Animal care and all procedures in this protocol follow the institutional and national guidelines.
Prepare the preparations that are indicated by "Π-" beforehand.
1. Preparation of BMMs
- Perform the culling of the mice by cervical dislocation.
- Remove femur and tibia bones, free bones from tissue and trim both ends for the accessibility of the bone marrow.
- Keep bones in ice-cold PBS or ice-cold DMEM medium (supplemented with 100 U/ml penicillin and 100 μg/ml streptomycin, on ice until the next step.
Note: Conduct the following steps under a class II biosafety cabinet to minimize the risk of contamination.
- Flush the medullary cavity with cold PBS +penicillin/streptomycin using a 26 G (0.45 mm) needle attached to a 1 ml syringe.
- Pellet cells by gentle centrifugation at 350 x g for 10 min, resuspend the pellet in BMM medium and plate in sterile microbiology noncoated Petri dishes.
- Preparation of the BMM medium
- Dulbecco's Modified Eagles Medium DMEM
- 10% inactivated FCS
- 20% mouse fibroblast L929 cell line culture supernatant (source of macrophage colony-stimulating factor, M-CSF)
- 5% horse serum
- 2 mM glutamine
- Preparation of the L929 cell line culture medium;
- RPMI (Roswell Park Memorial Institute) 1640 medium
- 10% inactivated FCS
- 2 mM glutamine
- Preparation of mouse fibroblast L929 cell line culture supernatant;
- Confluent L929 cells were split 1:4, cultured in 175 cm2 flasks for 2 days using 20 ml L929 medium and the culture supernatant was collected after 48 hr, filtered and added to the BMM-medium
- Incubate the cells flushed from the femur in an incubator at 37 °C in 5% CO2 atmosphere.
- After every 48 hr (maximum 72 hr) of incubation, aspirate the medium and replace by fresh BMM medium, for up to 10 days. More than 95% of the cells were positive for CD14 as tested by flow cytometry. CD14 is a pattern recognition receptor expressed mainly by macrophages. By determining the percentage of cells positive for this receptor, a pure culture of adherent BMMs has been generated.
Note: prepare and culture the cells accordingly if other cell types are used.
2. Coating of Microbeads as Phagocytic Cargo
- For preparation of 1 ml bead suspension, use 400 μl of 2.5% 3 µm carboxylated polystyrene microparticles, or alternative microparticles.
- Transfer the bead suspension to a 1.5 ml microcentrifuge tube, wash 3x with PBS and add 100 μl of 500 mM 2-(N-morpholino)ethanesulfonic acid sodium salt, MES buffer at pH 6.7 to the bead pellet.
- Dissolve 50 μg mouse IgG (polyclonal IgG antibody) in 50 μl sterile ddH2O and add to the bead suspension.
- Fill the suspension up to 1 ml with sterile ddH2O (450 μl).
- Incubate the solution for 15 min on a rotating wheel at RT.
- Prepare EDAC cross-linker, N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride in a concentration of 10 mg/ml and add 14 μl to the bead suspension.
Note: EDAC cross-links amino groups of the IgG with the carboxyl groups on the surface of the beads and facilitates the immobilization of the IgG on the bead surface. This is critical for bead uptake and therefore the solution should be prepared freshly.
- Incubate the suspension on a rotating wheel for 1 hr at RT.
- Add 14 μl of EDAC cross-linker and incubate the suspension on a rotating wheel for 1 hr at RT.
- Centrifuge the suspension at 10,000 x g for 2 min in a microcentrifuge.
- Wash the beads 3x in stop buffer (1% Triton-X 100 in 10 mM Tris, pH 9.4) in order to stop the cross-linking reaction, by resuspending the pellet in stop buffer and spinning the solution at 10,000 x g for 2 min.
- Wash beads 3x in PBS and resuspend the pellet in 1 ml PBS.
Optional: Prepare working aliquots of 30-50 μl.
- Store the IgG-coated bead suspension at 4 °C for no longer than 4 weeks and never allow the suspension to be frozen.
Note: A preservative such as Sodium azide at a final concentration of 0.02% (w/v) can be added to the suspension to prevent bacterial growth and contamination. In this case washing of the beads prior to its use has to be performed to avoid cytotoxic effects of the preservative. Centrifuge an aliquot of the suspension at 10,000 x g for 2 min and wash the beads by resuspending the pellet in PBS. Repeat washing 3x.
