Kynurenines are associated with immune response regulation in several diseases, including cancer. Reliable and validated methods for identifying multiple kynurenines aid in the development of more effective therapies. Our protocol uses liquid chromatography coupled with mass spectrometry to identify the different tryptophan metabolites generated by the kynurenine pathway in medium collected from cancer cell cultures.
Unexperienced users may have some difficulty during the sample preparation or data acquisition and interpretation steps. By following our protocol and recommendations, one can avoid mistakes and obtain reliable data. To prepare stock solutions of the reagents, weigh out 0.3 milligrams of each reagent in a vial to the highest accuracy and dissolve each reagent in 300 microliters of the appropriate solvent to obtain one gram per liter stock solutions of each reagent.
To prepare charcoal-treated culture medium, weigh out 280 milligrams of activated charcoal in a conical tube and add five milliliters of the liquid medium prepared for culturing the cells of interest. Shake the tube with the medium and charcoal on a seesaw rocker for two hours at room temperature and 50 oscillations per minute. At the end of the incubation, sediment the charcoal by centrifugation and carefully collect the supernatant without disturbing the charcoal, then filter the medium using a 0.45 micrometer syringe filter.
To prepare the calibration solution, spike the charcoal-treated culture medium with 0.75 microliters of 0.1 gram per liter 3NT solution and add 3-H kynurenine, 3-HAA kynurenine, and xanthurenic acid to at least six different concentrations to cover all of the calibration ranges to a final volume of 150 microliters per sample. After vortexing, add 150 microliters of minus 20 degrees Celsius cold methanol supplemented with 1%formic acid to each tube for sample deproteinization and tightly cap and vortex the tubes again. After a 40-minute incubation at minus 20 degrees Celsius, centrifuge the samples and use an automatic pipette to transfer 270 microliters of each supernatant into individual flat bottom glass vials.
Place the vials into an evaporator and use the appropriate program for water methanol fractions to gently evaporate the volatile components for about 30 minutes. When the tubes are dry, reconstitute each sample in 60 microliters of 0.1%formic acid in water and vortex the samples before transferring each solution into individual 1.5 milliliter tubes for centrifugation. Without disturbing the sediment, transfer the supernatants into chromatographic vials with conical glass inserts and place the vials into an LC-MS auto-sampler.
Before running the samples, purge the LC system with the mobile phase to remove bubbles and to prime all of the solvent channels. Next, flush the guard and analytical column with 100%acetonitrile for about 30 minutes before flushing the system with 100%solvent A until a stable pressure is observed in the column, then set the appropriate LC parameters in the data acquisition software and construct a work list for running the samples on the LC system. To construct the calibration curve, in the data acquisition software, add the calibration standards into the work list and run the standards in triplicates, then integrate and measure the peak area corresponding to 3-hydroxykynurenine, kynurenine, 3-hydroxyanthranilic acid, 3-nitrotyrosine, and xanthurenic acid at the retention time of about 4.4, 10, 16, 21, and 30 minutes respectively.
To collect supernatant samples from an in vitro cell culture, after 48 hours of standard cell culture of the cells of interest, transfer 500 microliters of supernatant from each well into individual 1.5 milliliter tubes and remove the cell debris by centrifugation, then transfer the medium supernatants into new tubes for minus 80 degrees Celsius storage until the analysis and maintain the cell pellets at minus 20 degrees Celsius until protein estimation analysis. To prepare samples for LC-MS analysis, transfer 149.25 microliters of each thawed culture medium sample into a new 1.5 microliter tube and add 0.75 microliters of 0.1 gram per liter 3NT solution to each tube. After preparing the samples as demonstrated, add 150 microliters of minus 20 degrees Celsius methanol supplemented with 1%formic acid to each tube and prepare the sample for LC-MS analysis as demonstrated.
When the work list is complete, measure the peak area of each analyte and use an individual linear calibration equation dedicated for each analyte to calculate concentrations of the analytes present within each experimental sample. To assess cellular protein content corresponding to the sample of culture medium, resuspend each cell pellet in 100 microliters of PBS and freeze the samples at minus 20 degrees Celsius for one hour before thawing them on ice. After freeze-thawing the samples three times, collect the cell lysates by centrifugation and transfer the supernatants into new tubes without disturbing the pellets.
Dilute the sample 10 times with fresh PBS and add the appropriate volumes of bovine serum albumin standard solution in duplicate to the appropriate wells of a 96-well plate. Load 10 to 15 microliters of each cell lysate sample supernatant to the appropriate wells of the 96-well plate and fill both the standard and sample wells to a final volume of 50 microliters of PBS per well. Next, add 200 microliters of a Bradford reagent diluted five times with ultra pure water to each well and incubate the plate for at least five minutes at room temperature.
At the end of the incubation, load the plate onto a microplate reader and measure the absorbance at 595 nanometers, then construct a calibration curve to allow calculation of the amount of protein in each sample and divide the concentration of each kynurenine by the total protein content to normalize the kynurenine amount in each sample per one microgram of protein. Here are single quadrupole mass spectrometry results obtained during the analysis of medium containing 4.5 grams per liter of D-glucose and 10%fetal bovine serum. Note the small peak indicating the presence of kynurenine within the sample.
Run a quality control sample before requiring the actual sample data to confirm the appropriate retention times of the analytes as a shift in LC signals or mismatches can be observed. Co-eluting matrix components can generate ions with the master charge ratio selected for the target analytes. For example, in this analysis, the peak from the unknown compound appeared in the scan period during which the ion of master charge ratio 206 was monitored.
Due to the incompatibility of the retention time, the signal did not correspond to the analyte. Although the tryptophan isotope shared the same ion as master charge ratio 206, chromatographic analysis revealed that the tryptophan signal was well separated from the xanthurenic acid signal, indicating that the level of tryptophan present in the tested cancer cell medium did not impact xanthurenic acid quantification. This analysis of the culture medium from two types of cancer cell lines demonstrates that the evaluated human epithelial breast cancer cells released different amounts of tryptophan metabolites while the tested human ovarian cancer cells produced significantly higher levels of kynurenine.
Using an internal standard during the sample preparation helps with reliable data acquisition. Normalization of the data to the protein content corrects for cell number variabilities within individual wells. Our protocol can be further expanded to determine additional analytes, but may accumulate in the culture medium under different experimental conditions.
