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

Summary

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

Abstract

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-CSF^k/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.

Introduction

Chimeric antigen receptor T (CAR-T) cell therapy exhibits great promise in the treatment of cancer.^1,2 Two CAR-T cell therapies targeting CD19 (CART19) were recently approved in the United Stated and in Europe for the use in B cell malignancies after demonstrating striking results in multicenter clinical trials.^3,4,5 Barriers to more widespread use of CAR-T cells are limited activity in solid tumors and associated toxicities including cytokine release syndrome (CRS) and neurotoxicity (NT).^3,5,6,7,8,9 To enhance the therapeutic index of CAR-T cell therapy, genome engineering tools such as zinc finger nucleases, TALENs, and CRISPR are employed to further modify CAR-T cells in an attempt to generate less toxic or more effective CAR-T cells.^10,11

In this article, we describe a method to generate CRISPR/Cas9 edited CAR-T cells. The specific goal of this method is to genetically modify CAR-T cells during CAR-T cell manufacturing via CRISPR/Cas9 to generate less toxic or more effective CAR-T cells. The rationale for developing this methodology is built on lessons learned from clinical experience of CAR-T cell therapy, which indicates an urgent need for novel strategies to increase the therapeutic window of CAR-T cell therapy and to extend the application into other tumors and is supported by the recent advances in synthetic biology allowing multiple modifications of CAR-T cells that have started to enter the clinic. While several genome engineering tools are being developed and applied in different settings, such as zinc finger nucleases, TALENs, and CRISPR, our methodology describes CRISPR/Cas9 modification of CAR-T cells.^10,11 CRISPR/Cas9 is an RNA-based bacterial defense mechanism that is designed to eliminate foreign DNA. CRISPR relies on endonucleases to cleave a target sequence identified through a guide RNA (gRNA). CRISPR editing of CAR-T cells offers several advantages over other genome engineering tools. These include precision of the gRNA sequence, simplicity to design a gRNA targeting the gene of interest, high gene editing efficiency, and the ability to target multiple genes since multiple gRNAs can be used at the same time.

Specifically in the methods described here, we used a lentivirus encoding CRISPR guide RNA and Cas9 to disrupt a gene during CAR transduction of T cells. In selecting an appropriate technique to edit CAR-T cells, we suggest the technique described here is an efficient mechanism to generate research grade CAR-T cells, but because the long term effect of permanent integration of Cas9 into the genome is unknown, we propose this methodology to develop proof of concept research grade CAR-T cells but not for producing good manufacturing practice grade CAR-T cells.

In particular, here we describe the generation of granulocyte macrophage colony stimulating factor (GM-CSF) knockout CAR-T cells targeting human CD19. These CAR-T cells were generated by transduction with lentiviral particles encoding a guide RNA specific to GM-CSF (gene name CSF2) and Cas9. We previously found that GM-CSF neutralization ameliorates CRS and NT in a xenograft model.¹² GM-CSF^k/o CAR-T cells allow for the inhibition of GM-CSF during the manufacturing process, effectively reducing production of GM-CSF while enhancing CAR-T cell anti-tumor activity and survival in vivo compared to wildtype CAR-T cells.¹² Thus, here we provide a methodology to generate CRISPR/Cas9 edited CAR-T cells.

Protocol

This protocol follows the guidelines of Mayo Clinic's Institutional Review Board (IRB) and Institutional Biosafety Committee (IBC). 1. CART19 cell production T cell isolation, stimulation, and ex-vivo culture Carry out all cell culture work in a cell culture hood utilizing appropriate personal protective equipment. Harvest peripheral blood mononuclear cells (PBMCs) from de-identified normal donor blood cones collected during apheresis as these are known to be a viab…

Representative Results

Figure 1 shows reduction of GM-CSF in GM-CSFk/o CART19 cells. To verify that the genome of the T cells was altered to knockout GM-CSF, TIDE sequencing was used in the GM-CSFk/o CART19 cells (Figure 1A). CAR-T cell surface staining verifies that the T cells successfully express the CAR surface receptor in vitro by gating on live CD3+ cells (Figure 1B). Intracellular staining…