3. Preparation of the Dextran Probe Stock Solution
- Dissolve the Texas Red 70,000 kiloDaltons Dextran (Dex70kD) in PBS at 20 mg/ml and store at -20 °C, according to the manufacturer's instructions.
Note: Keep stocks at -20 °C for up to several months, or at 4 °C for few weeks, see the manufacturers documentation.
- Prepare the dextran solution for the experiment from the stock by diluting it in complete DMEM cell culture medium (DMEM, 10% FCS, 2 mM L-glutamine) at approximately 1 mg/ml (several-fold concentrated solution that will be diluted to the final working concentration of 20 μg/ml before addition to the cells).
- Use a ultrasound water-bath to sonicate the dextran aliquot for 5 min to homogenize the solution and dissolve aggregates that could later lead to artifact generation during imaging.
- Centrifuge at maximum g for 5 min in a microcentrifuge to remove any undissolved clumps or contaminants from the solution.
- Carefully move the supernatant to a fresh tube while avoiding the pellet at the bottom of the tube and dilute the solution to the final working concentration of 20 μg/ml in complete DMEM cell culture medium.
- Filter-sterile the solution using a 0.2 μm syringe mounted filter.
4. Dextran Preloading
- Seed cells in a live cell imaging glass bottom dish and incubate for at least 12 hr (at 37 °C in 5% CO2 atmosphere) to ensure attachment and acclimatization.
Note: There are segmented glass bottom dishes available that allow performing multiple experiments (up to four compartments) per dish.
- Prepare the dextran in DMEM solution as described in Protocol 3. Warm up the prepared dextran in DMEM solution, using a water bath at 37 °C.
- Aspirate medium and add dextran solution to the cells carefully and incubate at 37 °C in 5% CO2 atmosphere for 2-8 hr for uptake.
Note: Plan and optimize the protocol based on the probe and cell type that is used and strictly keep to this duration when repeating experiments. This is essential for the profile of dextran accumulation in the endocytic pathway and thus reproducibility of experiments.
- Wash cells 3x with prewarmed complete DMEM medium; aspirate medium and rinse cells carefully with fresh medium.
- Incubate cells with complete DMEM medium for 4-12 hr at 37 °C in 5% CO2 atmosphere.
- Wash cells once with prewarmed complete filtered phenol red-free DMEM medium.
- For optimal imaging results, change to prewarmed complete filtered phenol red-free DMEM medium at least 30 min before the start of imaging. Phenol red may cause quenching of fluorescent signals, increasing background noise and thus reduce image contrast and clarity.
Note: Set up the microscope and the imaging settings in advance, according to preplanned and optimized protocol based on the type of probe and cells that are used.
5. Adding IgG-coated Beads
- Equilibrate an aliquot of preprepared 1% bead suspension to RT and sonicate in an ultrasound water bath for 2-3 min.
- Add 1-6 μl of the 1% bead suspension to the complete filtered phenol-red free DMEM medium under a class II biosafety cabinet to minimize the risk of contamination (a good starting concentration is 1 μl/2 cm2 dish surface).
Note: Here BMMs were seeded at 25,000 cells/well and a 6 μl of 1% stock bead suspension was added to the medium in the dish. This roughly equals a bead/cell ratio of 15:1. The ratio has to be adjusted to the type of the cells that is used and to the bead material; i.e. latex beads have low density and do not sink to the bottom quickly, whereas polystyrene beads sink and come in contact with the adherent cells much faster and thus in larger numbers.
Note: Depending on the experiment, it may be of advantage to select the region that will be observed in advance. Bead suspension can then be added only to that specific region of the glass bottom dish, therefore increasing the probability of observing favorable uptake events.
- The dense cloud of beads can be diffused by gently pipetting the suspension in the glass bottom dish.
- Wait until beads sink to the bottom of the glass bottom dish and are approximately in the same plane with the adherent phagocytic cells.
- Focus on the region of interest (ROI) and start the time-lapse imaging.
Note: It may be necessary to fine-tune the focus while imaging is in progress, depending on the imaging system that is used, its stability and the mobility of the observed cells. However, note that this may render impossible, the proper analysis of phagosomes that strongly deviate from the plane of focus as a result of refocusing.
