The overall goal of this novel RNA in-situ hybridization assay is to visualize single RNA molecules in a specific brain area which are critical for clarifying dopaminergic dysfunction during central nervous system disease. This method can help answer key questions in the neuroscience field such as dopaminergic abnormalities mediating behavioral responses and modulating working memory function. The main advantage of this method is that it provides a novel in-situ hybridization technique to investigate dopamine system dysfunction during the progression of central nervous system diseases.
Though this method can provide insight into overall expression levels of a target mRNA in a given brain region, it can also be applied to determine how mRNA transcripts are distributed throughout the cells of a given region. To begin this procedure, within five minutes after harvesting an adult rat brain, submerge it in liquid nitrogen for 15 seconds. Next, equilibrate the brain at minus 20 degrees Celsius in a cryostat for one hour.
After an hour, cut 30 micron sections containing nucleus accumbens from 2.76 millimeters to 2.28 millimeters anterior to bregma and mount them onto the slides. Then dry the sections at minus 20 degrees Celsius for 10 minutes. Subsequently, immerse the slides in pre-chilled 4%paraformaldehyde for one hour at four degrees Celsius.
Next, place the slides in an increasing ethanol gradient at room temperature then transfer the slides to fresh 100%ethanol for another five minutes. Afterward, place the slides on the absorbent paper to allow air dry. Draw a barrier around each section with a barrier pen.
Let the barrier dry completely for one minute. To pre-treat the brain sections, turn on the oven and set the temperature to 40 degrees Celsius. Add three drops of pre-treatment reagent on each brain section.
Then incubate the sections for 30 minutes at room temperature. Next, submerge the slides in 1X PBS for one minute at room temperature and transfer the slides to fresh 1X PBS for another minute. Slides should not stay in 1X PBS for longer than 15 minutes.
To run the multiplex assay, warm the target probe for 10 minutes at 40 degrees Celsius in a water bath and then cool to room temperature. Place the RNA reagent at room temperature. Remove excess liquid from the slides with absorbent paper and place them back on the slide rack.
Then add three drops of the Drd1alpha as probe on each sample slice and incubate the samples for two hours at 40 degrees Celsius. Afterward, wash the slides in 1X wash buffer for two minutes at room temperature twice. Then remove excess liquid from the slides with absorbent paper and place them back on the slide rack.
Do not let brain sections dry out between incubation steps. Add three drops of AMP 1FL on each sample slice and incubate the samples for 30 minutes at 40 degrees Celsius. Afterward, wash the slides twice in 1X wash buffer for two minutes each time at room temperature.
Then remove excess liquid from the slides with absorbent paper and place them back on the slide rack. Subsequently, add three drops of AMP 2FL on each sample slice. Incubate the samples for 15 minutes at 40 degrees Celsius.
Next, submerge the slides in 1X wash buffer for two minutes at room temperature twice. Remove excess liquid from the slides with absorbent paper and place them back on the slide rack. Add three drops of AMP 3FL on each sample slice and incubate the samples for 30 minutes at 40 degrees Celsius.
Next, wash the slides in 1X wash buffer for two minutes at room temperature twice. Remove excess liquid from the slides with absorbent paper and place them back on the slide rack. Then add three drops of AMP 4FL ALT A on each sample slice and incubate the samples for 15 minutes at 40 degrees Celsius.
Wash the slide in 1X wash buffer for two minutes at room temperature twice. Remove excess liquid from the slides and immediately place two drops of mounting reagent onto each section. Next, place a 22 millimeter by 22 millimeter coverslip over each brain section.
Then store the slides in the dark at two to eight degrees Celsius until dry. For imaging, turn on the confocal microscope and switch to a 60X objective. Obtain Z stack images and acquire images of Drd1alpha-labeled cells in the nucleus accumbens region.
For images from the nucleus accumbens that displayed the discrete dots staining pattern, the dynamic range of expression was assessed using a semi-quantitative analysis. Each cell was scored from zero to nine based on the number of dots per cell. This hybridized signal score method can thus assess the extent and variability for Drd1alpha expression across individual cells.
Here are the representative confocal images of Drd1alpha expression in male and female rats which have the discrete dots staining pattern. To account for the nested data structure, average count values were calculated for each category and used for statistical analysis. A Mann-Whitney U test was conducted to assess differences in median cell count in male and female rats.
The frequency of cells in each category is analyzed using relative frequency and cumulative frequency. Female animals displayed a significant shift in the distribution with the greater frequency of cells in lower ordered categories relative to male animals. Overall, the results suggest clear sex differences in Drd1alpha expression in the nucleus accumbens.
Once mastered, this technique can be done in seven hours if it is performed properly. While attempting this procedure, it's important to remember to work quickly as temperature changes or drying out of the tissue can damage the mRNA and hinder our ability to obtain a reliable signal. After watching this video, you should have a good understanding of how to perform the in-situ hybridization technique in cortical tissues, fluorescently image signal mRNA transcripts within chosen brain regions, and characterize the distribution of mRNA transcripts for statistical analysis.
