General cell culture methods

Cell suspension was diluted 1:10 with PBS and 10 µl of this suspension was diluted 1:2 with trypan blue. 10 µl were counted in a Neubauer hematocytometer.

Trypan blue is a vital dye that stains broken cell membrane. Thus, stained (dead) cells are not counted. Cells were counted in each of the four corner quarters. One corner quarter represents the area of 1 mm² and the height of 0.1 mm, thus holds 0.1 µl cell suspension. The mean of the cell number per quarter was calculated. Mean cell number multiplied by 10⁴ (volume of the chamber) and the dilution factor (10 x 2) resulted in the number of cells per ml.

2.2.1.2. Freezing cells

Cell suspensions of approximately 1 x 10⁷ cells were centrifuged at 1000 x g for 8 min. Cell pellets were resuspended in 10 ml ice cold FCS containing 5 % DMSO and 1 ml aliquots were prepared in sterile polypropylene tube for cryogenic storage. Tubes were slowly cooled down over night at -80 °C in a polystyrene box. Long term storage took place in liquid nitrogen.

2.2.1.3. Thawing and maintaining cells

Frozen cell suspensions were thawed in a water bath at 37 °C and were added to 50 ml cell growth medium immediately to dilute toxic DMSO. Cells were subsequently centrifuged at 1000 x g for 8 min. Cell pellets were resolved in 12 ml growth medium containing 10 % FCS and seeded into a sterile 75 cm² plastic flask. Cells were split every 3

48

– 5 days, depending on confluence. For splitting old medium was removed and cells were washed once with PBS. Cells were subsequently incubated for 2 – 5 min with 2 ml Trypsin/EDTA at 37 °C. When all cells were detached from the surface, fresh medium was added to the suspension. Cells were transferred to a 15 ml tube and spun down for 5 min at 1000 x g. Supernatant was discarded and cell pellet was resuspended in 5 ml growth medium and seeded at adequate cell density.

2.2.2. Transfection of cells

Cell lines were transfected by lipofection or electroporation. Lipofection is a method to introduce nucleic acids into cells by using vesicles, so called liposomes.

Liposomes are positively charged and entrap the negatively charged genetic material.

They are made of a phospholipid bilayer, thus they can easily pass the cell membranes as it also consists of lipid bilayer and is negatively charged. Electroporation is a very effective method of transfection. The permeability of the cell plasma membrane is increased by applying an electric field. After disruption of the phospholipid bilayer DNA can penetrate the cells. The membrane spontaneously reassembles and leaves the cell intact. However, many cells die during this method.

2.2.2.1. Transient transfection by lipofection

Cells were seeded in a density of 5 x 10⁴ cells per well in a 24-well plate and incubated over night for attachment. Plasmids harboring the gene of interest or a control empty vector were diluted in serum-free OPTIMEM in a final concentration of 20 ng/ml. For reporter assays reporter plasmids containing promoter binding sites and firefly luciferase (200 ng/ml) and transfection control plasmids containing renilla luciferase (20 ng/ml) were added to the mix and cells were transfected with 15 µl Lipofectamine 2000 (Invitrogen) per 24-well plate according to manufacturer’s recommendations. For transfection cells were cultured in serum-free OPTIMEM for 24 h.

Medium was changed to normal growth medium the day after transfection. Lysates for analysis were taken 48 h to 72 h after transfection, depending on experimental procedures.

49

2.2.2.2. Transient transfection by electroporation

1 x 10⁶ cells in 500 µl OPTIMEM were inserted to a 0.4 cm gap electroporation cuvette together with a plasmid containing the gene to analyze (20 ng/ml), reporter plasmids (200 ng/ml) and transfection control plasmids harboring renilla luciferase (20 ng/ml). Electroporation was carried out in a BioRad electroporator applying 165 V and 1000 µF. 25 µl of cell suspension was subsequently seeded in each well of a 24-well-plate and 500 µl serum-free OPTIMEM was added. Medium was changed to normal growth medium the day after transfection. Lysates for analysis were taken 48 h to 72 h after transfection.

2.2.2.3. Titration of antibiotics (Killing curve)

To determine the optimal concentration for selection of stable cell clones (see below) killing curve experiments were performed. Different cell lines were seeded in 24-well-plates in a density of 5 x 10⁴ cells per well. Antibiotics were applied to the cells after attachment. Zeocin was added in concentrations from 100 µg/ml to 1000 µg/ml, blasticidin was added in concentrations from 10 µg/ml to 100 µg/ml. Cell viability was analyzed microscopically after three and seven days. Optimal selection concentration was defined as the lowest concentration of antibiotic in which all cells were dead by seven days at the latest.

2.2.2.4. Stable transfection of cells

Cells were seeded in a 6-well-plate in a concentration of 1 x 10⁵ cells per well and incubated over night for attachment. Transfection of cells with a plasmid containing the gene of interest and a eukaryotic antibiotic resistance cassette was achieved by lipofection or electroporation (see above). Each well was transfected with 1 µg of plasmid DNA in OPTIMEM. 24 h after transfection cells were trypsinized, diluted 1:2, 1:5 and 1:10 and seeded into 150 mm cell culture dishes containing 20 ml growth medium and the selective drug. Growth medium and antibiotic was changed every 3 to 7 days.

After 2 to 3 weeks, single colonies began to appear and could be harvested. For isolation of colonies, growth medium was removed and cells were rinsed twice with PBS. Cell separating cylinders were dipped into autoclaved vaseline to make the rim sticky.

Subsequently, cylinders were put over a cell colony and gentle pressure was applied to

50

prevent movement. 50 µl of Trypsin/EDTA was added into cylinders and cell culture plates were incubated for 2 min at 37 °C to allow cells to detach. Each trypsin-treated colony was placed into one well of a 24-well-plate containing growth medium and selective antibiotic. Cells were grown until 80 % confluence and split into 24-well-plates and 6-well-plates to check if the gene of interest was present via promoter analysis and protein expression. Positive cell clones were expanded and frozen.

2.2.2.5. Inducible cell clones

The Tet-On system was used to express dnSOX2 at certain time points after induction. The Tet-On system is an aberrant version of the initially established Tet-Off system invented by Bujard and colleges in 1992. In this dual system the regulatory plasmid is a constitutively expressed tetracycline-responsive transcriptional activator (tTA), a fusion protein of tetracycline repressor (TetR) found in Escherichia coli and the VP16 domain of herpes simplex virus under the control of a CMV promoter. The second plasmid of the system, a responsive plasmid, harbors the gene of interest under the control of a tetracycline responsive element (TRE). In absence of tetracycline, tTA binds to TRE and activates transcription of the gene of interest. When tetracycline is added to the cells it binds to tTA. This complex can no longer bind the TRE and thus transcription is inhibited [176]. The Tet-On system is based on a mutated version of tTA (reverse tTA).

It only binds to TRE in presence of tetracycline or a tetracycline derivate, e.g. doxycycline (Dox) and thus induces expression of the gene of interest [177].

A vector containing rtTA was stably transfected into cell lines (see above).

Selection took place via transient transfection of clones with a reporter plasmid for rtTA (TO-Luc) and subsequent reporter assays (see below). Successfully transfected stable cell clones were expanded and again stably transfected with a plasmid containing the TRE and dnSOX2 cDNA. Stable clones were selected by reporter assay. Therefore, cells were transiently transfected with a SOX2 reporter plasmid (SOP-Flash), induced with doxycycline 3 h after transfection and analyzed 48 h later.

51