6. Imaging
Follow the general guidelines below for optimal imaging quality;
- Use a confocal imaging system such as a laser-scanning or spinning disc system.
Note: A Leica TCS SP5 AOBS Laser scanning confocal microscope controlled by the Leica LAS AF software and equipped with an environmental control chamber was used here for time-lapse video imaging.
- Optimize the imaging settings such as scanning speed, magnification, resolution, etc. in a manner to allow for a rate of a frame in every 7-20 sec, depending on system used.
Note: Here, a 200 Hz scanning speed, 2x scanner zoom and a line averaging of 2-3x at a resolution of 512 x 512 pixels resulted in a recording time between 3-5 sec/rame. A rate of a frame in every 10 sec was used to record time-lapse movies with durations of at least 120 min.
- Use appropriate excitation/emission settings based on the used imaging system and probe(s).
- Optimize the settings to prevent excessive photo-bleaching.
Note: Here, the Texas Red Dextran 70kD was excited using a DPSS (561 nm) laser and emission light was detected by a Leica hybrid detector (HyD) at 600-650 nm with the emission peak at 610 nm. Laser intensity has to be adapted to the signal intensity and kept as low as possible to minimize photo-bleaching of the fluorophore(s) and photo toxicity effect of the laser light on the cells. Generally, it is important to balance the scanning speed, line averaging, scanning resolution, frame interval and duration of the imaging to obtain proper and stable signal intensity and capture the complete duration of bead uptake and phagosome maturation process.
- Include a bright-field (BF) channel for observing the beads if they are not conjugated with a fluorophore.
Note: Beside the Texas Red channel, BF channel was used to visualize the beads, the same DPSS laser was used as the light source and signal was detected with a photo multiplier (PMT) detector.
Note: Make sure to apply identical recording settings when acquiring data that is to be collated. Most important parameters are: excitation laser intensities, detector setting, acquisition settings, magnification and frame intervals. Not using identical frame intervals will necessitate a curve-averaging step as the observation data points will not overlap (e.g. to collate an observation with frames acquired at every 7 sec with another set with frames at every 12 sec). This would increase the steps required for data evaluation and require additional software with curve-averaging function, such as OriginLab's Origin Pro statistics software (http://www.originlab.com/).
- Preferably, save the time-lapse video in the native file-format of the used imaging system and avoid exporting in compressed formats.
Note: Here, time-lapse movies were saved in the native Leica LAS AF format (.LIF) files, which were then directly imported to open in Fiji. Fiji is able to read the native file formats from most microscope manufacturers using the included Bio formats importer plug-in. Exporting the time-lapse movie file in an image series with JPG or TIFF or as a video file in an AVI container format is not necessary or recommended. In addition to preserving the best possible image quality from the original observation by avoiding lossy compression algorithms (e.g. JPEG), using the native microscope file format insures that the file's meta-data (time stamps, magnification, laser and acquisition intensities, detector settings etc.) is preserved and available to Fiji. However, if for any reason, time-lapse video files need to be exported in a different format for analysis, make sure to use uncompressed file formats such as TIFF image series and separate RGB color (red, green, blue) channels already at this step, as Fiji often cannot successfully separate the BF channel from other color channels in exported files. Also, make sure to preserve the original microscope files as a reference.
7. Analysis of the Time-lapse Movies
- Use ImageJ, Fiji or any other software that provides an analogues signal association analysis capability.
Note: Here, Fiji was used for the analysis of time-lapse movies. Fiji is an ImageJ distribution containing an image processing package with reorganized tool menus and additional native plug-ins, available for free download at http://fiji.sc. The process described in this section is depicted in Figure 2.
- Open the file in Fiji by clicking "File", "Open" and choosing the file, or by dragging and dropping the file to Fiji.
- Choose the following options;
- Stack viewing: View stack with Hyperstack,
- Color options: Color mode Colorized,
- Split channels into separate windows: Split channels (for every RGB color-channel that was recorded a separate window will be opened).
- In case an image series is to be used, load the series to Fiji by going to "File", "Import", "Image Sequence" and choose any image file in the folder that contains the target image series.
- Set filters and conditions for loading selected images in the series, for instance;
- Number of images: how many frames are to be loaded.
- Starting image: which image is the starting frame in the series.
