Cell Biological Methods

2.4.1 General mammalian cell culture

Mammalian cell lines were cultured in humidified incubators at 37°C and 5% CO2. Media were purchased from Invitrogen. We used Dulbecco’s modified Eagle’s medium (D-MEM) containing glutamine or glutamax, sodium pyruvate, pyridoxine and either 1 g/l (Cos7, Hela) or 4.5 g/l glucose (HEK293, NIH-3T3, PC12). Media were supplemented with 10% heat inactivated fetal calf serum (FCS) and antibiotics (50 units/ml penicillin, 50 µg/ml streptomycin). For PC12 cells, the medium was supplemented with 10% horse serum and 5% FCS. Cells were generally passaged every 3-5 days using trypsin/EDTA solution (Invitrogen) and plated at 1:5-1:20 dilutions onto new culture dishes.

2.4.2 Transfection of plasmid DNA and siRNAs

Mammalian cells were transfected with vectors for eukaryotic expression at 80-90% confluency using Lipofectamine 2000 transfection reagent (Invitrogen) according to the manufacture’s instructions with changes in the amount of DNA and Lipofectamine 2000 used (2.5 µg DNA and 5 µl Lipofectamine per 9.5 cm2 well). DNA/ Lipofectamine complexes were prepared in Opti-MEM (Invitrogen) and added to the cells cultured in antibiotics free medium. Cells were incubated for 4 hours before the medium was changed. Cells were further processed 24 hours after transfection.

For siRNA transfections, Oligofectamine (Invitrogen) was used and cells were transfected at 30-50% confluency. For efficient knockdowns (>90%) two rounds of transfections were done with an interval of 48 hours. We used 5 µl Oligofectamine and 300-400 pmol siRNA per 9.5 cm2-well prepared in Opti-MEM. Medium was exchanged to antibiotics free medium (half the normal volume) prior to addition of the complexes.

Cells were incubated for 3 hours and full medium was added up to the normal volume. The cells were usually passaged between the first and second transfection. Experiments with siRNA treated cells were usually performed 48 hours after the second transfection. When vector DNA and siRNAs were co-transfected in the second round of transfection, Lipofectamine 2000 was used and transfections were performed 24 hours before the experiment.

2.4.3 Generation of stable cell lines

Cell lines stably expressing a certain gene were generated by selection with geneticin, an analog of neomycin. Eukaryotic expression vectors usually contain a neomycin resistance cassette, which allows transfected cells to grow in medium containing geneticin. Cells were transfected as described above and passaged in different dilutions 24 hours after transfection using medium containing 500 µg/ml geneticin (Invitrogen). Medium was changed every 2 days until all non-transfected control cells had died and single colonies could be observed (between 1-3 weeks). Single colonies were picked, dissociated and transferred to 48- or 96-well plates. Cells were expanded in selective medium and checked for gene expression by immunoblotting. Several positive clones were chosen and aliquots were stored in liquid nitrogen.

2.4.4 Immunofluorescence staining

Cells seeded on glass coverslips were fixed either with 4% PFA (para-formaldehyde), 4% sucrose in PBS pH 7.4 for 20-30 min at room temperature or in pre-cooled 100% methanol for 10 min at -20°C. Afterwards, coverslips were washed 3 times in PBS and cells were permeabilized and blocked in PBS containing 30% goat serum and 0.3% Triton X-100 (blocking solution). Primary antibodies were diluted in blocking solution, applied to the coverslips in a humidity chamber (30-50 µl per coverslip upside down onto parafilm) and incubated for 1 hour at room temperature. Coverslips were washed 3 times with PBS and incubated with Alexa Fluor labeled secondary antibodies (1:100 – 1:200 dilutions) for 1 hour at room temperature. Afterwards, coverslips were washed again 3 times in PBS and mounted onto glass slides using Immumount mounting solution (Thermo Electron) supplemented with 1 µg/ml DAPI.

In order to reduce background by unspecific binding of antibodies, in some cases high- salt PBS (containing 500 mM NaCl) was used instead of PBS. For some antibodies (e.g

Materials and Methods 49 LAMP-1), it was necessary to leave out the detergent in all steps after fixation with methanol.

