Fluorescence Activated Cell Sorting (FACS) and Gene Expression Analysis of Fos-expressing Neurons from Fresh and Frozen Rat Brain Tissue

All experiments were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) of the National Institutes of Health Guide for the Care and Use of Laboratory animals ¹⁶.

Note: All the steps below use low-binding centrifuge tubes that were kept on ice unless otherwise specified.

1. Preparation Before Tissue Collection

1. Set the centrifuge to 4 ^oC.
2. Fire polish a set of three glass Pasteur pipettes with decreasing diameters of approximately 1.3, 0.8, and 0.4 mm for each sample.
3. Prepare labeled 1.7 ml-tubes containing 1 ml cold Buffer A and keep the tubes on ice.
4. Prepare an ice tray containing the brain slicing matrix, spatulas and glass plates (or inverted glass Petri dish) on which to perform the dissection. Pre-chill two or more razor blades on the glass plates and use tissues paper to dry all instruments that touch the tissue.
5. Thaw the Enzyme solution at room temperature (RT) for 30 min before tissue collection.

2. Tissue Collection and Dissection

1. Initiate the behavioral or pharmacological treatment 90 min before tissue collection.
   NOTE: For the results shown here, acute intraperitoneal injections of 5 mg/kg methamphetamine on rats in a novel environment (test condition) and naïve rats kept in their home cages (control condition) were performed.
2. Anesthetize the rat by placing it in a glass desiccator jar with saturated isoflurane and decapitate the rat 30 – 60 sec later using a guillotine.
   Use scissors to remove the skin and muscle from the head and expose the skull. Use rongeurs to cut the skull and open up the foramen magnum and remove the back part of the skull. Use rongeurs to cut along the top edges of the skull to expose the brain. Be careful not to damage the brain. Use a small spatula to gently scoop under and elevate the brain. Raise the brain and cut the nerves until the brain is free ¹⁷.
3. Dissect tissue using razor blades.
   NOTE: Obtain tissue samples using either of the following methods: (2.3.1) freshly dissected tissue; (2.3.2) frozen tissue after dissection; or (2.3.3) frozen tissue dissected from frozen whole brain. Keep the brain slicing matrix, razor blades and glass plate dry throughout the dissection and mincing processes as condensed water can lead to hypotonic lysing of cells. Use magnifying glasses to ensure accurate dissection.
   1. For freshly dissected tissue, place the freshly extracted brain into a brain slicing matrix (a rat brain-shaped metal mold with slots for the razor blades at 1 mm intervals) that has been chilled on ice. Insert two or more pre-chilled razor blades into the slots to cut coronal slices that contain the brain region(s) of interest. Place the cut slice on the chilled glass plate.
      Note: Dissect the brain regions of interest on a chilled glass plate.
   2. For frozen tissue after dissection, dissect the brain region(s) of interest from slices of freshly extracted brain, similar to that described above in 2.3.1. Place the dissected tissue into a microtube and rapidly freeze the tissue by submerging the microtube in -40 ºC isopentane for 20 sec. Keep dissected tissue frozen at all times in a -80 ºC freezer until further processing.
   3. For frozen tissue, immediately freeze the freshly extracted brain in -40 ºC isopentane and store in a sealed bag at -80 ºC for up to 6 months.
      1. On the day of dissection, place the frozen brain in a cryostat set at approximately -20 ºC (no warmer than -18 ºC) for approximately 2 hr to equilibrate the temperature.
         NOTE: Brains can be cut easily at this temperature, while much cooler temperatures make the brain too brittle to be cut safely.
      2. Use razor blades to cut 1 – 2 mm coronal slices of the frozen brains in a cryostat. Use a blunted 12- to 16-gauge needle to obtain tissue punches from these slices under freezing conditions. Keep dissected tissue frozen at all times until further processing.
4. Add 1 – 2 drops of Buffer A to cover the dissected tissue before mincing. Remove most of the white matter from the tissue using two razor blades to prevent loss of neurons during the rest of the trituration process. If starting with frozen tissue, then allow the tissue to thaw on the cold glass plate for no more than 1 min before applying Buffer A solution.
5. Mince the tissue 100 times in each orthogonal direction with a razor blade on a chilled glass plate. Hold the razor blade vertical to the glass plate when mincing.
   NOTE: Thorough mincing is critical for all protocol steps.
6. Use razor blades to transfer the minced tissue into microcentrifuge tubes containing 1 ml of cold Buffer A. Invert the tube 3 – 5 times to keep all minced tissue in the solution.

3. Cell Dissociation

NOTE: Use gentle end over end mixing for all of the following steps. Do not use a vortex mixer and avoid air bubbles that cause cell damage.

