2.3.1 Thawing of cells
Cells are stored in liquid nitrogen. First the cryovial was removed from the storage unit and set into a 37 ℃ water bath. After fast thawing, the cells were transferred into 15 ml reaction tubes. The appropriate cell culture medium was added dropwise to the cell suspension to limit the probability of an osmotic shock. Afterwards, the reaction tube was centrifuged at 800 rpm for 5 min. Then the supernatant was replaced by fresh medium, the pellet was resuspended and transferred to a clean cell culture flask and stored ON in a cell incubator at 37℃ and 5 % CO2. On the next day, the medium was again replaced by fresh medium to remove dead detached cells from the culture flask.
2.3.2 Maintenance
The cell lines grew in 75 cm2 cell culture flasks at 37 ℃ supplemented with 5 % CO2 and approximately 96 % H2O. Cells were splitted when the cell monolayer covered ap-proximately 70 to 90 % which occurred every second or third day.
The standard splitting procedure was as follows: After the medium was fully re-moved from the cells, the monolayer was rinsed one time with 1x PBS (see table 6).
Afterwards, 1.5 ml Trypsin/EDTA-solution (see table 5) were added to the monolayer to detach the cells from the flask. Detaching reaction was performed in the cell incubator at 37 ℃ for 5 to 10 minutes. The completely detached cells were dissolved in 8.5 ml medium and transferred into a new 15 ml reaction tube followed by 5 min centrifugation at 800 rpm. After complete removal of the supernatant the cell pellet was redissolved in 10 ml fresh medium. 1 to 5 ml of the cell suspension, depending on the time, when a full flask was needed the next time, was then refilled into the cell culture flask and supplemented with fresh medium to get 10 ml total volume. Alternatively, the cells were frozen or seeded appropriately for an experiment.
2.3.3 Freezing
To store cells for future experiments, cells were frozen in liquid nitrogen. After splitting, the cell pellet was resuspended in 1.5 ml medium supplemented with 10 % DMSO and transferred into a cryovial. To avoid destruction of the cells by the formation of ice crystals a slow decrease in temperature was necessary. The vial was put into a cryobox filled with IPA and stored first in a -80℃ freezer. After the vial was completely frozen, it was transferred into the liquid nitrogen hold.
2.3.4 Cell treatment procedures
During this work several colorectal cancer cell lines were treated with several different compounds. These experiments were done either in 96-well plates with a cell growth
area of 0.31 cm2 per well, in 24-well plates with 1.9 cm2, 6-well plates with 9 cm2 or 10 cm petri dishes with 60 cm2. The 96-well plates were used for growth determination experiments (XTT), the 24-well plates were used for protein phosphorylation analysis and the other two devices enabled the collection of supernatant for protein analysis or RNA for RNA-expression analysis.
In general, four timepoints were analyzed per experiment. Three wells of a 96-well plate were used per treatment for growth determination, one 96-well of a 6-96-well plate or one petri-dish was used per treatment for RNA and supernatant sample collection per timepoint. The timepoints analyzed for cells treated with EGF-receptor inhibitors were 24, 48, 72 and 96 h. For cells treated with epigenetic interfering compounds, the timepoints tested included 72, 96, 120 and 144 h, because these compounds can only interfere during cell cycle and therefore are supposed to be effective after a longer period.
The number of cells seeded per well or plate depended on the overall duration of the experiment and the cell growth rate to avoid overgrowth. The number of seeded cells was approximately 2500 to 5000 cells per cm2 growth area for the shorter experiments up to 96 h, whereas the number of seeded cells was approximately 1000 to 4200 cells per cm2 growth area for the longer experiments up to 144 h. After seeding, the cells incubated at 37 ℃ for 24 h. Then treatment was performed daily by replacing the complete medium with fresh medium or fresh medium containing the compound or the solvent. The concentrations of the compounds used and the appropriate solvents are shown in table 18.
Table 18: Compounds in treatment experiments
Name Type Solvent Concentration
Cetuximab EGFR inhibitor NaCl 9 g/l 10 µg/ml
Erlotinib EGFR inhibitor DMSO 10 µM
Gefitinib EGFR inhibitor DMSO 10 µM
DAC DNMT inhibitor NaCl 9 g/l 2.5 µM
Cambinol HDACi DMSO 20 µM
SAHA HDACi MetOH 1 µM
TSA HDACi DMSO 25 ng/ml
Valproat HDACi MetOH 1 mM, 2mM
Zebularine DNMT inhibitor NaCl 9 g/l 100µM
2.3.5 Cell post-treatment experiments
After treating the cells for 144 h with DNA methyltransferase inhibitors (DNMT in-hibitors) or HDACis the cells were replated into 96-well plates as follows. The super-natant was removed and stored for ELISA. Afterwards, the plates or wells were rinsed with 1x PBS (see table 6) and treated with 1 ml of Trypsin/EDTA solution (see ta-ble 5). After 5 minutes of incubation at 37 ℃ the cells were redissolved in 5 ml fresh medium and centrifuged for 5 minutes at 800 rpm. Then the pellet was redissolved in
fresh medium and cells were counted using a Neubauer improved cell counting chamber or the TC10 cell counter. 1500 cells per well of untreated, solvent treated and compound treated cells were replated into four 96-well plate, reflecting four different timepoints in a cell proliferation assay (Cell Proliferation Kit II (XTT) ).
After 24 h of incubation the supernatant of each well was replaced by medium or medium plus EGFR inhibitors (see table 18) or the appropriate solvent. For the next four days cellular viability was measured as described by the manufacturer. XTT absorbance was measured 4 h and 24 h after dispension of the XTT solution. Also for the next four days the medium of the remaining plates was replaced daily by fresh medium or medium plus inhibitor/solvent.
2.3.6 Cell transfection experiments
To transfect cells with DNA using LipofectamineT M 2000, cells were seeded into a suitable well that they were 70% - 90% confluent at the time of transfection. In table 19 the composition of each transfection reaction is shown for the appropriate well size, as used during this work.
Table 19: Compounds in transfection experiments
6 well 12 well 96 well
Solution 1
Optimem 250µl 100µl 8.3 µl
DNA 1 µg - 2µg 250 ng 21 ng - 55 ng
Solution 2
Optimem 250µl 100µl 8.3 µl
LipofectamineT M 2000 9 µl 4µl 0.33 µl
Solution 1 and 2 were incubated at RT for 5 minutes before they were mixed. After a second incubation step for 20 minutes at RT, the transfection solution was applied to the cells dropwise. The cells were then incubated at 37 ℃in the cell incubator for four hours. Afterwards, the medium was completely replaced by fresh medium. The cells were then put into the cell incubator until progression of the experiment.
2.3.7 Sample collection
To detect proteins in the supernatant of cells, the medium was transferred into a new reaction vessel. Detached cells were pelleted by centrifugation at 10000 rpm and 4 ℃.
The supernatant was then transferred into a new reaction tube and stored for ELISA-experiments at -20 ℃ (see table 7). To analyze the mRNA, the cells were processed as described in section 2.6.