2.4.5 Fluorescence microscopy and quantification

For fluorescence image acquisitions and analysis we used a Zeiss Axiovert 200M Digital Research Microscopy System equipped with a special light source and the Slidebook Digital Microscopy software package provided by Intelligent Imaging Innovations. This setup allows quasi-confocal imaging by deconvolution of the acquired images. The deconvolution algorithm used by the software reverses the optical distortion that takes place in a microscope, thus greatly improving z-resolution.

For quantification of fluorescence intensities we made use of the mask creation and statistics functions provided by the software. Details about quantification procedures can be found in the respective figure legends.

Alternatively, images were acquired using a confocal spinning disc microscopy system (Ultra VIEW ERS Rapid Confocal Imager) and the Image Suite software (Perkin Elmer).

2.4.6 Transferrin uptake and recycling assays

2.4.6.1 Microscopy-based transferrin assays

Transfected cells were seeded on matrigel coated glass coverslips and starved the next day for at least 1 hour in serum free medium before the assay. Alexa Fluor 594 labeled Tf (Molecular Probes) was diluted to a concentration of 25 µg/ml in serum free medium containing 0.2% BSA and centrifuged for 10 min to remove precipitates. The solution was added to the coverslips (100 µl per coverslip) in a humidity chamber and incubated for 20 min at 37°C in a humidified incubator to allow internalization of the Tf (“pulse”). The humidity chamber was immediately placed on ice and the coverslips were washed three times with ice-cold Hank’s balanced salt solution (HBSS) supplemented with 20 mM Hepes. Alternatively, PBS supplemented with 0.5 mM CaCl2 and 0.5 mM MgCl2 was used for washing. For the analysis of Tf-uptake, coverslips were fixed with 4% PFA, 4% sucrose in PBS pH 7.4 for 30 min at room temperature. For recycling (“chase”), 100 µl of pre-warmed medium containing 10% FCS and 1 mg/ml unlabelled holo-Tf (Sigma) were added to the coverslips and incubated at 37°C (humidified

incubator). Coverslips were removed after different periods of time (15, 20, 30 min), dipped twice into ice-cold HBSS + Hepes (or PBS + 0.5 mM CaCl2 + 0.5 mM MgCl2) and fixed as described. After fixation, coverslips were washed 3 times in PBS and mounted on glass slides or processed for immunofluorescence staining.

2.4.6.2 Quantitative transferrin assays

Cells were seeded on 12-well plates after transfection with siRNAs as described above and starved the next day for at least 2 hours in serum free medium. Plates were chilled on ice and 250-300 µl medium containing 20 µg/ml unlabeled holo-Tf and 300 ng/ml [125I]-labeled Tf (Perkin Elmer; specific activity: 0.3-1.0 µCi/µg) were added to each well. Plates were incubated at 37°C in a humidified incubator and removed after several periods of time (5, 10, 20 and 30 min for the uptake assay) or complete internalization of Tf was allowed for 30 min (for the recycling assay). As a control for unspecific binding, one plate was kept on ice. Afterwards, plates were chilled on ice and washed 3 times with ice-cold 0.5% BSA in PBS. For uptake assays, plates were kept on ice in PBS + 0.1% BSA. For recycling, pre-warmed medium containing 100-fold excess of Tf (2 mg/ml) was added and the plates were incubated at 37°C (incubator). They were removed at several time points (3, 6, 9 and 12 min), chilled on ice and the medium was changed to 0.1% BSA in PBS. Plates were kept on ice until all plates were ready for further processing. Washing was done alternating with 0.1% BSA in PBS and 0.1% BSA in PBS + 25 mM acetic acid pH 4.2 three times for three min each (everything on ice) to remove surface bound Tf. After the last short washing step (0.1% BSA in PBS), the solution was completely removed and 1 ml PBS containing 1% Triton X-100 was added. Plates were incubated for 10 min at room temperature to solubilize the cells, the solution of each well was transferred to liquid scintillation tubes containing 10 ml Ultima-Gold liquid scintillation cocktail (Perkin Elmer) and the counts per minute (CPM) were measured in a scintillation counter.