- Increment: the increment between frames to be loaded (every frame, every second frame, etc.).
- File name contains: filtering for specific channel using the file name (for instance by setting "c001", which is how normally the images from "channel 1" are labeled after color-separation of a multichannel time-lapse video).
- Remove scaling by going to "Analyze", "Set scale…", checking the box "Global" and clicking "Click to remove scale".
Note: This step allows pixel based analysis of the images in case different magnifications have been used for the various experimental sets that are to be evaluated. If the magnification settings have always been kept constant and the native microscope file was directly imported to Fiji, this step can be skipped, as Fiji can understand and use the magnification and scale data from the microscope file's metadata.
- Set up measurement parameters by going to "Analyze", "Set Measurements" and checking the following boxes: "Area", "Standard deviation", "Integrated density", "Display label" and "Mean gray value".
- Redirect to the color channel that contains the signal from the probe that is to be measured and confirm with "OK".
- Go to the frame in which the measurements are to be started and select the BF channel window by clicking on the upper edge of the window.
- Use the "oval selection tool" to select a region of interest (ROI), i.e. a circular ROI on the internalized bead. Ensure that the selection is fitted tightly to the outer edge of the bead as visible in the BF channel.
Note: When using a PC, hold the Shift-key while using the selection tool to ensure a circular ROI.
- Start the measurement optimally a few frames before the full engulfment of the bead is completed and note the frame in which a fully formed nascent bead-phagosome is formed and the phagocytic cup is closed. This should be relatively clearly discernable in the BF channel.
- Go to "Analyze" and click "Measure" to execute the measurement; the result will be displayed in a separate window titled "Results".
- Go to the next frame, adjust the position of the ROI in case the bead has moved, and repeat the measurement. The result will be added to the list in the result window; each analyzed frame can be identified based on the value in the "Label" column.
Note: Using shortcut keys (e.g. "M" for measure) can significantly speed up the evaluation process; see the list of shortcuts and assign costume ones under the menu "Plugins".
- After completing the measurement of all relevant frames, the results can be copied to a spreadsheet application such as MS Excel. The column "IntDen" depicts the intensities of the selected area in the channel that the measurement was redirected to.
8. Bleaching Correction
Depending on the used probe and imaging settings, photo-bleaching may occur. Depending on its extent, this could strongly affect the outcome of the evaluation. However, this effect can be partially corrected by applying an equal but opposite rate of change to the measured values. If present, the photo-bleaching coefficient can be calculated by measuring the time-dependent signal intensity decrease in the whole frame, or specifically cropped area of the frame, during the time-span relevant to analysis of each phagosome. This process is depicted in Figures 3 and 4.
- Under the "Plugins" menu of Fiji, use the "Time Series Analyzer" plug-in to determine the general decrease in the whole-frame, or ROI specific probe signal intensity over time (Figure 3).
Note: Time Series Analyzer plug-in is available for download at http://rsbweb.nih.gov/ij/plugins/time-series.html, in case not already present in the Plugins menu.
- Plot the measurement against time (in seconds) in MS Excel, only for the frames that correspond to the frames of an analyzed phagosome.
- Apply a linear trend-line (Figure 4A) to the plot; a negative slope for the decreasing signal indicates the presence of photo-bleaching effect.
- Apply the reversed slope to values from an analyzed phagosome(Figures 4B and 4C): Corrected signal intensity (SI) = raw SI + (time in seconds * reverse slope)
Note: each single analyzed phagosome will have a specific time-span (starting at complete uptake frame) during a recorded time-lapse movie; the photo-bleaching must be recalculated for that specific span and will be only valid for correcting the measured values from that specific phagosome.
9. Data Evaluation
- Collate the data and calculate the average and statistical error of the bleaching-corrected values in appropriate software.
- Plot the evaluated data in an appropriate form.
Note: Here, the scientific statistics and plotting software GraphPad Prism (http://www.graphpad.com/scientific-software/prism/) was used. Prism software is able to generate and plot an average curve with the corresponding error indicators as long as all the data have the same frame rate (i.e. all were acquired with at the same intervals, such as one frame every 10 sec).
Note: Wide variations of the absolute SI values within repeats of the same experiment set will introduce very large statistical error and render the data unusable. This can be the case if the protocol, e.g. imaging settings, are not held strictly identical among different experiment repeats that are to be collated.