Home3D Cell CultureCultrex® 3-D Spheroid Colorimetric Proliferation/Viability Assay Protocol

Cultrex® 3-D Spheroid Colorimetric Proliferation/Viability Assay Protocol

Reagent kit for investigating spheroid cell proliferation and/or viability

Catalog Number 3511-096-K

I. Background

Current in vitro tumor models lack either a physiological context and/or reproducible format for evaluating tumor cells in vitro. At present, the most popular method for compound screening and pathway analysis involves culturing cancer cells on rigid, tissue culture treated plastic surfaces where the cells adhere non-specifically and proliferate as a monolayer, and as a result, these cells lose both morphology and gene expression profiles associated with tumors in vivo. Alternatively, single cell suspensions may be embedded in extracellular matrix (ECM) hydrogels to construct 3-D cultures; however, the resulting structures are dispersed throughout the gel and exhibit significant variability in morphology and size, limiting the establishment of physiological gradients and adversely affecting the reproducibility of each assay.

To address issues of reproducibility and to build more physiological tumor systems, well-established methods for multicellular spheroid formation were incorporated into 3-D culture models. Researchers have been using spheroid cultures for cancer research for over 40 years;1-3 however, there have been limitations regarding which cell lines could spontaneously form spheroids. For spontaneously spheroid assembly, it was shown that the cells produce an ECM that is deposited on the outer surface of the spheroid and that cell lines that could not spontaneously form compact spheroids were deficient or lacking in the formation of this ECM.4,5 It was later shown that the addition of ECM proteins to non-spheroid forming cells induced spontaneous spheroid formation, making the spheroid format compatible with most solid cancer cell models6. We have optimized this process, providing the necessary reagents to evaluate your cells using this method. Simply harvest cells, resuspend in spheroid formation ECM, and then culture in a 96 well spheroid formation plate. Spheroids generally form in 48 to 72 hours. Cell number and culture time determines spheroid size, and since each well produces one spheroid, researchers have complete control over spheroid dimensions with virtually no well to well variability.

For most tumor models, we recommend spheroids between 400 and 500 μm in diameter. This is sufficient to establish physiological gradients for nutrients, oxygen, pH, and catabolites due to limitations in diffusion through the multicellular layers. Another effect of these gradients is the establishment of heterogeneous cell populations with necrotic cells in the core, quiescent cells in the deeper layers, and proliferating cells on the spheroid surface; all of these factors reminiscent of an avascular tumor.7-10 Once formed, these multicellular tumor cell aggregates can be treated with pharmacological compounds to evaluate the effect on tumor spheroid growth; alternatively, specific genes or pathways may be manipulated to evaluate their effect on expansion of the in vitro tumor. This process can be monitored in real-time and label-free using image analysis software to measure spheroid area, and the kit is supplied with the colorimetric cell viability reagent MTT for quantitative end point analysis. The MTT tetrazolium ring is cleaved by mitochondrial dehydrogenases yielding purple formazan crystals which are subsequently solubilized for quantitation using Detergent Reagent.11

II. Product Description

The 3-D Spheroid Colorimetric Proliferation/Viability Assay provides a useful tool for modeling tumor response in vitro. The kit uses 3-D Culture Qualified 96 Well Spheroid Formation Plate alongside a specialized Spheroid Formation ECM to drive aggregation and/or spheroid formation of cells. Upon completion of spheroid formation, the spheroid may be treated with pharmacological agents to evaluate tumor viability after drug treatment. Tumor spheroid expansion is visualized microscopically and can be quantitated through image analysis software for real-time and label free evaluation. At the conclusion of the assay, cell viability may be assessed by absorbance using MTT. The 3D Spheroid Colorimetric Proliferation/Viability Assay offers an in vitro, standardized, three dimensional, high-content format for inducing multicellular tumor spheroid (MCTS) formation and quantitating cell viability within the spheroids in response to pharmacological treatment.

Steps Comprising the 3-D Spheroid Colorimetric Proliferation/Viability Assay

Figure 1.Steps comprising the 3-D spheroid colorimetric proliferation/viability assay.

