Cerebellar Regional Dissection for Molecular Analysis

Traditional molecular studies of the cerebellum have been done on whole cerebellar extracts, which may mask any distinctions across specific cerebellar regions. This protocol makes it possible to assess distinct regions of the cerebellum separately and allows for the exploration of molecular mechanisms that may underlie their unique contributions to a variety behaviors and disease progression. The main advantage of this technique is that it allows for the reproducible and quick dissection of four cerebellar regions, the deep cerebellar nuclei, the anterior and posterior cerebellar cortex of the Vermis and the cerebellar cortex of the hemispheres.

After decapitating the euthanized mouse, make an incision with a razor blade along the medial sagittal line of the head, starting at the nose and continuing all the way back. Separate the skin and use the razor blade to cut away the muscle on each side, cutting down past the ear canals. Using dissecting scissors, trim many spinal cord regions up to where the brain stem meets the cerebellum, taking care to not damage the cerebellum.

Insert one of the vascular scissor blades into the space between the brainstem and vertebral column and cut toward the ear canal, lifting upward while cutting to limit damage to the tissue. Continue to cut along the edge of the skull up toward the olfactory bulbs. Using the blunt forceps, gently peel off the back of this skull to uncover the posterior region of the brain and cerebellum.

Position the blunt forceps along the cut edge of the skull and peel the skull up and over the brain. Trim the rest of the skull with the vascular scissors and blunt forceps, clearing most of it from the top of the brain. Slightly lift the brain with the micro spatula to remove the olfactory bulbs from the remaining skull and disconnect optic tract fibers.

The brain should come free easily at this point. Place the brain into the Petri dish, sitting on ice and remove any remaining skull or other debris. Gently place the brain into the brain matrix with the dorsal side up.

Make sure that it is set level in the matrix and that the midline is in the center. Place one razor blade along the sagittal midline, making sure that the blade pushes all the way to the bottom of the matrix. Place another razor blade one millimeter to the side of the first blade.

Place two more blades resulting in three blades placed on one side of the brain, all one millimeter apart. Repeat this on the other side. carefully grab the front and back end to the razorblades, and lift them straight up out of the matrix.

Discard the tissue on the outside of the razor blades. Slowly, separate one razor blade at a time from the others being careful not to damage the tissue sections. Slide the tissue section off the razor blade and onto the glass slide with the micro spatula.

Six sagittal brain sections should be collected. The foremost lateral sections will have DCN visible. To isolate the DCN, hold a trim to 200 microliter pipette tip perpendicularly over the DCN and push down through the tissue firmly rocking in all directions.

Lift the pipette up and visually confirm the presence of the tissue in the tip. Place one finger at the top of the tip and push down, causing the tissue to bulge out. Insert the tip into a correctly labeled microfiche tube and ensure that the tissue punch is placed in the bottom of the tube.

Repeat this for the remaining three sections, placing the DCN punches in the same tube. Flash freeze the tube in liquid nitrogen. Push away the rest of the brain tissue around the cerebellum in the sections where the DCN was extracted.

Use blunt forceps to gently pick up these hemisphere cerebellar cortex sections and place them into respective microfiche tubes, then flash freeze them. For the last two vermal sections, push away surrounding brain tissue to leave only the cerebellum. Using a razor blade, make a cut separating the anterior labials from the posterior labials.

Ensure that the cut is just after the formation of labial six and does not include labial 10. Using blunt forceps, carefully placed the anterior cerebellar cortex sections and posterior cerebellar cortex sections into their respective microfiche tubes and flash freeze them by leaving the tubes in liquid nitrogen for five minutes. Place the microfiche tubes on ice to keep the tissue from thawing too quickly and apply 150 microliters of cold RNA isolation solution in the microfiche tube, then homogenize with a sterilized pestle.

Once the tissue is homogenized pipette the solution up and down to ensure there is no remaining intact tissue. Further, break up any small tissue pieces by pulling it up into an insulin syringe a few times. Add another 350 microliters of the reagent, pipette up and down to mix thoroughly and let it sit at room temperature for five minutes.

Add 150 microliters of chloroform to the tube and shake it vigorously, then let it rest for two to three minutes. Centrifuge at 12, 000 times G at 15 degrees Celsius for 10 minutes. Carefully remove the tubes from the centrifuge and set the temperature of the centrifuge to four degrees Celsius.

Transfer only the clear aqueous phase into a new tube, taking care not to disrupt the opaque interphase. Save or discard the remaining solution in the tubes. Add 100%isopropyl alcohol at a one to two ratio and mix thoroughly by pipetting up and down.

Let the sample rest at room temperature for 10 minutes to precipitate the RNA out of the solution. Centrifuge at 12, 000 times G and four degrees Celsius for 10 minutes, placing all tubes in the same orientation to make it easier to visualize the pellet. After centrifugation, carefully remove the tubes and remove the supernatant with the pipette, making sure to not disrupt the pellet.

The pellet is gel like and difficult to see, so estimate where it is based on the orientation of the tubes in the centrifuge. After removing all supernatant, add 500 microliters of 75%ethanol, vortex briefly and centrifuge at 7, 500 times G and four degrees Celsius for five minutes. Remove the supernatant carefully, without disrupting the pellet.

Leave the caps open to dry the sample for five to 10 minutes. Once dry resuspend the pellet in DNA's free water at 20 microliters to the samples for DCN and 30 microliters for all others. Store the samples at minus 80 degrees Celsius until further analysis.

This protocol was used to dissect four distinct regions of the mouse cerebellum and to explore regional differences in gene expression. The expression levels of Aldolase C, parvalbumin and KCNG4 were assessed using real-time quantitative PCR. Aldolase C is more highly expressed in the posterior cerebellar vermis.

But lower in the DCN and the anterior region of the vermis when compared to the bulk cerebellar dissection. Parvalbumin is similarly present in the DCN anterior vermis, posterior vermis and hemisphere cerebellar cortices, when compared to bulk cerebellar extracts. KCNG4 is significantly enriched in the DCN and the interior vermis, but not in the posterior vermis or hemispheres when compared to the bulk extraction.

To directly compare the expression of aldolase C across the cerebellar cortex, the expression levels were compared to the anterior vermis. The expression level of aldolase C was significantly higher in the posterior Vermis and trending higher in the cerebellar hemispheres. The RNA extracted from these regions can also be used in RNA sequencing, experiments.

RNA seq comparing these for cerebellar regions would provide more detailed information on molecular mechanisms, underlying discrete functions of these regions. As well as potential differences in their vulnerability in disease.