External ID: CF Folding
Protocol:
A high throughput 384-well microplate based fluorescence assay was developed using HeLa cells engineered to express F508del-CFTR. Cells were maintained in cell culture media (High Glucose DMEM (Gibco) supplemented w/ 10% FBS (Gibco)). For the assay, cells were trypsinized (0.25% Trypsin-EDTA solution (Gibco)) and resuspended in assay media (cell culture media + 1% Pen/Strep (Gibco)) at a density of 320,000 cells per ml. Cells were dispensed to the assay plates (Corning 3712) in 25 ul using a Wellmate (Matrix/Thermo). Plates were incubated overnight at 37C, 5% CO2 and high humidity. The next day, compounds were prepared by making a dilution in assay media to a concentration of either 150 uM or 60 ug/ml (6x) depending on the library being screened. Then 5 ul of the diluted compound was transferred to the assay plate containing the cells. Assay plates were incubated for 24 hours 37C, 5% CO2 and high humidity. Following incubation with the compounds, relative cell number was determined by adding 3 ul of alamarBlue (TREK Diagnostics) and incubating the plates at 37C, 5% CO2 and high humidity, until cell control values reached ~4 million, as measured with a fluorescent intensity protocol on an Envision multimode plate reader (Perkin Elmer) (excitation 535 nm, emission 595 nm wavelengths) . Following the alamarBlue read, the media was removed and the cells were fixed with the addition of 13 ul of 4% paraformaldehyde in PBS (pH 7.4) and incubated for 10 minutes at room temperature. Plates were washed twice with PBS to remove the fixative. Cells were permeabilized with the addition of blocking solution (PBS, 0. 1% Triton X-100, 10 mg/ml BSA) and incubated at room temperature for 30 minutes. The blocking solution was removed and the primary antibody mixture was added in 13ul (Antibodies UNC570 and UNC596; CFF Therapeutics, Inc., Bedford, MA) at a 1/5000 dilution of each antibody in blocking solution. Plates were then incubated over night at 4oC. Primary antibody was removed by washing three times with 50 ul of wash solution (PBS, 0.1% Triton X-100) with at least 5 minutes between wash cycles. Secondary antibody (Alexa 488 anti-mouse IgG Invitrogen) was then added in a volume of 13 ul (1/1000 dilution in blocking solution) and incubated for two hours at room temperature in the dark. To remove excess secondary antibody, plates were washed three times with 50 ul of wash solution and one time with 50 ul of PBS. Plates were read from the bottom using a fluorescent intensity protocol on an Envision multimode plate reader (485 nm excitation and 535 nm emission).
To minimize the disruption of the cell monolayer during the numerous washes, the following process was used. The removal of media or other reagents for the wells of the microtiter plate was done using a Biomek FX (Beckman, Fullerton CA) with a 384 tip multichannel head. Aspiration was done at a slow rate following the liquid level with the tip positioned in the top right corner of the well. All solution additions, starting with the fixative, were done with a Matrix Wellmate. Again to avoid disturbing the cell monolayer, the plate offset was adjusted so that the liquid dispensed to the left wall of the well rather than directly on the cell monolayer.
For the screen, approximately ten thousand compounds from a mix of FDA and diverse libraries (MicroSource Pharmacon-1600 (FDA), Enzo (FDA), Selleck (FDA) and Enamine) were tested at a final concentration 25 uM (Enzo, Selleck & MS Pharmakon) or 10 ug/ml (Enamine 30K diversity set). The proteasome inhibitor ALLN was used as the positive control (50 uM) and 100 uM Hyamine was used as a viability control on all microtiter plates. All wells including the cell controls contained 0.5% DMSO. In-plate controls were used to normalize the data and results were reported as fold increase above the cell control and normalized to relative cell number derived from the alamarBlue data.
Ninety six compounds identified in the single dose screen were evaluated further in dose response. Compound high dose was twice the screening concentration and a ten point series of two fold dilutions were done for each compound. DMSO concentration was 1% for in all wells. Compounds were evaluated in both the immunostain assay and in the cell viability assay.
Data Analysis: Thirty two control wells containing cells only, 24 wells containing Hyamine and 8 wells containing ALLN were included on each assay plate and used to calculate Z' value for each plate and to normalize the data on a per plate basis. Data were analyzed using the IDBS Activity Base software. Results were expressed as Fold Increase (FI) for the immunostain assay and cell viability (V) for the alamarBlue assay. Final data was reported as Normalized fold increase (NFI). Data was analyzed as follows FI=DataValue/Median cell control, V= (DataValue-median Hyamine control)/(median cell control -median Hyamine control) and NFI=FI/V.
For the immunostain dose response assay, IC50 values were calculated for active compounds by plotting the FI for each concentration, and using a 4 parameter Levenburg-Marquardt algorithm with the minimum limit set at 0. Similarly, EC50 values were calculated for the cell viability dose response assay, plotting the % Viability at each concentration and also using a 4 parameter Levenburg-Marquardt algorithm with the minimum limit set at 0 and the maximum limit set at 100.
Outcome- From the primary screen, compounds selected as Active were those that met one of the following two criteria: (1) Fold Induction >/= 1.5, Cell Viability >/= 50% and the ratio of Fold Induction to Cell Viability >/= 1.5; or (2) Fold Induction >/= 1, Cell Viability >/= 50% and the ratio of Fold Induction to Cell Viability >/=1.75. While 101 compounds met this criteria, 96 were ultimately selected for confirmatory screening. For the dose response screen, compounds were labeled as "Active" if they showed at least 8 fold increase over the ALLN control at any concentration.
Comment:
Possible Artifacts: Possible artifacts in this assay include, but are not limited to, compounds that are fluorescent, absorb at the excitation or emission wavelengths, or non-specifically upregulate protein expression