III. Components

IV. Reagents and Equipment Required but not Provided

  1. Equipment
    • Laminar flow hood or clean room
    • 37 ⁰C CO2 incubator
    • Low speed swinging bucket 4 ⁰C centrifuge and tubes for cell harvesting
    • Hemocytometer or other means to count cells
    • –80 ⁰C storage
    • Ice bucket
    • Standard light microscope (or inverted)
    • Pipettes and pipette aid
    • Bright-field microscope with 4X objective and digital camera
    • Timer
    • Computer
    • Image analysis software, such as ImageJ
    • Graphing software, such as Microsoft® Excel®
    • Colorimetric plate reader (excitation 530-560 nm and emission 590 nm)
  2. Reagents
  3. Disposables
    • Greiner culture flasks, tissue culture treated, 25 cm2 (Product No. C6231) or 75 cm2 (Product No. C7106)
    • Centrifuge tubes, 10 mL (Product No. SIAL0790) and 50 mL (Product No. SIAL0828)
    • Serological pipettes, 1, 5, and 10 mL (Product No. SIAL1485, SIAL1487, SIAL1488)
    • 1 - 200 µL (Product No. P5037) and 200 – 1000 µL pipette tips
    • Gloves

V. Precautions and Limitations

For Research Use Only. Not for use in diagnostic procedures.

  1. The physical, chemical, and toxicological properties of these products may not yet have been fully investigated; therefore, we recommend the use of gloves, lab coats, and eye protection while using these chemical reagents.
  2. The CULTREX® 3-D Spheroid Colometric Proliferation/Viability Assay contains reagents that may be harmful if swallowed, or come in contact with skin or eyes. In case of contact with eyes, rinse immediately with plenty of water and seek medical advice.
  3. MTT Reagent (Product No. 4890-25-01) contains less than 1% (w/v) MTT (3-(4,5-dimethylthiazolyl-2)-2, 5-diphenyl-tetrazolium bromide (CAS # 298-93-1). MTT is toxic and may cause heritable genetic defects. In case of contact, immediately flush eyes or skin with copious amounts of water. If swallowed, wash out mouth with water provided person is conscious. Call a physician.
  4. Detergent Solution (Product No. 4890-25-02) contains SDS which is an irritant. In case of contact, immediately flush eyes or skin with copious amounts of water. If swallowed, wash out mouth with water provided person is conscious.

VI. Preparation Instructions

  1. 10X Spheroid Formation ECM
    10X Spheroid Formation ECM should be thawed on ice at 4 ⁰C and diluted with Tissue Culture Growth Medium chilled to 4 ⁰C; pipet up and down with a serological pipet to mix. Cells are resuspended in 1X Spheroid Formation ECM, and 50 μL of cell suspension is added to each well of the 3D Culture Qualified 96 Well Spheroid Formation Plate.
    See Table 1 for recommended dilution schedules.
  2. MTT Reagent
    The MTT Reagent is supplied ready for use. The MTT Reagent is stable at 4 ⁰C provided there is no contamination. Care should be taken not to contaminate the MTT reagent with cell culture medium during pipetting. It is recommended that the appropriate volume required for each experiment is aliquotted and placed into a separate clean tube under sterile conditions and the stock bottle is returned to 4 ⁰C in the dark.
    If the MTT Reagent is blue-green in color do not use and refer to the Troubleshooting Guide.
  3. Tissue Culture Medium with Proliferation/Viability Modulating Compounds
    Add 2X concentration of Proliferation/Viability Modulating compounds within the tissue culture medium to compensate for changes in total volume due to the spheroid formation ECM. Tissue culture medium should be at 37 ⁰C when added.
  4. Detergent Reagent
    The Detergent Reagent is supplied ready for use. Before use, warm the bottle for 5 minutes at 37 ⁰C then invert gently while mixing to avoid frothing.

VII. Assay Protocol

Perform these procedures in a biological hood using aseptic technique to prevent contamination.

A. Cell Harvesting

Culture cells per manufacturer’s recommendation. The following procedure is suggested and may need to be optimized to suit the cell type(s) being studied.

