A Strategy to Identify Compounds that Affect Cell Growth and Survival in Cultured Mammalian Cells at Low-to-Moderate Throughput

1. NSC culture

NOTE: Manipulation of a human NSC line will be described below but any cell line can be used for this protocol. All cell culture work is performed in a biological safety cabinet.

1. Coat a 96-well plate with basement membrane/extracellular matrix (ECM).
   1. Thaw aliquot of ECM (Table of Materials), which will facilitate attachment of NSC, on ice. Dilute ECM to the appropriate concentration (generally 1:100) in 10 mL base medium (Table of Materials) and add 50 µL per well to each of 60 interior wells of a 96-well plate (Figure 1). Use only the interior 60 wells to avoid artifacts that may result from the edge effect¹⁶.
   2. Let the plate sit at room temperature or in a cell culture incubator (37 °C, 5% CO₂) for at least 30 min.
2. Dissociate and plate neural stem cells.
   NOTE: Cells for use in this method should be grown to at least 80% confluence in a T75 flask.
   1. Culture cells in a T75 flask in a cell culture incubator at 37 °C and 5% CO₂ in NSC medium that is composed of base medium, B27, non-essential amino acids, 2 mM glutamine, and 10 ng/mL basic fibroblast growth factor (FGFb or FGF2).
   2. Remove cells from the incubator once they reach 80% confluence and aspirate off NSC medium. Add an appropriate amount of cell dissociation reagent (3 mL for a T75 flask; Table of Materials) and incubate for 5 min in the incubator.
   3. After incubation, add 7 mL of NSC medium in the T75 flask and pipette vigorously to ensure all cells become detached. Transfer the dissociated cell solution to a 15 mL tube and centrifuge at 200 x g for 5 min.
   4. After centrifugation, remove supernatant from the tube and resuspend cells in 10 mL of NSC medium and count cells.
   5. Readjust concentration of cells to 200,000 cells/mL with NSC medium. Ensure cells are fully resuspended for homogeneous plating into wells.
   6. Plate 100 µL of the cell mixture (20,000 cells) in the 60 interior wells of three 96-well plates that have been coated as described in section 1.1. Use six of the eight slots of an 8-channel multichannel pipettor to plate cells column-by-column.
   7. Add 100 µL of base medium or NSC medium to all wells without cells to minimize potential evaporation from outermost wells.
   8. Under a cell culture microscope, visually inspect at least 10 wells on each of the three 96-well plates to confirm that the cells are seeded at the expected density. Do not proceed with the assay if cells are plated at a density too sparse or dense.

2. Treating cells with compounds

NOTE: The home-made library tested in this demonstration contains compounds that modulate wingless/integrated (Wnt), retinoic acid, transforming growth factor-beta (TGF-β), and sonic hedgehog signaling pathways as well as a variety of tyrosine kinases.

1. Exploratory primary screen for toxicity/cell number
   1. Aliquot 50−100 μL of up to 57 test compounds (Supplemental Table 1) at a concentration of 10 mM in 100% dimethyl sulfoxide (DMSO) into the interior 60 wells of a U-bottomed, V-bottomed or round-bottomed 96-well plate with three DMSO wells as a control (see Figure 1 for a plate map). This will serve as the master compound plate with 25 µL of compound that can be frozen and thawed several times.
      NOTE: Flat bottomed plates should not be used as it will be more difficult to aspirate small volumes of compounds from them with a bench top pipettor.
   2. Remove cell culture plates from incubator 16-24 h after splitting as described in section 1 and aspirate off NSC medium column-by-column with an 8-channel multi-well pipettor using only six of the eight multi-well slots. Add 95 µL of fresh NSC medium to cells in each of the three replicate plates and place plates back in incubator until step 2.1.4 below is completed.
   3. Add 49 µL of NSC medium to each of the interior 60 wells of an empty U-bottomed, V-bottomed or round-bottomed 96-well plate with an 8-channel multi-well pipettor. Unseal the master compound plate and use a bench top pipettor or equivalent instrument to pipette 1 µL of compound from the master plate into the 49 µL of NSC medium in each of the interior 60 wells.
   4. Mix the diluted compound 3x with the bench top pipettor.
   5. Remove the three 96-well plates of NSCs from the incubator, pipette 15 µL of each diluted compound with the bench top pipettor and dispense a 5 µL aliquot of compound into each of the three plates.
      NOTE: This 1:20 dilution of compound into the cells in combination with the initial 1:50 dilution in step 2.1.3 yields a 1:1000 dilution such that the final concentration of the compounds on the NSCs will be 10 µM with a DMSO concentration of 0.1% and the final concentration for the DMSO controls will be 0.1%.
   6. Incubate cells with compound for 72 h and proceed with cytotoxicity assays. Shorter intervals can be used but a 72-hour incubation period should maximize the potential cytotoxic effects of tested compounds.
2. Dose response assay
   NOTE: The set-up for the 96-well used for the dose-response is displayed in Figure 2.
   1. Use column 2 for six DMSO control replicates and test triplicates of up to three different compounds at two-fold serial dilutions at six doses starting with a high dose of 10 µM.
   2. Dilute 4 µL of DMSO or test compound in DMSO into 196 µL of NSC medium in a 1.5 mL microcentrifuge tube. Add 25 µL of DMSO to the column of wells from B2-G2 and 50 µL of test compounds to the row from B3-B11 with the three tested compounds in 10 mM triplicates in rows B3-B5, B6-B8, and B9-B11.
   3. Pipette 25 µL of NSC medium to the remaining empty columns in the interior portion of the 96-well plate. Remove 25 µL of compound from wells B3-B11 with a multichannel pipettor, add to wells C3-C11, and mix at least five times. Repeat the process for the remaining rows to generate triplicates at two-fold dilutions for a total of six doses for each of the compounds.
   4. Generate NSCs for the dose response exactly as described for the primary screen in section 2.1. The compounds for the dose response are added to and incubated on the cells exactly as described in steps 2.1.5 and 2.1.6.
      NOTE: Three biological replicates of the dose response assay are performed by repeating the assay on the NSCs at different passages on separate days.