1. Centrifuge the sample tubes at 110 x g for 2 min at 4 ºC. Discard supernatant. Slowly add 1 ml of cold freshly thawed Enzyme solution (containing a mix of proteolytic enzymes) down the inner wall of the microtube. Immediately suck up the entire pellet and gently pipette up and down only 4 times with a moderately large tip diameter pipette to disperse the minced tissue pellet.
2. Invert the microtubes immediately to prevent the pellet from sticking to the bottom and incubate the samples with end-over-end mixing for 30 min at 4 ^oC.
3. After enzymatic tissue digestion, centrifuge the tubes at 960 x g for 2 min at 4 ºC. Remove the supernatant and add 0.6 ml of cold Buffer A. Immediately after adding the Buffer A, use the same pipette tip to disperse the pellet by sucking up the entire pellet and gently pipette up and down 5 times.
4. Mechanically triturate the digested tissue and collect in 15 ml tubes using the following steps. For each sample, use a separate set of 3 fire-polished glass Pasteur pipettes with descending diameters of approximately 1.3, 0.8 and 0.4 mm attached to latex bulbs.
   1. Gently triturate each sample 10 times with the 1.3 mm glass pipette. Let the sample settle for 2 min on ice (the debris and undissociated cells will settle to the bottom). Collect the supernatant (~ 0.6 ml) and transfer to a 15 ml conical tube (tube #1).
   2. Add 0.6 ml Buffer A solution to the remaining pellet. Triturate the sample 10 times with the 0.8 mm glass pipette. Let the sample settle for 2 min on ice. Collect the supernatant (~ 0.6 ml) and transfer to the same 15 ml conical tube #1.
   3. Add 0.6 ml Buffer A solution to the remaining pellet. Triturate the sample 10 times with the 0.4 mm glass pipette. Let the sample settle for 2 min on ice. Collect the supernatant (~ 0.6 ml; without touching the pellet with non-dissociated cells) and transfer to the same 15 ml conical tube #1.
      NOTE: Keep the 0.4 mm diameter pipette in the tube #1 for the following trituration steps.
   4. Repeat step 3.4.3 three more times using the smallest glass pipette (~ 0.4 mm diameter), and collect the supernatant into a separate 15 ml conical tube (tube #2).
   5. Triturate the collected cell suspensions in tubes #1 and #2 for 10 more times using the 0.4 mm glass pipette and keep on ice.

4. Cell Fixation and Permeabilization

1. Prepare 4 microtubes per sample (two microtubes for cells from tube #1 and two for cells from tube #2) by adding 800 µl of 100% cold ethanol (stored at -20 ^oC before use) into each tube and keep them on ice. Note: The final ethanol concentration will be 50%.
2. Pipette ~ 800 µl of the cell suspensions (from tube#1 and tube#2) into each of the 4 tubes containing cold ethanol and invert the tubes to mix the samples.
3. Incubate tubes on ice for 15 min while inverting the tubes every 5 min.
4. After fixation/permeabilization, centrifuge the tubes at 1,700 x g for 4 min at 4 ºC and discard the supernatant. Leave 50 µl of solution to prevent cell loss.
   NOTE: The pellets at this stage are white and stick less to the wall of the tubes than before permeabilization. Therefore, remove the supernatant carefully by touching the wall of the microtube where there is no pellet and draw up the supernatant slowly using a micropipette.

5. Cell Filtration

1. Re-suspend the pellets from step 4.4 with cold PBS as follows:
   1. Add 550 μl of cold PBS to one of the two microtubes coming from tube #1, and use a moderately large diameter pipette tip to gently pipette the cell suspension up and down 5 times. Repeat the same for one microtube coming from tube #2.
   2. For cells from tube #1, using the same pipette, transfer the first cell suspension to the second pellet. Resuspend the second pellet by gently pipetting the combined cell suspension up and down 5 times.
   3. For cells from tube #2, resuspend and combine the pellets (i.e., third and fourth microtubes) as described in 5.1.2.
2. Filter the two cell suspensions from steps 5.1.2 and 5.1.3 separately using two different pairs of cell strainers (100 µm and 40 µm pore sizes) as follows:
   1. Pre-wet each cell strainer by adding PBS to the inside of the strainer. Use a pipette to remove the excess PBS from the outside of the strainer.
   2. Pipette the cell suspension from step 5.1.2 evenly onto the first cell strainer with 100 µm pore size. Collect the flow-through in a 50 ml tube on ice. Use the pipette to collect the flow- through attached on the outer side bottom of the cell strainer.
   3. Use the same pipette to transfer the flow-through from the 100 μm cell strainer to the 40 μm cell strainer. Collect this flow-through in another 50 ml tube on ice. When transferring the flow through from 40 μm cell strainer, change to new pipette tips to avoid contamination from 100 μm cell strainer.
   4. Repeat these steps for the cell suspension from step 5.1.3 using a new set of filters.
3. Combine the two flow-through from each sample for a final volume of approximately 1 ml per sample.

