We acknowledge the Human Immunology Core for providing normal donor T cells and the Flow Cytometry Core at University of Pennsylvania.

Human T cells were procured through the University of Pennsylvania Human Immunology Core, which operates under principles of Good Laboratory Practice with established standard operating procedures and/or protocols for sample receipt, processing, freezing, and analysis conform to MIATA and University of Pennsylvania ethics guidelines.
1. Lentiviral vector production
NOTE: The viral products have been made replication-defective by separation of packaging constructs (Rev, gag/pol/RRE, VSVg and transfer plasmid) into four separate plasmids, greatly reducing the likelihood of recombination events that may result in replication-competent virus.
<ol>
	<li>Prepare HEK293T cells one day prior to the transfection. Plate approximately 6 x 106 cells in T150 culture vessels in 30 mL of standard culture media (referred to as R10:RPMI 1640 supplemented with 10% fetal calf serum, 10 mM HEPES, 1% Pen/Strep, 1% L-glutamine) and incubate overnight at 37 &#176;C. 18-24 h later, cells should be 60-70% confluent and look healthy (dendritic projections and uniform distribution across the flask). If cells look healthy, proceed to step 1.2.</li>
	<li>Prepare the transfection mix containing lipofection reagent (96 &#181;L), pTRP gag/pol (Lot# RR13SEP19A) (18 &#181;g), pTRP RSV-Rev (Lot# RR13SEP19B-3) (18 &#181;g), pTRP VSVG (Lot# RR13SEP19C) (7 &#181;g) packaging plasmids and 15 &#181;g of expression plasmid (CD19bbz scFv cloned in pTRPE).
	<ol>
		<li>For each transfection reaction, prepare one tube containing 1 mL of reduced-serum minimal essential media plus the four plasmids described in step 1.2 as well as one tube containing 2 mL of reduced-serum minimal essential media plus 90 &#181;L of lipofection reagent. Combine these two solutions by dropwise addition of the 1 mL plasmid mix to the 2 mL of lipofection reagent mix. Be sure to vigorously mix the solution by pipetting up and down several times. Incubate the solution for 15 min at room temperature.</li>
		<li>In the meantime, aspirate the media from the HEK293T cell flask and gently wash cells with 10 mL of reduced-serum minimal essential media and aspirate again.</li>
		<li>Gently add the transfection mix (3 mL) from step 1.2.1 to the bottom corner of cell culture flask using a 5 mL serological pipette. Gently tilt the flask to evenly distribute the transfection mix across the cell culture flask and incubate for 10 min at room temperature. Make sure to not disturb the cell monolayer. After a 10 min incubation, add 35 mL of R10 media and return flask to the incubator for 24 h.</li>
	</ol>
	</li>
	<li>After 24 h, collect the supernatant from the HEK293T cell culture flasks and transfer into 50 mL conical tubes. Add fresh R10 to the HEK29T cells and put the cells back into the incubator for another 24 h. Spin down the supernatant (300 x g) to remove cell debris and filter the supernatant through a 0.45 &#181;m filter.</li>
	<li>Concentrate the filtrate from step 1.3 by high-speed ultracentrifugation (25,000 x g for 2.5 h or 8000 x g overnight (O/N)). Store the 24 h virus pellet at 4 &#176;C while pooling the 48 h virus.</li>
	<li>Repeat steps 1.3-1.4 for the 48 h collection and combine 24 h and 48 h virus collections. Pellets from the 48 h collection will contain a combined harvest of the lentivirus.</li>
	<li>Resuspend viral pellet in approximately 1 mL of cold R10 and aliquot into 100 &#181;L vials. Immediately snap freeze the aliquots using dry ice and store at -80 &#176;C.</li>
	<li>Calculate functional viral titer in transducing units/mL by transducing a fixed amount of CD3/CD28 bead-activated primary human T-cells with serial dilutions of the lentiviral supernatant. Measure CAR-Transduction after 72 h by flow-cytometry.
	<ol>
		<li>Stain for the CD19-directed CAR with an anti-FCM63 scFv antibody. For other chimeric antigen receptors, stain using fluorophore-labeled recombinant protein that is specific to the CAR scFv. Virus dilution that generates under 20% CAR positive cells by flow-cytometry is the most accurate dilution to calculate viral titer from. Above 20% CAR-positive cells, the chance for each positive cell to be transduced twice increases, resulting in an underestimation of the number of transducing particles. Calculate the transducing units per mL(TU/mL ) = (number of cells transduced x percent CAR positive cells x dilution factor)/(transduction volume in mL).</li>
	</ol>
	</li>
</ol>
2. Designing of sgRNAs and gene disruption in primary human T cells
<ol>
	<li>Designing CRISPR sgRNA&#39;s 
	NOTE: Several servers and programs facilitate the design of target-specific sgRNA&#39;s. In this protocol, CRISPR sgRNAs were designed using CHOPCHOP (https://chopchop.cbu.uib.no), and the gRNA design portal from the Broad institute (https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design).
	<ol>
		<li>For each target gene, design six to ten sgRNA sequences to target early coding exon sequences. 