3. Imaging cells on a plate reader

1. After cells have been incubated with compounds for the allotted time, image cells on a plate reader to determine the pre-treatment cell number per well.
   NOTE: Instructions for imaging cells are reader-specific but generally follow a similar strategy. The directions below apply to the reader used in this demonstration (Table of Materials).
2. Remove the plate from the incubator and place it inside the plate reader. Open the imager software to set up protocol and experiment files for the study. Go to Imager Manual Mode on Task Manager and click Capture now….
3. Choose 96-well plate as the vessel type, select 10x for the magnification, and red fluorescent protein (RFP) 531 and 593 for imaging tdTomato. Pick a well, then click Autofocus to focus image, and Auto Expose for proper exposure time. Manually adjust focus and exposure if needed.
4. Once proper focus and exposure have been obtained, click the camera icon to capture the picture. Then click PROCESS/ANALZYE above image to continue building the protocol and select the ANALYSIS tab.
5. Click Cellular Analysis in ADD ANALYSIS STEP to the right of the image and click START. Image will show highlighted cells to indicate each individual cell. The Options selection may be clicked to alter parameters to better select cells based upon the fluorescence threshold or cell size. If the imager is properly counting the cells, then click ADD STEP at the bottom of the screen.
6. Click the icon at the top of the screen to Create experiment from image set, which will open a window with the experiment. Once open, click Procedure under the Protocol tab and in the new window that opens select Read, then in the new window click full plate to select only the 60 wells that contain the cells (B2…G11). Click OK to save changes, then click OK in the Procedure window.
7. The plate can now be imaged by this protocol and the experimental file can be saved. Click the play icon to run the plate. Once the first plate has been imaged, image the other two plates. Upon completion of the imaging, download the cell count data to a spreadsheet for analysis. Take all images at 10x magnification.

4. Terminal MTT cytotoxicity assay

NOTE: Begin the MTT assay within two hours of completing tdTomato imaging.

1. Make a 5 mg/mL MTT stock solution by weighing out 25 mg of MTT and resuspending it in 5 mL of NSC medium. Vortex the solution until there are no visible precipitates of MTT, which could take several minutes.
2. Remove cell culture plates from the incubator and aspirate off cell culture medium. Dilute MTT 1:10 in cell culture medium and add 100 µL of MTT to each well of cells.
3. Incubate cells at 37 °C for 2 h. A purplish precipitate should be visible roughly in proportion to the number of cells in the well. Either aspirate the MTT solution off plates or invert the plate quickly to flick solution out of the plate.
4. Add 50 µL of 100% DMSO to each well and shake plates at room temperature for 10 min at 400 rpm. Read the absorbance of each well at 595 nm in a plate reader and export data to a spreadsheet for analysis.

5. Data analysis

1. Perform an analysis of tdTomato cell counts and absorbances with appropriate software (commercial spreadsheet, R). Calculate averages for absorbance or cell count of the three DMSO replicates on each plate for normalization purposes, then divide the value for the cell counts or absorbances for each well on the plate by this average and convert to a percentage. This yields the normalized cell count or absorbance relative to DMSO control for each plate.
2. Calculate the mean normalized count or absorbance and standard deviation for replicate wells on the three plates.
   NOTE: At this point there should be four different sets of normalized values: one for each of the plates and one mean for the three replicate plates.
3. Be conservative and use a normalized value at or below 25% for the average across the three replicate plates to classify a compound as toxic. Also, because only a single treatment per compound is performed on each plate, only label compounds that fall below this threshold on all three replicate plates as toxic. Examine fluorescent images of all compounds that this analysis filters as toxic to visually confirm toxicity.
   NOTE: The identification of compounds with a growth inhibitory or growth enhancing effect is more difficult to assess in an exploratory assay of this type due to the lack of replicates on each plate. However, the following is a quick way to identify compounds that may either slow down or enhance cellular growth.
4. Calculate the standard deviation for the three replicate DMSO controls on each plate and then filter for any compounds that have average values at least two standard deviations above or below the DMSO control. Compounds that fall out of this filter on each of the three plates may warrant further investigation.
5. Use the same analysis strategy for the dose response as the primary toxicity screen. Calculate the averages for the DMSO controls for each biological replicate and use these values to normalize the percent live cells or percent absorbances for each compound/dose combination. Calculate the means and standard error of the means for all compound/dose combinations for the three biological replicates.
6. Transform the concentration to its log value, generate a dose response curve for the log of concentration versus normalized viability, and fit the curve with a non-linear regression analysis (analysis can be performed in R or various commercial statistical packages). Calculate the lethal dose 50 (or technically in this case the viable dose 50) or concentration of compound that results in 50% toxicity from the equation of this curve. Many software packages will automatically calculate this figure.