Using CRISPR/Cas9 Gene Editing to Investigate the Oncogenic Activity of Mutant Calreticulin in Cytokine Dependent Hematopoietic Cells

The overall goal of this experiment is to utilize CRISPR/Cas9 gene editing to model calreticulin mutations in cytokine dependent hematopoietic cells in order to study their oncogenic activity. This method can help answer key questions in the hematological malignancies field such as the biological function of driver mutations when they are expressed at physiological levels. The main advantage of this technique is that it utilizes the CRISPR/Cas9 gene editing system to model and study the biological function of genes involved in cancer.

To anneal and phosphorylate the oligos, add the reagents to a total of 10 microliters in a PCR tube kept on ice. Set the program in the thermocycler. Use water to dilute the reaction after cycle is complete.

To digest the lentiGuide-Puro vector, prepare 50 microliters of digestor reaction. Then, start the digestion reaction at 55 degrees Celsius at a heat block. After one hour, add an additional microliter of BsmB1 restriction enzyme and continue the reaction for another hour.

To dephosphorylate the cut back bone, add seven microliters of phosphatase reaction buffer and two microliters of phosphatase enzyme to the digestive vector. Then, incubate the mixture at 37 degrees Celsius for 30 minutes. Purify the already cut and dephosphylated back bone using a commercial kit.

To prepare the ligation mixture, add 15 nanograms of digested back bone and other reagents to a PCR tube kept on ice and adjust the volume to 10 microliters with water. Incubate the reaction at room temperature for one hour. Then transform STBL3 compatible cells with two microliters of the ligation mixture.

And then plate on the lysogeny broth agar plate containing 100 micrograms per milliliter of ampicillin. After this, incubate the plate overnight at 37 degrees Celsius. Pick three colonies and inoculate them.

Perform mini prep for each culture and sequence the oligo insertion site with a U6 promoter region primer. Seed hek293t cells on a 10 centimeter dish. And leave it for overnight incubation.

To prepare the DNA mixture for transfection, pipette 45 microliters of the transfection reagent to the DNA. Use a pipette to mix the DNA and transfection reagent carefully, and allow it to stand for 20 minutes. After this, add the DNA transfection mixture drop-wise on the seeded cells.

Gently swirl the plates. And incubate at 5%carbon dioxide and 37 degrees Celsius for a day. Harvest the virus containing supernatent after 24 and 48 hours by passing it through a 0.22 micromiter filter.

And aliquot 1.6 milliliters of supernatent in each cryo vial. Next aspirate the supernatent and resuspend the Ba/F3 cells in media by pipetting the cells up and down several times. Add 500 microliters of the resuspended cells, 1.5 milliliters of viral supernatant, four microliters of polybrene, and 10 nanograms per milliliter of murine interleukin 3 in a six well tissue culture plate.

Centrifuge the plate at 440 G for 120 minutes at 37 degrees Celsius. After centrifugation, transfer the plate to an incubator for overnight incubation at 37 degrees Celsius with 5%carbon dioxide. After this, spin the cells down at 440 G for three minutes.

And resuspend in five milliliters of fresh warm media in a six well plate. To select the Cas9 infected cells, first spin down the cell. And then resuspend in fresh warm media supplemented with five micrograms per milliliter of blasticidin after 48 hours of spinfection.

Continue selecting cells for nine days with blasticidin til all the uninfected cells are dead. Then, transfer the resistant cells to a medium with one microgram per milliliter of blasticidin. Transduce the parental cells and the cells stably expressing Cas9 with pXPR-011 reporter construct through lentiviral infection.

Continue selecting cells with two micrograms per milliliter of puromycin for three days, 48 hours after spinfection. Infect the Cas9 expressing cells with single guide ribonucleic acid using lentivirus. Then, use two micrograms per milliliter of puromycin to select the cells for three days, 48 hours post spinfection.

Bin the exponentially growing Ba/F3 cells expressing ectopic Cas9 and the single guide ribonucleic acid of interest. Aspirate the supernatent and wash the cells with five milliliters of phosphate buffered saline. Spin the cells down, and wash with phosphate buffered saline three times.

Then, count the number of cells using a cell viability analyzer. After this, seed cells in triplicates in two milliliters of fresh media without interleukin 3 in six well culture plates. Start monitoring and counting the cells every two days for eight days.

Representative flow psychometric data demonstrating Cas9 activity in parental Ba/F3 cell and Ba/F3 overexpressing Cas9 cells is shown here. Green fluorescent protein signal is reduced by 76%in Ba/F3 overexpressing Cas9 cells, indicating robust Cas9 activity, whereas in parental Ba/F3 cells, the green fluorescent protein signal remains at 100%Representative growth curves for cells demonstrating oncogenic activity of calreticulin are shown here. CRISPR/Cas9 mediated plus one base pair frame shift mutation was introduced in the exon nine locus of calreticulin using m1 and m2 single guide RNase.

Growth curves for calreticulin targeted Ba/F3 thrombopoietin receptor Cas9 cells shows murine interleukin 3 independent growth. However, the growth curves for the other cell types do not show any cytokine independent growth. Sequencing results confirm the on target editing of endogynous calreticulin exon nine in calreticulin targeted Ba/F3 thrombopoietin receptor Cas9 cells using the m1 and m2 single guide RNase.

The plus one base pair frame shift mutations are indicated in black. Once mastered, this technique can be done in two weeks if performed properly. While attempting this procedure, it's important to understand what kind of mutations in the gene of interest may be responsible for the phenotype that is desired.

Following this procedure, other methods to further characterize the mutation, such as its role in cell signaling or in protein protein interactions can be performed in order to further understand the mechanism by which is causes disease. After its development, this technique paved the way for researchers in the field of hematology to explore the effect of gain-of-function mutations at physiological levels on cell transformation in Ba/F3 hematopoietic cells. After watching this video, you should have a good understanding of how to utilize the CRISPR/Cas9 gene editing methodology to investigate the oncogenic activity of gain-of-function mutations in cytokine dependent hematopoietic cells.

Don't forget that working with lentivirus can be extremely hazardous and precautions such as working in a BL2 plus facility should always be taken while performing this procedure.