		NOTE: sgRNA should have high on-target efficacy and low off target efficacy. Each machine learning algorithm for determining sgRNA efficacy works slightly differently. Therefore, comparing multiple sgRNA design tools and curating a list of six to ten sgRNA for screening is recommended.</li>
	</ol>
	</li>
	<li>Gene disruption in primary human T-cells
	<ol>
		<li>Obtain autologous peripheral blood mononuclear cells (PBMC&#39;s) from healthy volunteer donors. A schematic timeline of the protocol is described in Figure 2A and described below.</li>
		<li>Isolate CD4+ and CD8+ T-cells using commercially available CD4 and CD8 selection kits.</li>
		<li>Combine CD4+ and CD8+ T-cells at a 1:1 ratio and incubate overnight at 3x106 cells/mL in R10 supplemented with 5 ng/mL huIL-7 and huIL-15 each. Addition of IL-7 and IL-15 is recommended as they are known to promote a central memory phenotype and CAR-T cells expanded with IL-7 and IL-15 have superior anti-tumor efficacy compared to IL-2 expanded CAR-T cells22,23,24.</li>
		<li>The next day, count T-cells and centrifuge 5-10 x 106 cells at 300 x g for 5 min. Discard all the supernatant and wash the cell pellet in reduced-serum minimal essential media. Resuspend the pellet in 100 &#181;L of nucleofection solution according to the manufacturer&#39;s instructions (Table of Materials).</li>
		<li>While washing the cells, prepare ribonucleoprotein (RNP) complex with Cas9 and gRNA by incubating 10 &#181;g of Cas9 nuclease with 5 &#181;g of sgRNA for 10 min at room temperature (RT). The molar ratio of Cas9 to sgRNA is 1:2.4. A mock control that contains Cas9 and electroporation enhancer, but no sgRNA, is recommended. 
		NOTE: Multiplex gene editing can be performed at this step by making RNP complexes for each target separately and combining them with cells at the time nucleofection as described in the next step. Choosing the reagents to assemble the RNP complex are key to getting high KO efficiency. For example, Cas9 nucleases from different vendors have varying off-target effects and chemically modified gRNA decrease toxicity to T cells, thereby increasing KO efficiency.</li>
		<li>Combine the resuspended cells from step 2.2.4 with the RNP complex from step 2.2.5 and add 4.2 &#181;L of 4 &#181;M electroporation enhancer (ssDNA oligonucleotide that is non-homologous to human genome). Mix well and transfer into electroporation cuvettes. Avoid bubbles as they impair electroporation efficiency.</li>
		<li>Electroporate cells using pulse code EH111. After electroporation, incubate cells in R10 supplemented with 5 ng/mL huIL-7 and huIL-15 at 5x106 cells/mL at 30 &#176;C for 48 h in 12-well plates. After 48 h, proceed with T-cell activation and expansion.</li>
	</ol>
	</li>
</ol>
3. T cell activation, lentiviral transduction and expansion
NOTE: For screening sgRNA&#39;s, lentiviral transduction (Step 3.2) of the CAR construct is not necessary.
<ol>
	<li>Count electroporated T-cells and dilute to a concentration of 1 x 106 cells/mL using warm R10 supplemented with 5 ng/mL huIL-7 and huIL-15. Activate cells by adding anti-CD3/anti-CD28 monoclonal antibody coated magnetic beads at a ratio of 3 beads per live T-cell. 
	NOTE: Electroporation causes significant cell death resulting in roughly 60% &#177; 15% viable cells compared to non-electroporated cells. Use a live/dead cell count to determine the appropriate amount of beads. Transfer the cells to 37 &#176;C and incubate overnight.</li>
	<li>After overnight stimulation, transduce CRISPR-engineered T-cells with lentiviral supernatant from step 1. Add the appropriate volume based on the viral titer calculated in step 1.7 to achieve a multiplicity of infection (MOI) of 3 and incubate cells for 72 h at 37 &#176;C. 
	NOTE: The virus pellet resuspended in R10 is simply added on top of the cells according to the cell concentration, viral titer, and desired MOI.</li>
	<li>After 72 h, feed cells with 50% of the current culture volume R10 containing 10 ng/mL huIL-7 and huIL-15 and return them to the incubator for another 48 h. Do not disturb the clusters that have formed between the T-cells and the beads.</li>
	<li>After 48 h, remove the beads from the cells by gently resuspending the cell-bead mixture followed by magnetic separation. Count cells after bead removal and bring to a concentration of 0.8 x 106 cells/mL using R10 supplemented with 5 ng/mL huIL-7 and huIL-15. After de-beading, cell numbers should be similar to the cell count on Day 1 prior to electroporation (Figure 2B).</li>
	<li>After 24 h, count cells and feed to a concentration of 1 x 106 cells/mL with R10 + 5 ng/mL huIL-7 and huIL-15. Repeat this every 24 h until growth kinetics and cell size demonstrate cells have rested from stimulation. 
	NOTE: From this point, T-cells double approximately every 24h. T-cell usually undergo 5-7 population doublings and have a cell volume of approximately 300 &#177; 50 fL when rested.</li>
	<li>Once rested, spin down CRISPR-engineered CAR-T cells and resuspend in freeze media (1:1 X-Vivo and FBS plus 10% DMSO) for cryopreservation. CAR-T cells used should be thawed and rested at 37 &#176;C for 16 hours before an experiment. 