  1. Cells need to be healthy and proliferating prior to use in the assay. Cells should be passaged 2 or 3 times and evaluated for cell viability by trypan blue or equivalent assay. Do not start the assay until cell viability is greater than 90%.
  2. Each well requires approximately 2,000 - 5,000 cells, and 25 and 75 cm2 flasks yield at least 1 x 106 and 3 x 106 cells, respectively. Plan accordingly.
  3. Prior to harvest, visually inspect cells, and record cell health, relative number, and morphology.
  4. Wash cells two times with sterile PBS or HBSS. Use 5 mL per wash for a 25 cm2 flask and 10 mL per wash for a 75 cm2 flask.
  5. Harvest cells. For 25 cm2 flask or 75 cm2 flask, add 1 mL or 2 mL, respectively, of Cell Harvesting Buffer (see Materials Required But Not Supplied), and incubate at 37 °C for 5 to 15 minutes until cells have dissociated from bottom of flask.
  6. Transfer cells to a 15 mL conical tube, and add 5 mL of cell culture medium.
  7. Centrifuge cells at 200 x g for 3 minutes to pellet cells, remove medium, and resuspend cells in 2 mL of cell culture medium. Cells may need to be gently pipetted up and down with serological pipette to resuspend cells and break up cell aggregates. Visually inspect cells to verify formation of a single cell suspension, no aggregates prior to counting.
  8. Count cells and evaluate cell viability by trypan blue exclusion or equivalent test. Do not start the assay if cell viability is less than 90%.
  9. Dilute to 1 x 106 cells per mL in cell culture medium.

B. 3-D Spheroid Colorimetric Proliferation/Viability Assay

  1. Assay Preparation – Before Day 0
    1. Establish assay parameters and appropriate controls. Appropriate controls include samples with and without proliferation/viability modulating agents, as well as samples without cells for background determination.
    2. Determine optimal seeding density for each cell line used. In general, 3,000 cells per well is a good starting point. Optimal seeding density can be evaluated by analyzing the size of spheroid formation using the Spheroid Formation protocol (VI.B.2). Serial dilutions of cells may be placed in each well to create a standard curve; this may be useful in evaluating spheroid size and linearity of the MTT absorbance curve (VII.3).
    3. Culture cells per manufacturer’s recommendation; adherent cells should be cultured to no greater than 80% confluence.
    4. Thaw 10X Spheroid Formation ECM on ice overnight in a 4 ⁰C refrigerator.
  2. Spheroid Formation – Day 0
    1. Harvest and count cells, as directed in section VI. A.
    2. Prepare a single cell suspension in 1X Spheroid Formation ECM. See section V.1. for reagent preparation.
    3. Dispense 50 μL of the single cell suspension in 1X Spheroid Formation ECM per well of the 3D Culture Qualified 96 Well Spheroid Formation Plate.
    4. Centrifuge at 200 x g for 3 minutes at room temperature in a swinging bucket rotor.
    5. Incubate at 37 ⁰C in a tissue culture incubator for 72 hours to promote spheroid formation.
Table 1Dilution Schedules (10% overage for multiwell dispensing)
  1. 3D Culture Spheroid Treatment – Day 3
    1. Add 50 μL of warm (37 °C) cell culture medium containing proliferation/viability modulating compounds, if applicable. See section V.3 for reagent preparation.
    2. Incubate the plate at 37 °C in a tissue culture incubator for 3 to 6 days, and photograph the spheroid in each well every 24 hours using the 4X objective. Adjust the lighting and focus to provide the most contrast between the 3D structure and background. The use of fluorescence microscopy for cells that express fluorescent protein or have a fluorescent label may also improve contrast and subsequent analysis. Debris may transfer to the bottom of the 96 well plate during handling; wiping the bottom of the wells with lens paper prior to photographing may improve clarity. The assay may be conducted longer than 6 days if desired; however, changing cell culture medium may be required to maintain cell viability.
    3. Analyze images using image analysis software to measure changes in the area of the structures to determine the extent of 3-D culture spheroid expansion for each sample.
  2. Image Analysis
    Note: Images may be analyzed using free software such as ImageJ (; see below. Other image analysis software may be configured to make the same measurements; please consult your software supplier regarding capabilities and instructions.
    1. Photograph image of known size (eg. 1 mm) using 4X objective, and measure pixels in ImageJ.
      1. Open image. Go to File/Open, and select image.
      2. Select line tool.
      3. Draw a line the length of the object.
      4. Go to Analyze/Measure, and record pixel number.
      5. Calculate the number of pixels in each mm (eg. 600 pixels/mm). Record result ------- pixels/mm
    2. Set scale; this will need to be done each time ImageJ is opened.
      1. Go to Analyze/Set Scale.
      2. For “Distance in pixels” input value from VI.B.4.v. (above).
      3. For “Know distance” input “1,000”.
      4. For “Unit of Length” input “μm”.
      5. Check “Global”, and select “OK”.
    3. Analyze spheroid image.
      1. Open image. Go to File/Open, and select image.
      2. Convert to an 8 bit image: Go to Image/Type/8 bit (check).
      3. Adjust image threshold. Go to Image/Adjust/Threshold (check). The program will distinguish between dark and light pixels, and the threshold may be adjusted on the histogram using the sliding scale. Similar settings will work for photographs taken under the same conditions. Areas of dark pixels will be overlaid with red. Adjust the threshold so that only the spheroid image is overlaid.
      4. Select spheroid. Select the circle tool and surround the image. This will eliminate any dark pixels outside of the spheroid from the measure.
      5. Go to Analyze/Measure. This will measure the area of the spheroid structure (μm2) in a table. Multiple measurements may be made in one table. Save table.
      6. Convert the table to an Excel worksheet. Open with Excel and “Save As” an .xls or .xlsx file.
Process for analysis of spheroid expansion.

