Detection of Alternative Splicing During Epithelial-Mesenchymal Transition

The overall goal of the following experiment is to detect changes in alternative splicing during EMT. This is achieved by utilizing an inducible EMT model in which expression of the fusion protein twist er. In the human mammary epithelial cells triggers cells to undergo EMT upon tamoxifen treatment as a second step.

The expression of splice isoforms is analyzed by quantitative R-T-P-C-R using isoform specific primer sets, which reveals alternative splicing changes at the RNA level. Next, the abundance of protein corresponding to each isoform is determined by immuno blotting in order to confirm the expression of splice isoforms at the protein level, results are obtained that show changes in alternative splicing in genes of interest during EMT, based on quantitative R-T-P-C-R and immuno blotting analyses, This method can help answer key questions in the field of RN alternative splicing and EMT, such as how alternative splicing is regulated during EMT and how this regulation affects EMT and EMT related pathological processes. The implications of this technique is stand towards cancer therapy because EMT plays an important role in promoting tumor invasion and metastasis.

Though this method can provide insight into alternative splicing During EMT. The method for isoform specific MRA detection can also be applied in other systems, such as studying alternative splicing in neuron differentiation and the program cell deaths. The first step is to plate cells expressing the twist ER fusion protein seed the cells into a 10 centimeter tissue culture dish in duplicate next, prepare and light protect the Tamoxifen solution to induce the epithelial mesenchymal transition or EMT treat cells with 20 nanomolar tamoxifen containing media for a non tamoxifen treated control group add 0.01%ethanol to an additional set of cells two days after incubation.

Take pictures under a light microscope at 10 x magnification to record any morphological changes. Next, wash the cells with cold PBS. Scrape the cells from one half of the plate into RNA lysis buffer for RNA isolation and the other half in 100 microliters of ice cold ripa buffer for protein analysis passage the cells from both groups as shown earlier and continuously treat with 20 nanomolar tamoxifen or vehicle.

Repeat these steps every other day until day 14 at which time Tamoxifen treated twist ER cells should show a spindle shaped mesenchymal morphology. Whereas vehicle treated controls should maintain the cobblestone like epithelial morphology. Here a four exon prem NNA is used as an example for detection of exon inclusion.

Design a forward primer inside the variable exon three and a reverse primer inside the nearby constitutive exon four. Allowing for the specific amplification of the variable exon included isoform to specifically amplify exon skipping events. Design primers spanning the junction of the constitutive exon two and exon four that would otherwise be destroyed when variable exon three is included.

Design the other primer inside the constitutive exon four to detect the total transcripts of the gene and avoid PCR products amplified from genomic DNA or prem NA.Design primers within two constitutive exons when ready. Follows standard RNA extraction procedures to isolate the RNA from the cell samples collected earlier. Determine the concentration and quality of RNA by UV absorption to synthesize the first strand CD NA set up reverse transcriptase reactions in a final volume of 20 microliters.

Perform RT reactions at 42 degrees Celsius for one hour, followed by incubation at 70 degrees Celsius for five minutes. To inactivate the RT enzyme for real-time. PCR set up 20 microliter reactions that consist of 10 microliters of cyber green master mix 0.1 to 1.0 microliters of CD NA template and five picomoles forward and reverse primers.

Run real-time PCR with 40 cycles in triplicate. Check the dissociation curves and make sure that a single peak is observed for each primer set. Obtain the quantification cycle values by calculating the second derivative values of the amplification curves.

Calculate the relative quantity of target mRNAs in induced samples as compared to the un induced sample using the delta delta CQ method as shown by this formula. Leave the cells collected for protein analysis on ice for approximately 10 minutes before centrifuging and collecting the supernatant. After determining the protein concentration, dilute the samples in SDS loading, buffer and load 20 to 40 micrograms of proteins into 10%SDS page gels.

Run SDS page gels at 20 milliamps for 1.5 hours. After this time, transfer proteins to PVDF membranes in a wet transfer system at four degrees Celsius for three hours at 85 volts. Adjust the transfer time according to the molecular weight of the target proteins.

Next, block the membrane in 5%non-fat milk for 30 minutes to one hour. At room temperature, incubate the membrane with a primary antibody at four degrees Celsius overnight. The primary antibody recognizes the epitope in the constitutive exon coating region and detects slic isoforms simultaneously based on their different protein sizes.

At the same time, monitor EMT by immuno blotting. For EMT markers. Use eec, ahern, gamma catenin and occludin as epithelial markers and fibronectin n cadherin and menton as mesenchymal markers.

The next day, wash the membrane three times with TBST in five minute intervals. Next, incubate the membrane with an HRP conjugated secondary antibody in a one to 10, 000 dilution for one hour at room temperature. After this time, wash the membrane three times with TBST at five minute intervals.

Finally, visualize the proteins with a chemiluminescence detection system and expose the membrane to an auto radiography film. Twist induced EMT was characterized by a transition from a cobblestone like epithelial phenotype to an elongated fibroblastic phenotype, displaying the absence of epithelial markers, e cadherin, gamma catenin, and occludin, and the upregulation of mesenchymal markers, fibronectin n cadherin, and vimentin. Furthermore, EMT was assessed by the loss of EC cadherin localization at cell cell junctions depicted.

Here are the primer designs for the detection of CD 44 splice isoforms. The primer locations are indicated by the different colored arrows. The results from Q-R-T-P-C-R analyses indicate a significant decrease in CD 44 V mRNA and increase in CD 44 s mRNA after 14 days of TAM treatment.

By contrast, the total transcript of CD 44 remained unchanged during EMT consistent with the results of Q-R-T-P-C-R, the protein level of CD 44 V declined remarkably, whereas expression of the CD 44 s protein was greatly upregulated While attending this procedure. It's important to remember that successful induction of ENT is very crucial. Thus, ENT must be carefully confirmed with various methods such as detection of changes in cell morphology expression of ENT markers and localization of RIN on cell surface.

Following this Procedure, other methods like splicing reporter managing assay can be performed to answer additional questions like, how do these acting elements and the transacting factors affect alternative splicing regulation After its development? This technique paved the way for researchers in the field of RNA biology, developmental biology, and cancer biology to explore alternative splicing regulation in the EMT processes during normal development and cancer metastasis.