	NOTE: Keep approximately 10x106 cells reserved for measuring knockout efficiency and CAR integration. Expected population doublings and volume changes during the expansion have been shown in Figure 2B,2C. Additionally, Figure 2D shows levels of CAR expression on both Mock and gene edited CAR-T cells.</li>
</ol>
4. CRISPR Efficiency
<ol>
	<li>Genomic DNA extraction and target gene amplification
	<ol>
		<li>From each screening culture, spin down 3-5 x 106 T-cells. Cells can be either frozen down as a dry pellet or one can proceed with genomic DNA extraction. At time of DNA extraction, resuspend pellets in 200 &#181;L of Phosphate Buffer Saline (PBS) and extract genomic DNA from electroporated cells using a standard DNA extraction kit according to the manufacturer instruction.
		<ol>
			<li>Briefly, lyse cells with proteinase K and load lysate onto a DNA binding column. During centrifugation, DNA is binding to the membrane while contaminants will pass through. After two washing steps to remove remaining contaminants and enzyme inhibitors, elute DNA in water.</li>
		</ol>
		</li>
		<li>Amplify 200-300 ng of genomic DNA using standard PCR mix containing DNA polymerase, accessory proteins, salts, and dNTPs and 10 &#181;M forward and reverse primers flanking the region of the intended double-strand break. 
		NOTE: For PCR primer design, the reference genomic sequence (can be found using http://www.ensemble.org) flanking the gRNA cut site are entered into the NCBI primer blast tool (https://www.ncbi.nlm.nih.gov/tools/primer-blast). PCR primers should be designed such that the amplicon has a target size of 600-700bp. This length allows to design sequencing primers that bind within the amplicon with sufficient distance from the gRNA cut site (at least 150 bp) to ensure good sequencing quality around the Cas9 induced indels (see 4.2.1). Each gRNA requires a unique primer pair, unless the gRNA cut sites are in close proximity.&#160;</li>
		<li>Run the entire PCR product on a 1% agarose gel and purify the amplicon using a standard agarose gel purification kit. 
		NOTE: The process of determining the optimal Tm for PCR can take multiple rounds of troubleshooting. This is because the KO sequence has indels and the target gene should be primed for sequencing where there would be no indels usually 100 bp upstream or downstream of the cut site. This can vary widely due to indels resulting from non-homologous end joining. Designing nested sequencing primers to the PCR primers and increasing the concentration of product sequenced can eliminate problems with sequencing.</li>
	</ol>
	</li>
	<li>Sequencing and indel detection
	<ol>
		<li>Design sequencing primers that bind to the gel purified amplicon and send mock and knockout amplicons for Sanger sequencing. Once sequencing is complete, upload the trace files to the Desktop Genetics software (tide.deskgen.com, Desktop Genetics) for TIDE analysis.
		<ol>
			<li>For sequencing primer design, enter the sequence of the PCR amplicon into a standard primer design software (NCBI, Eurofins or other publicly available tools). The design software will suggest multiple primer sequences that are suitable to sanger sequencing.</li>
			<li>Choose forward and reverse primers that bind within the amplicon at least 150 bp upstream or downstream of the gRNA cut site to ensure good sequencing quality around the indels. The sequencing chromatogram will be used in 4.2 for TIDE analysis, therefore it is important that sequencing quality is good for accurate indel decomposition (see Hultquist et al.)25.</li>
		</ol>
		</li>
		<li>Use TIDE (Tracking of Indels by DEcomposition) analysis to detect knock out (KO) efficiency at the genomic level26. The algorithm accurately reconstructs the spectrum of indels from the sequence traces and calculates R2 values, reflecting goodness of fit after non-negative linear modeling by the TIDE software.</li>
	</ol>
	</li>
	<li>Target protein detection
	<ol>
		<li>For target genes whose gene product is expressed on the surface of T-cells, stain approximately 1 x 105 cells from each screening culture with a fluorochrome-tagged antibody specific for the target protein. Compare expression levels of the target protein between the mock control and knockout groups by flow cytometry as shown in Figure 3A,3B.</li>
		<li>For target genes whose gene product is expressed intracellularly, lyse approximately 3 x 106&#160;million cells per screening group in lysis buffer and follow standard protocols for SDS-PAGE and western blotting. Alternatively, surface or intracellular flow-cytometry can be used to probe for the target protein.</li>
	</ol>
	</li>
</ol>
5. Monitoring Off-target effects using iGUIDE - Library preparation, DNA sequencing, and analysis
NOTE: iGUIDE technique allows for detection of locations of Cas9 guided cleavage and quantify the distributions of those DNA double-stranded breaks.
<ol>
	<li>Perform iGUIDE as described by Nobles et al.21. The off-target effects of sgRNA targeting TRAC locus using the iGUIDE technique have been shown in Stadtmauer et al, 202013.</li>
</ol>