Figure 2.Process for analysis of spheroid expansion. A) Capture image and convert to 8 bit; B) Set threshold to capture the total structure; C) Select structure to calculate total area.

  1. Colorimetric Analysis
    1. Add one tenth volume (10 μL per 100 μL) of Resazurin per well and transfer the plate back to the 37 °C cell culture incubator. See section V.3 for reagent preparation.
    2. After 24 hours, warm Detergent Reagent to 37 ⁰C, and add an equal volume (100 μL per 100 μL) of Detergent Reagent. Transfer the plate back to the 37 ⁰C cell culture incubator for 24 hours to solubilize cells and MTT formazan crystals
    3. Read absorbance at 570 nm. If substantial cell debris is present after incubation, background values may be evaluated at 690 nm and deducted for each sample.
    4. Graph data.

VIII. Data Interpretation

  1. The CULTREX® 3-D Spheroid Colorimetric Proliferation/Viability Assay provides morphological and quantitative analysis of spheroid cell proliferation/viability. Spheroids expand in size as cells proliferate, and this results in changes in surface area that occur over time for proliferating cell lines(Figure 3). These changes in surface area can be measured and used to compare relative proliferation of different cell lines or cell lines subjected to genetic manipulation.
Spheroid growth of MDA-MB-231 breast cancer cells.

Figure 3.Spheroid growth of MDA-MB-231 breast cancer cells. Cells were seeded at 3,000 cells/well in the presence of spheroid formation ECM and incubated for 72 hours at 37 °C, 5% CO2 to induce spheroid formation. At that time, 50 µL of complete medium was added to each well, and spheroids were incubated at 37 °C, 5% CO2. Spheroids were photographed every 24 hours and images were analyzed using ImgaJ software.

  1. The changes in area can also be used to evaluate the effect of pharmacological compounds on spheroid growth. Once optimal assay conditions have been established, this can be evaluated as an endpoint assay. The following assay was conducted using MDA-MB-231 cells treated with varying concentrations of the inhibitor Bleomycin.

First the areas were calculated for each condition, and these values were used to generate average and standard deviations:

Spheroid bleomycin area

Next the area for each spheroid before treatment was subtracted to determine spheroid expansion.

Spheroid expansion area

Finally, the resulting areas were divide by the area obtained for the no inhibitor control, providing the proliferation index as a percentage of control:

Bleomycin proliferation index
  1. Colorimetric endpoint analysis using MTT Reagent can be used to generate a standard curve based on cell seeding density. The following assay was conducted using MDA-MB-231 cells serially diluted from 12,500 cells/well to 781 cells/well on Day 0 and evaluated on Day 3.

First, the absorbance was measured at 570 nm for each well, and the average and standard deviations were calculated for each sample using Excel:

Spheroid seeding density

Next, the background was subtracted from each sample, and the data was plotted with a trendline to evaluate the relationship between cell seeding density and absorbance (570 nm):

Spheroid seeding density trendline
  1. Colorimetric endpoint analysis using MTT Reagent can also be used to evaluate the effect of pharmacological compounds on cell viability. The following assay was conducted using MDA-MB-231 cells treated with varying concentrations of the inhibitor Bleomycin.

First, the absorbance at 570 nm was measured for each well, and the average and standard deviations were calculated for each sample using Excel:


Next, the background was subtracted from each sample:


Finally, the background-corrected absorbance was divided by the value obtained for the no inhibitor control, providing the viability index as a percentage of control:

Bleomycin viability index

Using the linear portion of the inhibition curve, the IC50 may be estimated:

Bleomycin viability index trendline

IC50 ~ 15 µM for MDA-MB-231 Spheroids

Troubleshooting Guide

Cultrex is a registered trademark of Trevigen, Inc.


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