2.4.7 Low density primary hippocampal neuron cultures

Primary hippocampal neurons from embryonic day E18 rat embryos were prepared and cultivated in low density cultures essentially as described by Goslin, Asmussen and Banker (in: Culturing Nerve Cells, 2nd edition, 1998). Briefly, hippocampi were dissected from the brains of E18 rat embryos, treated with 0.25% trypsin for 15 min at

Materials and Methods 51 37°C, washed in Ca2+ and Mg2+ free Hanks’ balanced salt solution (HBSS), and dissociated by repeated passage through a constricted Pasteur pipette. Cells were plated in horse serum-containing cell culture medium at a density of 150.000 cells per 6 cm tissue culture dish containing six 15 mm poly-L-lysine coated coverslips with wax dots at their surface. After cells had attached to the substrate (>5 hours after preparation), coverslips were transferred upside down to dishes with glial cell monolayers containing serum-free medium. Glial cells were prepared separately from embryonic rat brains and plated in the appropriate density or “left-over” cultures on dishes in which neurons have been plated were used. Details for preparation of coverslips, media composition, dissection, plating and culturing of neurons and astroglial cells can be found in the chapter “Rat Hippocampal Neurons in Low-Density Culture” of the book mentioned above.

2.4.8 Transfection of primary hippocampal neurons

Primary hippocampal neurons were transfected at day in vitro (DIV) 8 to 10 using the Effectene transfection reagent (Qiagen) essentially as described by the manufacture’s instructions. We used 0.3 µg DNA, 2.4 µl Enhancer and 6 µl Effectene per coverslip placed in one well of a 12-well plate. We used conditioned medium from the culture dish were neurons had grown in and incubated with the transfection mix overnight. Cells were fixed 20-24 hours after transfection and processed for immunofluorescence staining and microscopy.

Alternatively, primary neurons were transfected directly after preparation using the Amaxa Nucleofector II system with the Rat Neuron Nucleofector Kit following the manufacture’s instructions. We used 5x105 cells in 100 µl transfection solution and 3 µg DNA per transfection. After transfection, 500 µl of pre-warmed plating medium (containing horse serum) were added and the cells were plated onto two 6 cm tissue culture dishes with coverslips. Coverslips were transferred to the glial cell culture dishes the next day. Cell were fixed after different periods of time as described above and processed for immunofluorescence staining.

2.4.9 Immunofluorescence staining of cultured neurons

For immunofluorescence staining of cultured neurons grown on glass coverslips we used a modified protocol. Cell culture medium was removed from the coverslips and the

cells were fixed immediately in 4% PFA, 4% sucrose in PBS pH 7.4 for 15 min or in - 20°C methanol for 5-10 min. After fixation, cells were washed 3 times with PBS. PFA- fixed cells were quenched for 10 min in 50 mM NH4Cl and washed 3 times with PBS. Cells were permeabilized in PBS + 0.1% Triton X-100 for 3 min and washed again three times in PBS. Coverslips were transferred onto parafilm in a wet chamber, immediately covered with 100 µl blocking solution (2% FCS, 2% BSA, 0.2% Fish Gelatin in PBS) and incubated for 1 hour at room temperature. The blocking solution was aspirated and 100 µl primary antibody solution (diluted in 10% blocking solution in PBS) were applied for 1 hour. After three washes with PBS, 100 µl secondary antibody solution (in 10% blocking/ PBS) were added and incubated for 30 min. Coverslips were washed three times in PBS, the wax dotes were removed, the coverslips were briefly dipped into water and mounted onto glass slides in a drop of Gelmount mounting solution (Sigma).

2.4.10 Quantification of neurite lengths

Images were acquired with an inverted microscope (Zeiss) using the freely available software Scion Image (Scion Corporation). Neurite lengths were quantified by drawing a freehand line along the longest neurite of each neuron and calculating the length in µm from the length of the line in pixels using the appropriate factor for the objective that had been used for image acquisition.

Results 53