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The authors have no disclosures.

Here we describe approaches to gene edit CAR-T cells using CRISPR Cas9 technology and manufacture products to further test for function and efficacy. The above protocol has been optimized for performing CRIPSR gene editing in primary human T cells combined with engineering T cells with chimeric antigen receptors. This protocol allows high knockout efficiency with minimal donor-to-donor variability. Modification using CRISPR can improve both the efficacy and safety of CAR-T cells by eliminating receptors that inhibit T ce...

Chimeric antigen receptor (CAR)-T cell therapy has revolutionized the field of adoptive cell therapies and cancer immunotherapy. CAR-T-cells are engineered T-cells expressing a synthetic immune receptor that combines an antigen-specific single chain antibody fragment with signaling domains derived from the TCRzeta chain and costimulatory domains necessary and sufficient for T-cell activation and co-stimulation1,2,3,4. The manufacturing of CAR-T cells starts by extracting the patient&#39;s own T-cells, followed by ex vivo viral transduction of the CAR module and expansion of the CAR-T cell product with magnetic beads that function as artificial antigen presenting cells5. Expanded CAR-T cells are re-infused into the patient where they can engraft, eliminate target tumor cells and even persist for multiple years post infusion6,7,8. Although CAR-T cell therapy has resulted in remarkable response rates in B-cell malignancies, clinical success for solid tumors has been challenged by multiple factors including poor T-cell infiltration9, an immunosuppressive tumor microenvironment10, antigen coverage and specificity, and CAR-T cell dysfunction11,12. Another limitation of current CAR-T cell therapy includes the use of autologous T-cells. After multiple rounds of chemotherapy and high tumor burden, CAR-T cells can be of poor quality as compared to allogeneic CAR-T products from healthy donors in addition to the time and expense associated with manufacturing of autologous CAR-T cells. Gene-editing of the CAR-T cell product by CRISPR/Cas9 represents a new strategy to overcome current limitations of CAR-T cells13,14,15,16,17.
CRISPR/Cas9 is a two component system that can be used for targeted genome editing in mammalian cells18,19. The CRISPR-associated endonuclease Cas9 can induce site-specific double-strand breaks guided by small RNAs through base-pairing with the target DNA sequence20. In the absence of a repair template, double-strand breaks are repaired by the error prone nonhomologous end joining (NHEJ) pathway, resulting in frameshift mutations or premature stop codons through insertion and deletion mutations (INDELs)19,20,21. Efficiency, ease of use, cost-effectiveness and the ability for multiplex genome editing make CRISPR/Cas9 a powerful tool to enhance the efficacy and safety of autologous and allogeneic CAR-T cells. This approach can also be used to edit TCR directed T cells by replacing the CAR construct with a TCR. Additionally, allogeneic CAR-T cells that have limited potential to cause graft versus host disease can also be generated by gene editing the TCR, b2m, and HLA locus.
In this protocol, we show how CRISPR-engineering of T cells can be combined with viral vector mediated delivery of the CAR-Transgene to generate genome-edited CAR-T cell products with enhanced efficacy and safety. A schematic diagram of the entire process is shown in Figure 1. Using this approach, we have demonstrated high-efficiency gene knockout in primary human CAR-T cells. Figure 2A describes in detail the timeline of each step for editing and manufacturing T cells. Strategies for guide RNA design and knockout validation are also discussed to apply this approach to various target genes.

