Genome Engineering of Primary Human B Cells Using CRISPR/Cas9

Here we provide a detailed, step-by-step protocol for CRISPR/Cas9-based genome engineering of primary human B cells for gene knockout (KO) and knock-in (KI) to study biological functions of genes in B cells and the development of B-cell therapeutics.

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This protocol allows researchers to precisely eliminate a gene in B cells to study the loss of function effects of that gene or to insert a trans gene for stable trans gene expression that can be used for research or therapeutic purposes. The main advantage of this method is that it provides a universal platform that makes it possible to easily and precisely engineer B cells with high efficiencies. This method can be used to engineer B cells to express recombinant antibodies or enzymes and then transfer those B cells to treat infections or in enzymopathies.

To begin, thaw B cells in a 37 degree Celsius water bath. While waiting, transfer two milliliters of pre warmed FBS into a sterile, 15-milliliter conical tube. Once the B cells are completely thawed, immediately add one milliliter of pre-warmed FBS, drop-wise, into the sample.

Incubate at room temperature for one minute. Gently pipette to resuspend the sample and transfer the whole volume, drop-wise, into a conical tube containing two milliliters of prewarmed FBS. Bring the volume to 15 milliliters with sterile PBS, then cap the tube and invert it gently two to three times.

Centrifuge the sample at 400 times G for five minutes, then discard the supernatant without disturbing the cell pellet. Resuspend the pellet with one milliliter of pre-equilibrated B-cell expansion medium and count the cells. The total cell number should be approximately 10 to the seventh cells.

Transfer the cells into a flask containing 20 milliliters of the pre-equilibrated B-cell expansion medium. The final concentration of the cells, should be approximately five times 10 to the fifth cells per milliliter. Incubate the flask vertically in a tissue culture incubator.

Prepare the CRISPR/Cas9 transfecting substrate by mixing one microgram of chemically modified sgRNA with 1.5 micrograms of chemically modified streptococcus pyogenes Cas9 nucleus mRNA per transfection reaction. For control, add one microliter of TE buffer, instead of sgRNA, into a 0.2-milliliter tube of an eight tube strip. Turn on an electroporator and prepare the nuclear infection reagents.

Count and transfer 1 million B cells per transfection reaction, into a sterile conical tube. Bring the volume to 15 milliliters with sterile PBS and centrifuge at 400 times G for five minutes. After centrifugation, discard the supernatant.

Resuspend the cells with 10 milliliters of sterile PBS and centrifuge at 400 times G for five minutes, then discard the supernatant completely without disturbing the cell pellet. Add 0.5 micrograms of chemically modified GFP mRNA per 1 million B cells to the cell pellet. Resuspend the pellet with 20 microliters of primary cell transfection reagent per 1 million B cells and mix gently by pipetting five to six times.

Transfer 20.5 microliters per transfection reaction into the 0.2-milliliter tubes containing CRISPR/Cas9 reagent. Pipette up and down once to mix and transfer the entire volume into a transfection cuvette. Cap and tap the cuvette on the bench gently to ensure that the liquid covers the bottom of the cuvette.

Use the human primary B-cell protocol on the electroporator for transfection. Rest the electroporated cells in the cuvette at room temperature for 15 minutes. Then transfer 80 microliters of the pre-equilibrated B-cell expansion medium into the transfection reaction in the cuvette.

Place the cuvette in the tissue culture incubator for 30 minutes. Gently pipe head a couple of times to mix and transfer the whole volume of the sample from the cuvette to an appropriate well of a 48-well tissue culture plate containing one milliliter of the B-cell expansion medium. The final concentration of the cells should be 1 million cells per milliliter.

Performing a gene knock-in experiment, transfer recombinant adeno associated type-six viral vector at 500, 000 multiplicity of infection into the appropriate well containing electroporated cells. Place the plate in a tissue culture incubator at 37 degrees Celsius and 5%carbon dioxide with humidity. In the knockout experiment, the B-cell count showed more than 80%viable cells with a slight reduction in cell recovery in both the control and the CD19 knockout samples at 24 hours post electroporation.

B cells were collected on day five post-transfection for flow cytometry and tide analysis. Representative scatterplots of the control and knockout samples showed 14 and 95%CD19 negative cells respectively, demonstrating a significant reduction in CD19 expression in the knockout samples. Chromatograms of genomic sequencing showed double peaks in the CD19 knockout B cells, indicating insertions or deletions of nucleotides post-CRISPR/Cas9 mediated double-stranded breaks.

Indel analysis of the chromatographs of the knockout samples showed a high percent of indel formation at the CD19 locus, which is consistent with percent CD19 protein loss detected by flow cytometry. B cells from the knock-in experiment were collected on day 12, post engineering. Scatterplots showed 64%of EGFP positive cells in the sample that received the recombinant adeno associated type-six viral vector, together with RNP, whereas none or minimal EGFP positivity was observed in the control and vector-only samples respectively.

A junction PCR amplification, showed 1.5 kilobase pair amplicons in the knock-in sample and no PCR product was observed in either the control or vector-only sample. Cell counts showed that the engineering process affects cell recovery in the knock-in sample more than the control or the vector-only samples. However, all samples quickly rebounded within three days after engineering.

This procedure can also be used to introduce base editor agents to alter single base pairs in order to induce or correct single point mutations in the B-cell genome. It could also be used to introduce premature stop codons or to alter splice sites, allowing for multiple gene knockouts without the risk of chromosomal translocations. Before this technique was developed, engineering human B cells would inquire the use of other more challenging gene engineering approaches.

This technique is an easier, less expensive and quicker alternative. It could also potentially be used to synthesize cell therapy products for clinical use.

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Journal (Biology)

Journal (Biology)

Genome Engineering of Primary Human B Cells Using CRISPR/Cas9

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