity. For High-Throughput Screening assays, cells are grown in T175 flask (BD Falcon, Ref No. 353112) or Hyperflasks (Corning, Cat No. 10010), harvested at more than 80% confluence using 7 or 75 ml Trypsin-EDTA 0.25% (Cellgro, Cat. No. 25-053-CI) for 5 minutes and then the trypsin is inactivated with 7 or 75 ml of complete medium respectively. Cells should not be trypsinized more than 10 minutes because massive cell death will start to occur. Cells are centrifuged at 1000rpm/5min and resuspended in fresh complete DMEM media with phenol red (Invitrogen, SKU No.11995) as mentioned above (for normal cell propagation) or DMEM medium without phenol red (LONZA; Cat. No 12-917F) with 10% heat inactivated fetal bovine serum (Invitrogen, Cat. No. 16140089), 1% penicillin/streptomycin/glutamine (Invitrogen, 10378-016) without Geneticin (for compound screening). Cell number is counted using a Nexelcom Bioscience cell counter (Cellometer(r) Auto M10) and viability is measured by mixing one volume of cells with one same volume of Trypan Blue solution (0.4%)(dilution 1/2). Only cultures of >94% viability are utilized for HTS.
Compound Screening is carried out on the Broad Institute/Chemical Biology Platform Walkup automation system (Cy-Bi Well) and microscope (ImageXpress, Molecular Devices) units.
Day 1 (Cell plating):
1. U2OS-HIF1a-GFP cells are harvested and resuspended in DMEM without phenol red (LONZA, 12-917F) with 10% heat inactivated fetal bovine serum (Invitrogen, Cat. No. 16140089), 1% penicillin/streptomycin/glutamine (Invitrogen,10378-016) without Geneticin. U2OS HIF1a-GFP cells (from an initial cell suspension of 60,000 cells/ml) are dispensed using a MultiDrop Combi/Standard tube dispensing cassette (Thermo Scientific) in 384-well black with clear bottom tissue treated barcoded assay plates (Corning, Cat.No. 8816BC) at a final density of 2,000 cells per well in final volume of 50 ul. The cells are kept in suspension using a magnetic bar and a stirrer during the dispensing.
2. The assay plate (cell plate) are placed in Liconic Instruments cassettes (22 plates/cassette) and incubated for 24 hours at 37C in the Liconic incubators (Automation system)(Liconic Instruments) calibrated at 5% carbon dioxide, 21% oxygen, and 95% humidity.
Day 2 (Cherry pick compound pinning into assay plate):
3. The dose response test compounds plates ( 8 concentrations, dilution factor of 3, starting concentration at 33 microM) are double pinned (2x100 nl) along with the in-plate positive control (32 wells, 200 uM Desferrioxamine DFX, Sigma-Aldrich Cat No.D9533, BRD-K09821361-066-08-4) and transferred into one assay plate. Each compound plate is pinned twice in 2 different assay plates (duplicate).
4. The assay plates treated with compounds are moving back to Liconic carbon dioxide incubator to be incubated for an additional 24 hours.
Day 3 (Plate processing and reading assay plates on microscope):
5. The assay plates are washed twice with PBS (50 ul) and fixed with 2% formaldehyde in water for 20 minutes at room temperature. The assay plates are washed twice again and resuspended in 50 ul PBS with 40 ug/ml DAPI (Invitrogen, D3571). The assay plates are physically transferred to the microscope (ImageXpress, Molecular Devices) where the reading is occurring. Pictures are taken at magnification of 10X and images are processed using MetaXpress software. The average nuclear intensity was used as readout for this assay.
PRESENCE OF CONTROLS: Neutral control wells (NC; n=32) and positive control wells (PC; n=32) were included on every plate.
EXPECTED OUTCOME: Active compounds result in increasing readout signal.
ACTIVE CONCENTRATION LIMIT:
For each sample, the highest valid tested concentration (Max_Concentration) was determined and the active concentration limit (AC_limit) was set to equal Max_Concentration.
The raw signals of the plate wells were normalized using the 'Stimulators Minus Neutral Controls' method in Genedata Assay Analyzer (v7.0.3):
The median raw signal of the intraplate neutral control wells was set to a normalized activity value of 0.
The median raw signal of the intraplate positive control wells was set to a normalized activity value of 100.
Experimental wells values were scaled to this range.
PATTERN CORRECTION: No plate pattern correction algorithm from Genedata Condoseo (v.7.0.3) was applied.
MEASUREMENT USED TO DETERMINE ACTIVE CONCENTRATION (AC): absACnn, the concentration at which the curve crosses threshold 40.0
AC values were calculated using the curve fitting strategies in Genedata Screener Condoseo (7.0.3).
AC values were calculated up to the active concentration limit described for each sample.
pAC was set to equal -1*log10(AC)
Activity_Outcome = 1 (inactive) when:
a) compound shows activity but in a direction opposite to the expected outcome
in these cases, values describing curve fitting parameters (Sinf, S0, Hill Slope, log_AC50, log_AC50_SE) are set to null
b) curve fit is constant where activity is > -30% and < 30% at all tested concentrations, or
c) AC > AC_limit
Activity_Outcome = 2 (active) when:
AC <= AC_limit
Activity_Outcome = 3 (inconclusive) when:
a) Curve fitting strategy resulted in a constant fit with activity >= 30% but <= 70%, or
b) The fit was deemed not valid due to poor fit quality.
If PUBCHEM_ACTIVITY_OUTCOME = 1 (inactive) or 3 (inconclusive),
then PUBCHEM_ACTIVITY_SCORE = 0
If PUBCHEM_ACTIVITY_OUTCOME = 2 (active)
then PUBCHEM_ACTIVITY_SCORE = (10)(pAC)
Scores relate to AC in this manner:
120 = 1 pM
90 = 1 nM
60 = 1 uM
30 = 1 mM
0 = 1 M
When the active concentration (AC) is calculated to be greater than the highest valid tested concentration (Max_Concentration), the PUBCHEM_ACTIVITY_SCORE is calculated using Max_Concentration as the basis.
When the active concentration (AC) is calculated to be less than the lowest tested concentration, the PUBCHEM_ACTIVITY_SCORE is calculated using the lowest tested concentration as the basis.
The individual dose data point columns ('Activity_at_xxuM') reported here represent the median of valid (unmasked) replicate observations at each concentration. These values are the inputs to a curve fitting algorithm.
All other data columns represent values which are derived during the curve fitting algorithm; this may sometimes include automatic further masking of some replicate data points.
Occasionally this results in perceived inconsistencies: for example, between the derived 'Maximal_Activity' and the apparent most active data point.
Categorized Comment - additional comments and annotations
* Activity Concentration. ** Test Concentration.
Data Table (Concise)