<table><tbody><tr><td>4D-Nucleofactor Core Unit</td><td>Lonza</td><td>AAF-1002B</td><td></td></tr><tr><td>4D-Nucleofactor X-Unit</td><td>Lonza</td><td>AAF-1002X</td><td></td></tr><tr><td>Accuprime Pfx Supermix</td><td>ThermoFisher</td><td>12344040</td><td></td></tr><tr><td>Beckman Optima XPN ultracentrifuge</td><td>Beckman Coulter</td><td></td><td></td></tr><tr><td>Brilliant Violet 605 anti-human CD3 Antibody</td><td>Biolegend</td><td>317322</td><td>Clone OKT3</td></tr><tr><td>BV711 Anti-human PD1</td><td>Biolegend</td><td></td><td>Clone EH12.2H7</td></tr><tr><td>Cas9-Electroporation enhancers</td><td>IDT</td><td>1075915</td><td></td></tr><tr><td>CD3/CD28 Dynabeads</td><td>ThermoFisher</td><td>40203D</td><td></td></tr><tr><td>CD4+ T cell isolation Kit</td><td>StemCell technologies</td><td>15062</td><td></td></tr><tr><td>CD8+ T cell isolation Kit</td><td>StemCell technologies</td><td>15063</td><td></td></tr><tr><td>Corning 0.45 micron vacuum filter/bottle</td><td>Corning</td><td>430768</td><td></td></tr><tr><td>Corning T150 cell culture flask</td><td>Millipore Sigma</td><td>CLS430825</td><td></td></tr><tr><td>DMSO</td><td>Millipore Sigma</td><td>D2650</td><td></td></tr><tr><td>DNAeasy Blood and Tissue Kit</td><td>Qiagen</td><td>69504</td><td></td></tr><tr><td>DynaMag Magnet</td><td>ThermoFisher</td><td>12321D</td><td></td></tr><tr><td>Glutamax supplement</td><td>ThermoFisher</td><td>35050061</td><td></td></tr><tr><td>HEK293T cells</td><td>ATCC</td><td>CRL-3216</td><td></td></tr><tr><td>HEPES (1 M)</td><td>ThermoFisher</td><td>15630080</td><td></td></tr><tr><td>huIL-15</td><td>PeproTech</td><td>200-15</td><td></td></tr><tr><td>huIL-7</td><td>PeproTech</td><td>200-07</td><td></td></tr><tr><td>Lipofectamine 2000</td><td>ThermoFisher</td><td>11668019</td><td></td></tr><tr><td>Nucleospin Gel and PCR cleanup</td><td>Takara</td><td>740609.25</td><td></td></tr><tr><td>Opti-MEM</td><td>ThermoFisher</td><td>31985062</td><td></td></tr><tr><td>P3 Primary cell 4D-nucleofactor X Kit L</td><td>Lonza</td><td>V4XP-3024</td><td></td></tr><tr><td>Penicilin-Streptomycin-Glutamine</td><td>ThermoFisher</td><td>10378016</td><td></td></tr><tr><td>pTRPE expression Plasmid</td><td>in house</td><td></td><td></td></tr><tr><td>Rabbit Anti-Mouse FMC63 scFv Monoclonal Antibody, (R19M), PE</td><td>CytoArt</td><td>200105</td><td></td></tr><tr><td>RPMI1640</td><td>ThermoFisher</td><td>12633012</td><td></td></tr><tr><td>sgRNA</td><td>IDT</td><td></td><td></td></tr><tr><td>Spy Fi Cas9</td><td>Aldevron</td><td>9214</td><td></td></tr><tr><td>Ultracentrifuge tubes</td><td>Beckman Coulter</td><td>326823</td><td></td></tr><tr><td>Viral packaging mix</td><td>in house</td><td></td><td></td></tr><tr><td>X-Vivo-15 Media</td><td>Lonza</td><td>BE02-060F</td><td></td></tr></tbody></table>

production of human crispr-engineered car-t cells

Adoptive cell therapies using chimeric antigen receptor T cells (CAR-T cells) have demonstrated remarkable clinical efficacy in patients with hematological malignancies and are currently being investigated for various solid tumors. CAR-T cells are generated by removing T cells from a patient's blood and engineering them to express a synthetic immune receptor that redirects the T-cells to recognize and eliminate target tumor cells. Gene editing of CAR-T cells has the potential to improve safety of current CAR-T cell therapies and further increase the efficacy of CAR-T cells. Here, we describe methods for the activation, expansion, and characterization of human CRISPR-engineered CD19 directed CAR-T cells. This comprises transduction of the CAR lentiviral vector and use of single guide RNA (sgRNA) and Cas9 endonuclease to target genes of interest in T cells. The methods described in this protocol can be universally applied to other CAR constructs and target genes beyond the ones used for this study. Furthermore, this protocol discusses strategies for gRNA design, lead gRNA selection and target gene knockout validation to reproducibly achieve high-efficiency, multiplex CRISPR-Cas9 engineering of clinical grade human T cells.

We describe here a protocol to genetically engineer T cells, that can be used to generate both autologous and allogeneic CAR-T cells, as well as TCR redirected T cells.
Figure 1 provides a detailed description of the stages involved in the process of manufacturing CRISPR edited T cells. The process begins by designing sgRNA to the gene of interest. Once the sgRNA are designed and synthesized they are then used to make RNP complexes with the appropriate Cas protein...

Watch this Scientific Journal Video about Production of Human CRISPR-Engineered CAR-T Cells at JoVE.com

Production of Human CRISPR-Engineered CAR-T Cells

Here, we present a protocol for gene editing in primary human T cells using CRISPR Cas Technology to modify CAR-T cells.

Adoptive cell therapies using chimeric antigen receptor T cells (CAR-T cells) have demonstrated remarkable clinical efficacy in patients with ...

production-of-human-crispr-engineered-car-t-cells

Research

JoVE Journal

Immunology and Infection

12.7K Views.  University of Pennsylvania. Here, we present a protocol for gene editing in primary human T cells using CRISPR Cas Technology to modify CAR-T cells.

Video: Production of Human CRISPR-Engineered CAR-T Cells

Using CRISPR/Cas9 to Knock Out GM-CSF in CAR-T Cells

Chimeric antigen receptor T (CAR-T) cell therapy is a cutting edge and potentially revolutionary new treatment option for cancer. However, there are significant limitations to its widespread use in the treatment of cancer. These limitations include the development of unique toxicities such as cytokine release syndrome (CRS) and neurotoxicity (NT) and limited expansion, effector functions, and anti-tumor activity in solid tumors. One strategy to enhance CAR-T efficacy and/or control toxicities of CAR-T cells is to edit the genome of the CAR-T cells themselves during CAR-T cell manufacturing. Here, we describe the use of CRISPR/Cas9 gene editing in CAR-T cells via transduction with a lentiviral construct containing a guide RNA to granulocyte macrophage colony-stimulating factor (GM-CSF) and Cas9. As an example, we describe CRISPR/Cas9 mediated knockout of GM-CSF. We have shown that these GM-CSFk/o CAR-T cells effectively produce less GM-CSF while maintaining critical T cell function and result in enhanced anti-tumor activity in vivo compared to wild type CAR-T cells.