Discussion

In this report, we describe a methodology to utilize CRISPR/Cas9 technology to induce secondary modifications in CAR-T cells. Specifically, this is demonstrated using lentiviral transduction with a viral vector that contains gRNA targeting the gene of interest and Cas9 to generate GM-CSF^k/o CART19 cells. We had previously shown that GM-CSF neutralization ameliorates CRS and NT in a xenograft model.¹² As previously described, GM-CSF^k/o CAR-T cells allow for the inhib…

Materials

CD3 Monoclonal Antibody (OKT3), PE, eBioscience	Invitrogen	12-0037-42
CD3 Monoclonal Antibody (UCHT1), APC, eBioscience	Invitrogen	17-0038-42
Choice Taq Blue Mastermix	Denville Scientific	C775Y51
CTS (Cell Therapy Systems) Dynabeads CD3/CD28	Gibco	40203D
CytoFLEX System B4-R2-V2	Beckman Coulter	C10343	flow cytometer
dimethyl sulfoxide	Millipore Sigma	D2650-100ML
Dulbecco's Phosphate-Buffered Saline	Gibco	14190-144
Dynabeads MPC-S (Magnetic Particle Concentrator)	Applied Biosystems	A13346
Easy 50 EasySep Magnet	STEMCELL Technologies	18002
EasySep Human T Cell Isolation Kit	STEMCELL Technologies	17951	negative selection magnetic beads; 17951RF includes tips and buffer
Fetal bovine serum	Millipore Sigma	F8067
FITC Mouse Anti-Human CD107a	BD Pharmingen	555800
Fixation Medium (Medium A)	Invitrogen	GAS001S100
GenCRISPR gRNA Construct: Name: CSF2 CRISPR guide RNA 1; Species: Human, Vector: pLentiCRISPR v2; Resistance: Ampicillin; Copy number: High; Plasmid preparation: Standard delivery: 4 μg (Free of charge)	GenScript	N/A	custom order
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647	Invitrogen	A-21235
https://tide.nki.nl.	Desktop Genetics
Human AB Serum; Male Donors; type AB; US	Corning	35-060-CI
IFN gamma Monoclonal Antibody (4S.B3), APC-eFluor 780, eBioscience	Invitrogen	47-7319-42
Lipofectamine 3000 Transfection Reagent	Invitrogen	L3000075
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, for 405 nm excitation	Invitrogen	L34966
Lymphoprep	STEMCELL Technologies	07851
Monensin Solution, 1000X	BioLegend	420701
Mouse Anti-Human CD28 Clone CD28.2	BD Pharmingen	559770
Mouse Anti-Human CD49d Clone 9F10	BD Pharmingen	561892
Mouse Anti-Human MIP-1β PE-Cy7	BD Pharmingen	560687
Mr. Frosty Freezing Container	Thermo Scientific	5100-0001
NALM6, clone G5	ATCC	CRL-3273	acute lymphoblastic leukemia cell line
Nuclease Free Water	Promega	P119C
Olympus Vacuum Filter Systems, 500 mL, PES Membrane, 0.22uM, sterile	Genesee Scientific	25-227
Olympus Vacuum Filter Systems, 500 mL, PES Membrane, 0.45uM, sterile	Genesee Scientific	25-228
Opti-MEM I Reduced-Serum Medium (1X), Liquid	Gibco	31985-070
PE-CF594 Mouse Anti-Human IL-2	BD Horizon	562384
Penicillin-Streptomycin-Glutamine (100X), Liquid	Gibco	10378-016
Permeabilization Medium (Medium B)	Invitrogen	GAS002S100
PureLink Genomic DNA Mini Kit	Invitrogen	K182001
Puromycin Dihydrochloride	MP Biomedicals, Inc.	0210055210
QIAquick Gel Extraction Kit	QIAGEN	28704
Rat Anti-Human GM-CSF BV421	BD Horizon	562930
RoboSep-S	STEMCELL Technologies	21000	Fully Automated Cell Separator
SepMate-50 (IVD)	STEMCELL Technologies	85450
Sodium Azide, 5% (w/v)	Ricca Chemical	7144.8-16
X-VIVO 15 Serum-free Hematopoietic Cell Medium	Lonza	04-418Q