6. Incubation with Antibodies

NOTE: Use small aliquots of the brain cell suspensions to prepare multiple control samples for setting appropriate flow cytometer settings prior to running the main sample. For each antibody labeling, prepare control samples that include no antibodies, only the secondary antibody (or other fluorescent label), and then both primary and secondary antibodies (or other fluorescent label). Use these controls to set the gates that separate specific versus non-specific labeling in the flow cytometer. When possible, use fluorochromes that do not require compensation. Increase the final volume of the gating control samples to a final volume of 700 µl by adding PBS prior to adding the primary antibodies.

1. Prepare light-scattering and DAPI control sample by transferring a 100 µl sample of the filtered cells to a 1.7 ml microtube. Add 600 µl of cold PBS with 1 µg/ml DAPI for nuclei staining. Incubate for 10 min with end-over-end mixing, and wash (as indicated in steps 6.4.2 to 6.4.5) before passing through the flow cytometer.
   NOTE: This sample is used only to set the cell/nuclei gate prior to sorting the remaining cells in the FACS machine.
2. Prepare single immunolabeled control samples by transferring 100 µl of the filtered cells to a 1.7 ml microtube. Add 600 µl of cold PBS with one antibody (e.g., NeuN antibody). Add 600 µl of cold PBS to a microtube with another antibody (e.g., Fos antibody). Add the corresponding secondary antibody if it is not a direct-conjugated primary antibody.
   NOTE: These samples are used to determine the appropriate photomultiplier tube (PMT) voltage, and to assess the overlap of the two fluorescent signals if necessary. Antibody concentrations should be titrated to achieve the best signal-to-noise ratios in all channels. Overlapping fluorescent signals can also be compensated by internal calibration of different fluorescent channels within the flow cytometer.
3. Prepare double fluorescent-labeled negative control sample by transferring 100 µl of the filtered cells to a 1.7 ml microtube. Add 600 µl of cold PBS with the secondary antibodies alone or IgG direct-conjugated primary antibodies.
   NOTE: This control sample can be used every time before sorting to determine the background fluorescence for each fluorophore.
4. Prepare main sample to be sorted.
   1. Transfer 700 μl of the filtered cells into a 1.7 ml microtube. Add 7 µl (1:100) of primary Fos antibody conjugated directly to Alexa Fluor 647 (anti-Fos-AF647) and 1.4 µl (1:500) of primary NeuN antibody conjugated directly to Phycoerythrin (anti-NeuN-PE). Incubate tubes for 30 min at 4 ºC with end-over-end mixing.
   2. At the end of the incubation, add 800 µl of cold PBS to each microtube, including the main sample and the control samples, and mix by inversion.
   3. Centrifuge microtubes at 1,300 x g for 3 min at 4 ºC. Discard the supernatant, leaving 50 µl supernatant to prevent cell loss.
   4. Add 1 ml of cold PBS to the pellet and resuspend cells using a pipette with a moderately large tip diameter.
   5. Centrifuge at 1,300 x g for 3 min at 4 ºC. Discard the supernatant.
   6. Re-suspend the pellet in 500 µl cold PBS (adjust final volume depending the size of the pellet).
   7. Transfer and filter the suspension into a round-bottom FACS sample tube with a cell strainer cap (40 µm). Keep the immunolabeled cells on ice and immediately perform FACS. Note: For filtering, touch the pipette tip vertically on the strainer cap and push the cell suspension through it.
5. Set flow cytometer gates using control samples.
   1. Use the light-scattering and DAPI control sample to identify the neuronal cell population from the total events and cellular debris.
      NOTE: Cell bodies in this preparation are only 1 – 2% of the total events (the rest are debris and broken cellular processes). Based on DAPI fluorescent signal (indicating nuclei) and Forward scatter (size of the cell) it is possible to locate cell bodies and gate backwards based on the Forward and Side light-scattering properties of the cells (as shown in Figure 1 A,B).
   2. Use the single immunolabeled control samples to determine the PMT voltage settings, and to analyze spillover of emission from one specific fluorochrome into another filter/channel (e.g., Alexa Fluor 488/FITC or Phycoerythrine). If fluorescent signals overlap, correct the overlap by adjusting compensation levels manually.
   3. Use the double fluorescent-labeled negative control to set up the threshold for the positive population.
      NOTE: The signal coming from this sample is thought to be due to auto-fluorescence and the cells of the main sample located above this threshold can be considered as positive. Typically, the threshold parameters for sorting are more stringent and approximately the top 2/3 of the labeled cells above the negative control are actually sorted.
6. Sort the neurons from the main sample by FACS into 1.7 ml microtubes. Collect the cells into 50 µl of RNA extraction buffer. After sorting, vortex and centrifuge the tube and mix the suspension by pipetting up and down 10 times to recover all sorted cells from the walls of the tube.
7. Incubate the sorted cell suspension at 42 ºC for 30 min to ensure that all cells are lysed prior to RNA extraction, and then centrifuge at 2,800 x g for 2 min at 4 ºC.
8. Transfer the supernatant to an RNase-free tube for long-term storage at -80 ºC or immediately process the sample for RNA isolation, cDNA synthesis, target gene pre-amplification and qPCR, as described previously ^13-15.