Here, we present a protocol to genetically edit CAR-T cells via a CRISPR/Cas9 system.

Chimeric antigen receptor T (CAR-T) cell therapy is a cutting edge and potentially revolutionary new treatment option for cancer. However, there are ...

Cancer Research

Manufacturing Chimeric Antigen Receptor (CAR) T Cells for Adoptive Immunotherapy

Adoptive immunotherapy holds promise for the treatment of cancer and infectious disease. We describe a simple approach to transduce primary human T cells with chimeric antigen receptor (CAR) and expand their progeny ex vivo. We include assays to measure CAR expression as well as differentiation, proliferative capacity and cytolytic activity. We describe assays to measure effector cytokine production and inflammatory cytokine secretion in CAR T cells. Our approach provides a reliable and comprehensive method to culture CAR T cells for preclinical models of adoptive immunotherapy.

Manufacturing Chimeric Antigen Receptor CAR T Cells for Adoptive Immunotherapy

We describe an approach to reliably generate chimeric antigen receptor (CAR) T cells and test their differentiation and function in vitro and in vivo.

Adoptive immunotherapy holds promise for the treatment of cancer and infectious disease. We describe a simple approach to transduce primary human T cells ...

Clinical Application of Sleeping Beauty and Artificial Antigen Presenting Cells to Genetically Modify T Cells from Peripheral and Umbilical Cord Blood

The potency of clinical-grade T cells can be improved by combining gene therapy with immunotherapy to engineer a biologic product with the potential for superior (i) recognition of tumor-associated antigens (TAAs), (ii) persistence after infusion, (iii) potential for migration to tumor sites, and (iv) ability to recycle effector functions within the tumor microenvironment. Most approaches to genetic manipulation of T cells engineered for human application have used retrovirus and lentivirus for the stable expression of CAR1-3. This approach, although compliant with current good manufacturing practice (GMP), can be expensive as it relies on the manufacture and release of clinical-grade recombinant virus from a limited number of production facilities. The electro-transfer of nonviral plasmids is an appealing alternative to transduction since DNA species can be produced to clinical grade at approximately 1/10th the cost of recombinant GMP-grade virus. To improve the efficiency of integration we adapted Sleeping Beauty (SB) transposon and transposase for human application4-8. Our SB system uses two DNA plasmids that consist of a transposon coding for a gene of interest (e.g. 2nd generation CD19-specific CAR transgene, designated CD19RCD28) and a transposase (e.g. SB11) which inserts the transgene into TA dinucleotide repeats9-11. To generate clinically-sufficient numbers of genetically modified T cells we use K562-derived artificial antigen presenting cells (aAPC) (clone #4) modified to express a TAA (e.g. CD19) as well as the T cell costimulatory molecules CD86, CD137L, a membrane-bound version of interleukin (IL)-15 (peptide fused to modified IgG4 Fc region) and CD64 (Fc-&gamma; receptor 1) for the loading of monoclonal antibodies (mAb)12. In this report, we demonstrate the procedures that can be undertaken in compliance with cGMP to generate CD19-specific CAR+ T cells suitable for human application. This was achieved by the synchronous electro-transfer of two DNA plasmids, a SB transposon (CD19RCD28) and a SB transposase (SB11) followed by retrieval of stable integrants by the every-7-day additions (stimulation cycle) of &gamma;-irradiated aAPC (clone #4) in the presence of soluble recombinant human IL-2 and IL-2113. Typically 4 cycles (28 days of continuous culture) are undertaken to generate clinically-appealing numbers of T cells that stably express the CAR. This methodology to manufacturing clinical-grade CD19-specific T cells can be applied to T cells derived from peripheral blood (PB) or umbilical cord blood (UCB). Furthermore, this approach can be harnessed to generate T cells to diverse tumor types by pairing the specificity of the introduced CAR with expression of the TAA, recognized by the CAR, on the aAPC.

Clinical Application of Sleeping Beauty and Artificial Antigen Presenting Cells to Genetically Modify T Cells from Peripheral and Umbilical Cord Blood

T cells expressing a CD19-specific chimeric antigen receptor (CAR) are infused as investigational treatment of B-cell malignancies in our first-in-human gene therapy trials. We describe genetic modification of T cells using the Sleeping Beauty (SB) system to introduce CD19-specific CAR and selective propagation on designer CD19+ artificial antigen presenting cells.

The potency of clinical-grade T cells can be improved by combining gene therapy with immunotherapy to engineer  a biologic product with the potential for ...

Genome-Wide CRISPR Screens in CART Cells to Investigate Therapy Resistance

Performing an In Vitro Genome-Wide CRISPR Knockout Screen in Chimeric Antigen Receptor T Cells

Chimeric antigen receptor T (CART) cell therapy is an innovative form of targeted immunotherapy that has revolutionized the treatment of cancer. However, the durable response remains limited. Recent studies have shown that the epigenetic landscape of preinfusion CART cell products can influence response to therapy, and gene editing has been proposed as a solution. However, more work needs to be done to determine the optimal gene editing strategy. Genome-wide CRISPR screens have become popular tools to both investigate mechanisms of resistance and optimize gene editing strategies. Yet their application to primary cells presents many challenges. Here we describe a method to complete a genome-wide CRISPR knockout screen in CART cells from healthy donors. As a proof-of-concept model, we designed this method to investigate the development of exhaustion in CART cells targeting the CD19 antigen. However, we believe that this approach can be used to address a variety of mechanisms of resistance to therapy in different CAR constructs and tumor models.

The article describes a protocol for the application of an in vitro model for exhaustion to complete a genome-wide CRISPR knockout screen in healthy donor chimeric antigen receptor T cells.

Chimeric antigen receptor T (CART) cell therapy is an innovative form of targeted immunotherapy that has revolutionized the treatment of cancer. However, ...

A Nonviral Approach to Generate Transient Chimeric Antigen Receptor T Cells Using mRNA for Cancer Immunotherapy

Chimeric antigen receptor (CAR) T cell therapy has emerged as a pioneering cancer treatment, achieving unprecedented success in treating certain hematological malignancies such as lymphomas and leukemias. However, as more cancer patients receive CAR-T cell therapies, treatment-associated secondary primary malignancies are increasingly being reported partly due to unexpected CAR transgene insertion, raising serious safety concerns. To address this issue, we describe here a nonviral, non-integrating approach to generate transient CAR-T cells using mRNA. We electroporated T cells with modified mRNA encoding a human epidermal growth factor receptor 2 (HER2)-specific CAR and generated transient HER2-targeted CAR-T cells. The CAR was efficiently expressed on the T cell surface 1 day after electroporation, increased by day 2, and dramatically declined by day 5. The transient CAR-T cells exhibited potent cytotoxicity against HER2-positive SKOV-3 ovarian cancer cells and secreted high levels of IFN-&#978;. This protocol provides a step-by-step guide for developing small-scale transient CAR-T cells without permanent CAR transgene integration, describing detailed procedures for preparation of CAR mRNA, activation and transfection of T cells, assessment of CAR expression, and in vitro analysis of CAR-T cell function. This method is suitable for transient CAR-T cell generation in both preclinical and clinical studies.

This protocol outlines a detailed procedure for generating transient chimeric antigen receptor (CAR) T cells using non-integrating mRNA for cancer immunotherapy and provides reliable methods for evaluating CAR-T cells and their cytotoxic function.

Chimeric antigen receptor (CAR) T cell therapy has emerged as a pioneering cancer treatment, achieving unprecedented success in treating certain ...

Streamlined Protocol for Mouse CAR-T Cell Generation in Syngeneic Models

Efficient Generation of Murine Chimeric Antigen Receptor (CAR)-T Cells

Engineered cell therapies utilizing chimeric antigen receptor (CAR)-T cells have achieved remarkable effectiveness in individuals with hematological malignancies and are presently undergoing development for the treatment of diverse solid tumors. So far, the preliminary evaluation of novel CAR-T cell products has predominantly taken place in xenograft tumor models using immunodeficient mice. This approach is chosen to facilitate the successful engraftment of human CAR-T cells in the experimental setting. However, syngeneic mouse models, in which tumors and CAR-T cells are derived from the same mouse strain, allow evaluation of new CAR technologies in the context of a functional immune system and comprehensive tumor microenvironment (TME). The protocol described here aims to streamline the process of mouse CAR-T cell generation by presenting standardized methods for retroviral transduction and ex vivo T cell culture. The methods described in this protocol can be applied to other CAR constructs beyond the ones used in this study to enable routine evaluation of new CAR technologies in immune-competent systems.

Author Spotlight: Enhancing CAR-T Cell Function in Syngeneic Tumor Models 

This protocol streamlines retroviral vector production and murine T cell transduction, facilitating the efficient generation of mouse CAR-T cells.

Engineered cell therapies utilizing chimeric antigen receptor (CAR)-T cells have achieved remarkable effectiveness in individuals with hematological ...

Bioengineering

Engineering and Expansion of Human CAR Tregs for Immune Regulation Therapies

Generation of Human Chimeric Antigen Receptor Regulatory T Cells

Chimeric antigen receptor (CAR) T-cell therapy has reshaped the face of cancer treatment, leading to record remission rates in previously incurable hematological cancers. These successes have spurred interest in adapting the CAR platform to a small yet pivotal subset of CD4+ T cells primarily responsible for regulating and inhibiting the immune response, regulatory T cells (Tregs). The ability to redirect Tregs&#39; immunosuppressive activity to any extracellular target has enormous implications for creating cell therapies for autoimmune disease, organ transplant rejection, and graft-versus-host disease. Here, we describe in detail methodologies for bona fide Treg isolation from human peripheral blood, genetic modification of human Tregs utilizing either lentivirus or CRISPR/Cas9-aided knock-in using adeno-associated virus-mediated homologous directed repair (HDR) template delivery, and ex vivo expansion of stable human CAR Tregs. Lastly, we describe the assessment of human CAR Treg phenotypic stability and in vitro suppressive function, which provides insights into how the human CAR Tregs will behave in preclinical and clinical applications.

This protocol provides a streamlined workflow to generate and test human chimeric antigen receptor regulatory T cells (CAR Tregs).

Chimeric antigen receptor (CAR) T-cell therapy has reshaped the face of cancer treatment, leading to record remission rates in previously incurable ...

Automated Processor for Clinical-Scale CAR-T Cell Manufacturing

Chimeric Antigen Receptor T Cell Manufacturing on an Automated Cell Processor

Chimeric antigen receptor (CAR)-T cells represent a promising immunotherapeutic approach for the treatment of various malignant and non-malignant diseases. CAR-T cells are genetically modified T cells that express a chimeric protein that recognizes and binds to a cell surface target, resulting in the killing of the target cell. Traditional CAR-T cell manufacturing methods are labor-intensive, expensive, and may carry the risk of contamination. The CliniMACS Prodigy, an automated cell processor, allows for manufacturing cell therapy products at a clinical scale in a closed system, minimizing the risk of contamination. Processing occurs semi-automatically under the control of a computer and thus&#160;minimizes human involvement in the process, which saves time and reduces variability and errors.
This manuscript and video describes the T cell transduction (TCT) process for manufacturing CAR-T cells using this processor. The TCT process involves CD4+/CD8+ T cell enrichment, activation, transduction with a viral vector, expansion, and harvest. Using the Activity Matrix, a functionality that allows ordering and timing of these steps, the TCT process can be customized extensively. We provide a walk-through of CAR-T cell manufacturing in compliance with current Good Manufacturing Practice&#160;(cGMP) and discuss required release testing and preclinical experiments that will support an Investigational New Drug (IND) application. We demonstrate&#160;the feasibility and discuss the advantages and disadvantages of using a&#160;semi-automatic process for clinical CAR-T cell manufacturing. Finally, we describe an ongoing investigator-initiated clinical trial that targets pediatric B-cell malignancies [NCT05480449] as an example of how this manufacturing process can be applied in a clinical setting.

Author Spotlight: Advancements in CAR-T Cell Manufacturing and Gene Therapy Production 

This article details the manufacturing process for chimeric antigen receptor T cells for clinical use, specifically using an automated cell processor capable of performing viral transduction and cultivation of T cells. We provide recommendations and describe pitfalls that should be considered during the process development and implementation of an early-phase clinical trial.

Chimeric antigen receptor (CAR)-T cells represent a promising immunotherapeutic approach for the treatment of various malignant and non-malignant ...

Medicine

Non-Viral Engineering of Primary Human T Cells via Homology-Mediated End-Joining Targeted Integration of Large DNA Templates

Many current adoptive cellular therapies rely on lenti- or retroviral vectors to engineer T cells for the expression of a chimeric antigen receptor (CAR) or exogenous T cell receptor (TCR) to target a specific tumor-associated antigen. Reliance on viral vectors for the production of therapeutic T cells significantly increases the timeline, cost, and complexity of manufacturing while limiting the translation of new therapies, particularly in the academic setting. A process is presented for efficient non-viral engineering of T cells using CRISPR/Cas9 and homology-mediated end joining to achieve targeted integration of large, multicistronic DNA cargo. This approach has achieved integration frequencies comparable to those of viral vectors while yielding highly functional T cells capable of potent anti-tumor efficacy both in vitro and in vivo. Notably, this method is rapidly adaptable to current good manufacturing practices (cGMP) and clinical scale-up, providing a near-term option for the manufacturing of therapeutic T cells for use in clinical trials.

A detailed protocol is provided for using CRISPR/Cas9 technology to achieve highly efficient targeted knock-in of large, multicistronic constructs in primary human T cells via the homology-mediated end joining (HMEJ) DNA repair pathway. T cells engineered with this cGMP-adaptable protocol maintain excellent cell expansion, cytotoxicity, and cytokine production.

Many current adoptive cellular therapies rely on lenti- or retroviral vectors to engineer T cells for the expression of a chimeric antigen receptor (CAR) ...

Biology

A CRISPR-Cas9 Technique for Gene Editing in T Cells

Source: Agarwal, S., et al. <a href="https://app-jove-com.bdigitaluss.remotexs.co/v/62299">Production of Human CRISPR-Engineered CAR-T Cells.</a> J. Vis. Exp. (2021).
This video demonstrates an assay for performing gene editing in human T cells using the CRISPR-Cas9 technology. A mixture of primary CD4+ and CD8+ T cells is combined with a CRISPR-Cas9 ribonucleoprotein complex, targeting specific genes for knockout. Upon electroporation, the sgRNA guides Cas9 to the target DNA sequence, creating precise cuts. These cuts are then repaired by the cell&#39;s non-homologous end-joining mechanism, leading to gene knockout.

All procedures involving sample collection have been performed in accordance with the institute&#39;s IRB guidelines.
1. Designing of sgRNAs and gene ...

Production of Human CRISPR-Engineered CAR-T Cells

Summary

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A Nonviral Approach to Generate Transient Chimeric Antigen Receptor T Cells Using mRNA for Cancer Immunotherapy

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